Contacts of the helix formed by residues 108 - 124 (chain O) in PDB entry 3SDI
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 PRO 108 (chain O).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74O ILE* 4.5 0.4 - - - -
100O TYR* 3.7 18.4 - - + +
106O TYR 4.5 0.4 - - - +
107O PRO* 1.3 86.8 - - + +
109O THR* 1.3 68.9 + - - +
110O LYS* 4.7 8.5 - - + -
111O LEU* 3.0 34.3 + - + +
112O LEU* 3.2 9.4 + - - +
142O ASP* 3.4 33.2 - - + +
145O ASN* 4.2 8.3 - - - +
70W GLU* 3.5 18.8 - - - +
72W ARG* 6.0 1.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 109 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74O ILE* 3.9 15.7 - - + +
107O PRO 3.8 2.0 + - - -
108O PRO* 1.3 68.9 - - - +
110O LYS* 1.3 64.5 + - - +
111O LEU 3.1 0.3 + - - -
112O LEU* 3.3 1.9 + - - +
113O VAL* 2.9 34.0 + - + +
138O ILE* 4.4 11.2 - - + +
140O GLY* 3.2 40.9 - - - +
141O HIS 3.4 4.0 + - - -
142O ASP* 3.3 12.5 + - - +
147O SER* 3.6 21.0 - - + +
149O TYR* 4.0 17.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 110 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108O PRO* 4.7 13.7 - - + -
109O THR* 1.3 76.9 - - - +
111O LEU* 1.3 61.6 + - + +
113O VAL* 3.6 5.7 + - - +
114O SER* 2.9 26.0 + - - -
142O ASP* 5.2 0.9 - - - +
145O ASN* 3.2 44.0 + - + +
149O TYR* 3.5 33.0 - - + +
157O TYR* 4.6 7.0 + - + -
63P THR* 5.7 4.3 - - + +
69W LYS 4.6 8.7 - - - +
70W GLU* 3.1 31.7 + - - +
71W GLU* 4.0 19.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 111 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100O TYR* 4.2 7.4 - - + -
107O PRO* 4.7 4.0 - - + -
108O PRO* 3.0 26.9 + - + +
110O LYS* 1.3 82.3 - - + +
112O LEU* 1.3 65.7 + - - +
113O VAL 3.2 0.2 - - - -
114O SER* 3.1 14.3 - - - +
115O GLU* 3.0 30.1 + - + +
69W LYS* 3.8 40.2 - - + +
70W GLU* 3.3 43.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 112 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70O LEU* 4.1 22.4 - - + -
71O THR* 3.7 19.5 - - + -
74O ILE* 3.7 30.1 - - + -
92O SER* 3.7 24.2 - - - +
95O VAL* 4.0 14.4 - - + -
96O ALA* 4.1 13.7 - - + -
107O PRO* 4.1 13.6 - - + +
108O PRO 3.2 10.4 + - - +
109O THR 3.8 5.6 - - - +
111O LEU* 1.3 74.1 - - - +
113O VAL* 1.3 66.1 + - + +
115O GLU* 2.9 17.4 + - + +
116O VAL* 3.0 25.8 + - + +
138O ILE* 6.0 0.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 113 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109O THR* 2.9 26.4 + - + +
110O LYS* 3.6 5.6 - - - +
112O LEU* 1.3 74.6 - - - +
114O SER* 1.3 57.6 + - - +
115O GLU 3.3 0.2 + - - -
116O VAL* 3.3 9.6 + - - +
117O ALA* 2.9 28.2 + - - +
138O ILE* 3.6 36.8 - - + -
149O TYR* 4.0 17.9 - - + -
151O VAL* 4.0 11.6 - - + +
157O TYR* 3.6 39.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 114 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110O LYS 2.9 16.1 + - - -
111O LEU* 3.1 26.4 - - - +
113O VAL* 1.3 76.9 - - - +
115O GLU* 1.3 58.1 + - - +
117O ALA* 3.4 9.0 - - - +
118O LYS* 3.0 24.8 + - - +
157O TYR* 3.8 13.5 + - - -
86P GLU* 3.4 20.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 115 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95O VAL* 3.9 38.9 - - + +
99O SER* 4.1 16.5 + - - -
111O LEU* 3.0 21.1 + - + +
112O LEU* 2.9 10.1 + - + +
114O SER* 1.3 77.4 + - - +
116O VAL* 1.3 66.2 + - - +
118O LYS* 3.0 34.8 + - - +
119O ILE* 3.1 15.1 + - + +
69W LYS* 5.6 4.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 116 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70O LEU* 5.4 0.9 - - + -
