Contacts of the helix formed by residues 106 - 122 (chain P) in PDB entry 5A0Q
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 THR 106 (chain P).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71P ILE* 3.4 24.7 - - + +
104P ILE 3.4 1.0 + - - -
105P PRO* 1.3 72.4 - - - +
107P ALA* 1.3 63.5 + - - +
108P GLN 3.3 0.7 + - - -
109P LEU* 3.4 2.3 + - - +
110P VAL* 3.2 29.0 + - + +
135P ILE 4.7 2.0 - - - +
136P CYS 4.4 0.9 - - - -
137P GLY* 3.3 35.9 - - - +
138P TRP 3.9 0.3 + - - -
139P ASN* 2.7 21.0 + - - -
144P TYR* 3.1 33.3 - - + -
146P PHE* 4.0 10.1 - - + -
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Residues in contact with ALA 107 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105P PRO* 3.2 3.7 - - + +
106P THR* 1.3 81.1 - - - +
108P GLN* 1.4 67.5 + - + +
110P VAL* 3.6 4.2 + - - +
111P GLN* 3.1 31.2 + - + +
144P TYR* 5.2 7.9 - - + -
146P PHE* 3.6 24.4 - - + -
154P TYR* 4.7 3.8 + - + +
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Residues in contact with GLN 108 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96P TYR* 4.6 2.0 - - - +
104P ILE* 3.7 5.8 - - + -
105P PRO* 3.1 28.8 + - + +
107P ALA* 1.4 80.7 - - - +
109P LEU* 1.4 60.0 + - - +
111P GLN* 3.2 31.6 + - - +
112P ARG* 3.0 52.1 + - - +
73X TYR* 4.5 0.3 - - - -
76X LYS* 3.1 31.0 + - - +
77X GLU* 3.2 39.5 - - + +
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Residues in contact with LEU 109 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67P ILE* 3.5 31.2 - - + -
68P THR* 4.7 1.6 - - + -
71P ILE* 4.1 24.9 - - + -
89P ALA* 3.4 20.6 - - + +
92P LEU* 3.7 21.1 - - + -
93P ALA* 4.2 13.5 - - + +
104P ILE* 3.5 23.0 - - + +
105P PRO 3.2 4.8 + - - -
106P THR 3.4 6.0 + - - +
108P GLN* 1.4 73.5 - - - +
110P VAL* 1.3 60.1 + - + +
112P ARG* 4.5 1.3 - - + +
113P VAL* 3.0 40.2 + - + +
135P ILE* 5.6 4.3 - - + -
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Residues in contact with VAL 110 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106P THR* 3.2 18.3 + - + +
107P ALA 3.8 4.3 - - - +
109P LEU* 1.3 74.4 - - + +
111P GLN* 1.3 63.2 + - - +
113P VAL* 3.9 1.0 - - - +
114P ALA* 3.0 22.2 + - - +
135P ILE* 3.8 41.5 - - + -
146P PHE* 3.7 33.0 - - + -
148P SER* 4.7 4.1 + - - -
154P TYR* 3.6 36.1 - - + -
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Residues in contact with GLN 111 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107P ALA* 3.1 16.9 + - - +
108P GLN* 3.2 44.5 + - - +
110P VAL* 1.3 74.9 - - - +
112P ARG* 1.3 67.8 + - + +
114P ALA* 3.2 4.7 + - - +
115P SER* 3.1 24.2 + - - -
154P TYR* 3.2 36.9 + - + +
84Q ASN* 5.8 2.0 - - - +
91Q ARG* 6.1 0.6 - - - +
76X LYS* 3.7 27.9 + - - +
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Residues in contact with ARG 112 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92P LEU* 3.8 36.5 - - + +
96P TYR* 3.3 27.6 - - - -
100P TYR* 4.3 13.1 + - - -
104P ILE* 3.2 31.9 - - - +
108P GLN* 3.0 29.4 + - - +
109P LEU* 4.1 3.1 - - - +
111P GLN* 1.3 80.4 - - + +
113P VAL* 1.4 60.4 + - - +
115P SER* 3.2 21.8 + - - -
116P VAL* 3.3 12.0 + - - +
73X TYR* 4.6 4.9 - - - -
76X LYS* 3.8 28.7 - - + +
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Residues in contact with VAL 113 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85P LEU* 4.1 28.3 - - + +
89P ALA* 3.8 24.9 - - + +
92P LEU* 3.6 18.6 - - + -
109P LEU* 3.0 24.8 + - + +
110P VAL* 4.1 5.2 - - - +
112P ARG* 1.4 71.3 - - - +
114P ALA* 1.3 64.0 + - - +
116P VAL* 3.2 14.1 + - + +
117P MET* 3.2 27.4 + - + +
133P LEU* 5.5 0.4 - - + -
135P ILE* 4.7 16.4 - - + -
148P SER* 5.1 2.7 - - - +
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Residues in contact with ALA 114 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110P VAL 3.0 19.7 + - - +
111P GLN 3.2 6.9 + - - +
113P VAL* 1.3 76.3 - - - +
115P SER* 1.3 57.1 + - - +
117P MET* 3.2 2.6 + - - -
