Contacts of the helix formed by residues 111 - 134 (chain P) in PDB entry 5A31
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with SER 111 (chain P).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79P GLU* 3.7 29.4 + - - +
80P ASP* 3.8 13.0 + - - -
83P ASP* 3.2 25.5 + - - -
109P CYS 3.6 0.4 - - - -
110P ASN* 1.3 79.4 - - - +
112P LYS* 1.3 61.9 + - - +
113P LYS* 3.4 15.1 + - - +
114P ALA* 3.7 8.7 - - - +
115P TYR* 2.8 28.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 112 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46P ARG* 5.5 3.1 - - - +
79P GLU* 4.0 14.9 + - - +
110P ASN 3.6 3.8 + - - +
111P SER* 1.3 74.6 + - - +
113P LYS* 1.3 62.5 + - - +
115P TYR* 3.4 6.5 + - + +
116P PHE* 3.1 23.4 + - - +
166P GLU* 3.4 29.9 + - - +
167P LEU* 5.5 0.9 - - - -
168P ASP* 4.6 24.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 113 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45P GLU* 2.9 37.4 + - - +
46P ARG* 3.9 34.8 - - - +
80P ASP* 5.4 15.1 - - - +
87P TYR* 3.1 53.0 - - + +
111P SER* 3.4 9.6 + - - +
112P LYS* 1.3 78.7 - - + +
114P ALA* 1.3 63.2 + - - +
116P PHE* 3.4 6.0 + - - +
117P LEU* 3.1 22.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 114 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83P ASP* 3.8 12.3 - - + +
87P TYR* 4.2 16.4 - - + -
106P LEU* 3.9 16.0 - - + +
109P CYS* 3.7 28.0 - - + -
111P SER* 3.3 11.9 + - - +
113P LYS* 1.3 78.0 - - - +
115P TYR* 1.3 60.7 + - - +
117P LEU* 3.2 2.5 + - - +
118P TYR* 2.8 31.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 115 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109P CYS 4.9 13.2 + - - +
110P ASN* 5.3 3.4 - - - +
111P SER 2.8 17.6 + - - +
112P LYS* 3.6 8.5 - - + +
114P ALA* 1.3 76.4 - - - +
116P PHE* 1.3 68.4 + - - +
118P TYR* 3.4 22.9 - + - +
119P MET* 3.0 50.1 + - + +
157P GLU* 4.6 5.6 + - - +
158P LEU* 4.3 13.4 - - + +
161P LEU* 2.7 42.0 - - + +
167P LEU* 4.7 13.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 116 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46P ARG* 3.6 42.0 - - + +
48P LEU* 3.6 30.5 - - + -
112P LYS 3.1 11.2 + - - +
113P LYS* 3.6 9.4 - - - +
115P TYR* 1.3 84.4 - - - +
117P LEU* 1.3 62.6 + - - +
119P MET* 3.1 5.1 + - + +
120P TYR* 2.8 48.0 + + + +
170P PHE* 3.7 28.9 - - + -
171P GLY* 3.8 15.7 - - - +
173P TYR* 5.0 2.5 - + - -
174P LEU* 3.6 28.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 117 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46P ARG* 4.1 16.8 - - - +
87P TYR* 3.8 28.3 - - + +
90P ALA 5.1 0.2 - - - +
91P LYS* 3.9 32.5 - - + +
94P PHE* 3.5 32.8 - - + -
102P ALA* 4.9 2.5 - - + -
106P LEU* 3.7 20.0 - - + -
113P LYS 3.1 11.6 + - - +
114P ALA 3.2 6.0 + - - +
116P PHE* 1.3 85.0 - - + +
118P TYR* 1.3 57.1 + - - +
120P TYR* 4.5 2.7 - - - -
121P SER* 2.8 31.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 118 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103P ALA* 3.4 30.5 - - + -
106P LEU* 3.5 26.0 - - + +
107P HIS* 4.2 34.4 + + + -
114P ALA 2.8 17.3 + - - +
115P TYR* 3.4 26.2 - + - +
117P LEU* 1.3 72.3 - - - +
119P MET* 1.3 74.0 + - - +
121P SER* 2.7 20.5 + - - -
122P ARG* 2.9 50.2 + - - +
157P GLU* 4.3 7.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 119 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115P TYR* 3.0 36.9 + - + +
116P PHE* 3.1 5.6 + - + +
118P TYR* 1.3 89.7 - - - +
120P TYR* 1.3 60.4 + - - +
122P ARG* 3.1 36.6 + - - +
123P TYR* 2.9 27.2 + - - +
154P LEU* 4.1 13.8 - - + +
157P GLU* 3.5 33.9 - - + +
158P LEU* 3.8 28.5 - - + -
174P LEU* 4.0 15.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 120 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1M MET 3.7 26.6 + - - -
2M ASP* 4.7 7.6 - - + -
46P ARG 4.3 3.6 - - - -
47P GLY 3.9 9.3 + - - -
48P LEU* 3.6 26.2 - - + -
49P LEU* 5.7 1.9 + - - +
94P PHE* 3.8 20.6 - + - -
116P PHE* 2.8 41.7 + + + +
117P LEU* 4.0 2.7 - - - +
119P MET* 1.3 73.4 - - - +
121P SER* 1.3 56.2 + - - +
123P TYR* 3.1 22.6 + + - +
124P LEU* 2.9 61.8 + - + +
173P TYR* 5.3 6.3 - + - -
174P LEU* 3.6 23.0 - - + +
177P VAL* 6.6 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 121 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94P PHE* 4.0 25.8 - - - -
99P TYR* 3.5 29.5 - - - +
102P ALA* 4.6 0.7 - - - -
103P ALA* 3.3 19.6 - - - +
117P LEU* 2.8 23.3 + - - +
118P TYR* 2.7 22.3 + - - -
120P TYR* 1.3 73.2 - - - +
122P ARG* 1.3 61.5 + - - +
124P LEU 3.2 0.7 + - - +
125P SER* 3.0 21.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 122 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248J LYS* 5.0 9.5 - - - +
103P ALA* 4.7 9.0 - - + -
118P TYR* 2.9 38.2 + - - +
119P MET* 3.2 45.0 - - - +
121P SER* 1.3 83.8 + - - +
123P TYR* 1.3 59.5 + - - +
125P SER* 2.8 23.7 + - - +
126P GLY* 3.3 6.6 + - - -
153P GLU* 4.1 29.7 + - - +
154P LEU* 3.8 20.7 - - + +
157P GLU* 3.3 26.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 123 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2M ASP* 3.3 38.7 + - + +
119P MET 2.9 12.9 + - - +
120P TYR* 3.3 23.3 - + - +
122P ARG* 1.3 73.6 - - - +
124P LEU* 1.3 82.5 + - + +
126P GLY* 3.2 3.7 + - - -
127P GLU* 2.9 53.8 + - + +
151P LEU* 3.6 27.3 - - + +
154P LEU* 3.6 15.0 - - + +
174P LEU* 4.4 7.6 - - + -
177P VAL* 3.6 18.0 - - + +
178P VAL* 3.9 8.1 - - + -
181P LYS* 3.5 15.8 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 124 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1M MET 5.4 0.7 - - - +
2M ASP 5.1 0.7 - - - +
5M VAL* 3.8 41.6 - - + +
94P PHE* 3.9 4.7 - - + -
99P TYR* 3.8 41.5 - - + +
120P TYR* 2.9 63.1 + - + +
121P SER 3.9 0.4 - - - +
123P TYR* 1.3 89.2 - - + +
125P SER* 1.3 67.1 + - - +
127P GLU* 2.9 14.2 + - - +
128P LYS* 2.9 15.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 125 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99P TYR* 4.0 12.5 - - - +
100P ASP* 3.4 36.6 + - - +
121P SER 3.0 13.6 + - - -
122P ARG* 2.8 25.6 + - - +
124P LEU* 1.3 77.5 - - - +
126P GLY* 1.3 60.6 + - - +
128P LYS* 3.6 5.2 + - - +
129P LYS* 3.2 36.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 126 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122P ARG 3.3 5.1 + - - -
123P TYR* 3.2 7.6 + - - -
124P LEU 3.1 1.2 - - - -
125P SER* 1.3 84.4 + - - +
127P GLU* 1.3 57.3 + - - +
129P LYS* 3.5 11.1 + - - +
130P LYS* 3.0 26.7 + - - +
150P ALA* 4.6 21.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 127 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5M VAL* 4.3 22.7 - - + -