118P GLN* 3.1 22.9 + - - +
148P SER* 4.1 14.6 + - - +
152P GLY* 3.3 34.4 - - - +
154P TYR* 3.8 17.0 - - + -
84Q ASN* 5.9 2.2 - - - +
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Residues in contact with SER 115 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111P GLN 3.1 15.0 + - - -
112P ARG* 3.3 12.9 - - - -
114P ALA* 1.3 74.1 - - - +
116P VAL* 1.3 62.0 + - - +
118P GLN* 3.3 10.6 + - - +
119P GLU* 3.1 24.5 + - - +
84Q ASN* 5.1 9.2 - - - +
85Q VAL* 5.1 12.9 - - - +
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Residues in contact with VAL 116 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85P LEU* 5.9 4.7 - - + -
88P ARG* 3.5 59.5 - - + +
92P LEU* 4.2 4.7 - - + -
112P ARG 3.5 14.6 - - - +
113P VAL* 3.2 16.8 + - + +
115P SER* 1.3 77.3 - - - +
117P MET* 1.3 58.8 + - + +
119P GLU* 3.2 31.3 - - - +
120P TYR* 4.1 0.4 + - - +
129P PHE* 3.5 26.2 - - + -
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Residues in contact with MET 117 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85P LEU* 4.1 20.4 - - + -
113P VAL* 3.2 15.9 + - + +
114P ALA 3.2 9.2 + - - +
116P VAL* 1.3 76.8 - - + +
118P GLN* 1.3 59.4 + - - +
120P TYR* 4.2 4.8 + - - +
121P THR* 3.6 16.8 - - - +
129P PHE* 3.7 39.3 + - + -
131P VAL 3.3 25.4 - - - +
132P SER* 5.2 1.1 - - - -
133P LEU* 5.9 3.1 - - + -
148P SER* 3.6 23.8 - - - -
149P ASP* 3.2 29.2 - - - +
150P PRO* 3.7 11.5 - - + +
151P SER 4.2 0.7 - - - -
152P GLY* 3.9 8.5 - - - +
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Residues in contact with GLN 118 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114P ALA 3.1 14.6 + - - +
115P SER* 3.6 8.7 - - - +
116P VAL 3.2 0.2 - - - -
117P MET* 1.3 73.8 - - - +
119P GLU* 1.3 66.9 + - - +
120P TYR 3.2 2.2 - - - -
121P THR* 2.8 30.1 + - - -
122P GLN* 3.1 24.3 + - - +
151P SER 3.4 7.4 - - - +
81Q SER* 3.0 37.3 - - - +
82Q ASP* 2.4 32.7 + - - +
85Q VAL* 3.7 20.0 - - + +
128Q ARG* 3.8 0.6 - - - +
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Residues in contact with GLU 119 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88P ARG* 3.0 33.4 + - - -
115P SER 3.1 11.0 + - - +
116P VAL* 3.2 27.4 - - - +
118P GLN* 1.3 78.5 - - - +
120P TYR* 1.3 83.5 + - + +
122P GLN* 3.2 6.9 + - - +
123P SER* 2.9 32.9 + - - -
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Residues in contact with TYR 120 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127O GLN* 3.3 44.5 - - + +
10P THR* 4.2 6.8 - - - +
116P VAL* 4.1 1.6 + - - +
117P MET 4.2 1.7 + - - +
118P GLN 3.2 0.6 - - - -
119P GLU* 1.3 103.5 + - + +
121P THR* 1.3 59.8 + - - +
122P GLN 3.1 5.1 + - - -
123P SER* 3.8 15.3 - - - +
126P VAL* 3.8 34.9 - - + +
127P ARG 3.4 13.2 - - - +
128P PRO* 4.2 8.2 - - + +
129P PHE* 3.1 41.8 - + + -
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Residues in contact with THR 121 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10P THR* 2.8 27.2 + - - -
18P LEU* 5.1 0.6 - - - +
21P ILE* 3.5 37.8 - - + +
117P MET 3.6 19.7 - - - +
118P GLN* 2.8 30.7 + - - -
120P TYR* 1.3 78.2 - - - +
122P GLN* 1.3 55.7 + - - +
128P PRO* 4.0 11.4 - - + -
150P PRO 4.2 4.9 - - - +
151P SER* 4.3 5.4 - - - +
128Q ARG* 2.8 27.6 + - - -
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Residues in contact with GLN 122 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8P SER* 4.1 7.3 + - - -
10P THR* 4.3 2.2 - - - -
118P GLN* 3.1 25.5 + - - +
119P GLU* 3.2 8.1 + - - +
121P THR* 1.3 80.3 + - - +
123P SER* 1.3 56.8 + - - +
85Q VAL* 5.8 0.2 - - - +
121Q TYR* 3.8 17.5 - - + +
127Q LYS* 3.5 23.2 - - - +
128Q ARG* 3.0 38.1 + - - +
129Q PRO 3.9 0.6 - - - -
130Q PHE* 3.3 56.1 - - - +
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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) + - + + + + + -
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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