123P TYR* 2.9 57.4 + - + +
124P LEU* 2.9 8.8 + - - +
126P GLY* 1.3 75.4 - - - +
128P LYS* 1.3 65.4 + - - +
130P LYS* 3.2 24.9 + - - +
131P ASP* 3.0 29.9 + - - +
151P LEU* 4.3 10.2 - - - +
181P LYS* 3.6 23.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 128 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326C ILE 6.1 0.4 - - - +
327C ASP* 6.2 0.2 - - - +
5M VAL* 3.7 27.0 - - + +
6M GLN* 4.2 16.0 + - - +
7M ARG* 4.3 18.4 - - - +
97P LYS* 5.1 10.4 - - - +
99P TYR* 4.3 22.4 - - + -
100P ASP* 6.1 0.4 - - - +
124P LEU 2.9 12.9 + - - +
125P SER* 3.7 9.9 - - - +
126P GLY 3.4 0.2 - - - -
127P GLU* 1.3 74.8 - - - +
129P LYS* 1.3 59.9 + - + +
131P ASP* 3.2 8.7 + - - +
132P ASP* 2.9 45.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 129 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325C GLU* 3.6 32.7 + - + +
326C ILE 5.1 4.3 - - - +
328C LYS* 5.5 0.3 + - - -
100P ASP* 4.0 18.5 + - - +
125P SER* 3.2 25.8 + - - +
126P GLY* 3.7 9.6 - - - +
127P GLU 3.2 0.2 - - - -
128P LYS* 1.3 77.6 - - + +
130P LYS* 1.3 67.2 + - - +
132P ASP* 3.4 6.6 + - - +
133P GLU* 2.9 25.6 + - - +
150P ALA* 5.8 5.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 130 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126P GLY 3.0 17.1 + - - +
127P GLU* 3.2 23.7 + - - +
129P LYS* 1.3 77.4 - - - +
131P ASP* 1.3 78.7 + - - +
133P GLU* 3.2 15.2 + - - +
134P THR* 3.0 36.2 + - - +
147P LYS 5.9 5.2 - - - +
151P LEU* 6.5 0.9 - - + -
181P LYS* 5.0 11.0 - - - +
362P PRO* 4.5 18.4 - - - +
363P ARG* 5.8 5.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 131 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5M VAL 4.8 5.9 - - - +
6M GLN* 5.1 0.3 - - - -
7M ARG* 3.1 58.9 + - + +
20M ARG* 3.5 3.1 + - - -
127P GLU* 3.0 20.7 + - - +
128P LYS* 3.8 10.4 + - - +
130P LYS* 1.3 99.3 + - - +
132P ASP* 1.3 63.5 + - - +
134P THR* 3.5 10.5 + - - -
359P LYS 4.9 1.2 - - - +
360P LEU 4.9 3.3 - - - +
361P ASN 4.5 4.3 - - - +
362P PRO* 4.3 19.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 132 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326C ILE 5.8 0.5 - - - +
327C ASP* 6.0 0.5 - - - -
328C LYS* 4.0 25.9 + - - +
329C TYR* 3.4 36.6 - - + -
7M ARG* 5.2 3.5 - - - +
11M ILE* 5.7 1.4 - - - +
20M ARG* 3.5 31.8 + - - +
128P LYS* 2.9 35.3 + - - +
129P LYS* 3.9 6.8 - - - +
131P ASP* 1.3 77.8 - - - +
133P GLU* 1.3 64.7 + - - +
134P THR 3.4 4.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 133 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328C LYS* 4.3 10.0 - - - +
20M ARG 5.1 3.9 - - - +
21M GLU* 5.3 3.5 - - - +
23M LYS* 5.8 9.7 + - - -
129P LYS 2.9 17.1 + - - +
130P LYS* 3.5 13.3 - - - +
132P ASP* 1.3 75.8 - - - +
134P THR* 1.3 64.1 + - - +
147P LYS* 4.9 22.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 134 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7M ARG* 4.5 11.2 - - - +
17M ASP* 4.5 4.3 - - - +
20M ARG* 4.5 12.1 - - - -
21M GLU* 3.2 27.4 - - - +
130P LYS* 3.0 26.3 + - - +
131P ASP* 3.8 15.3 - - - -
132P ASP 3.3 7.7 - - - -
133P GLU* 1.3 82.0 - - - +
----------------------------------------------------------
Back to top of page
A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il