88O LEU* 4.4 9.9 - - + -
92O SER* 3.1 31.6 - - - +
95O VAL* 5.7 0.2 - - + -
112O LEU* 3.0 23.0 + - + +
113O VAL* 3.3 6.0 + - - +
115O GLU* 1.3 75.2 - - - +
117O ALA* 1.3 63.4 + - - +
119O ILE* 2.9 22.2 + - - +
120O MET* 3.1 21.7 + - - +
136O LEU* 3.7 29.4 - - + -
138O ILE* 4.3 17.7 - - + -
151O VAL* 5.0 2.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 117 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113O VAL 2.9 17.7 + - - +
114O SER 3.4 6.7 - - - +
116O VAL* 1.3 75.0 - - - +
118O LYS* 1.3 57.2 + - - +
120O MET* 3.5 0.8 + - - -
121O GLN* 2.9 30.7 + - - +
151O VAL* 4.0 15.3 - - + +
155O GLY* 3.2 29.5 - - - +
157O TYR* 3.7 20.4 - - + -
83P ALA* 5.6 1.1 - - + -
86P GLU* 5.8 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 118 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114O SER 3.0 13.8 + - - +
115O GLU* 3.0 30.5 + - - +
117O ALA* 1.3 76.3 - - - +
119O ILE* 1.3 60.8 + - + +
121O GLN* 3.3 6.6 + - - +
122O GLU* 3.0 55.7 + - - +
87P ILE* 3.9 26.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 119 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88O LEU* 3.8 23.3 - - + -
91O LYS* 4.2 46.0 - - + +
92O SER* 5.0 3.1 - - - +
95O VAL* 4.8 12.3 - - + -
115O GLU 3.1 19.4 + - - +
116O VAL* 2.9 14.2 + - - +
118O LYS* 1.3 77.1 - - + +
120O MET* 1.3 60.4 + - - +
122O GLU* 3.3 16.8 + - - +
123O ALA* 3.3 19.8 + - - +
132O PHE* 4.1 12.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 120 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88O LEU* 3.8 24.2 - - + -
116O VAL* 3.1 24.5 + - - +
117O ALA 3.9 3.1 - - - +
119O ILE* 1.3 72.8 - - - +
121O GLN* 1.3 66.9 + - - +
122O GLU 3.2 0.2 - - - -
123O ALA* 3.2 13.2 + - - +
124O THR* 3.3 12.0 + - - -
132O PHE* 4.0 18.0 + - + -
134O VAL* 3.7 26.9 - - + +
136O LEU* 4.3 4.3 - - + -
151O VAL* 3.8 25.4 - - + +
152O ASP 3.5 29.2 - - - +
153O PRO* 3.7 14.6 - - + +
155O GLY* 4.2 9.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 121 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117O ALA 2.9 22.2 + - - +
118O LYS* 3.6 7.0 - - - +
120O MET* 1.3 72.4 - - - +
122O GLU* 1.3 70.8 + - - +
124O THR* 2.8 27.6 + - + -
125O GLN* 2.9 30.1 + - - +
154O SER 3.7 11.9 - - - +
155O GLY* 4.0 1.8 - - - -
83P ALA* 3.7 32.3 - - + +
84P ASP* 2.9 31.3 + - - +
87P ILE* 3.7 21.6 - - + +
130P ARG* 3.8 4.2 - - - +
132P PHE* 4.7 1.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 122 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118O LYS* 3.0 50.0 + - + +
119O ILE* 3.6 17.7 - - - +
120O MET 3.2 0.4 - - - -
121O GLN* 1.3 86.4 - - - +
123O ALA* 1.3 55.0 + - - +
124O THR 3.0 0.2 - - - -
125O GLN* 2.9 4.3 + - - -
126O SER* 2.7 47.6 + - - +
87P ILE* 5.1 3.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 123 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13O THR* 4.6 0.9 + - - -
119O ILE 3.3 5.3 + - - +
120O MET 3.2 10.1 + - - +
122O GLU* 1.3 74.9 - - - +
124O THR* 1.3 59.2 + - - +
125O GLN 3.3 0.4 - - - -
126O SER 5.1 0.2 - - - +
129O VAL* 3.6 29.2 - - + +
130O ARG 3.7 13.0 - - - +
131O PRO* 3.7 20.4 - - + +
132O PHE* 3.6 33.2 - - + -
125U GLN* 4.1 2.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 124 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13O THR* 3.4 24.0 + - - +
24O ILE* 3.6 28.9 - - + +
120O MET 3.3 2.1 + - - -
121O GLN* 2.8 17.2 + - - +
123O ALA* 1.3 77.6 - - - +
125O GLN* 1.3 56.6 + - - +
126O SER 5.2 0.4 - - - -
131O PRO* 4.4 3.8 - - - +
153O PRO 3.2 22.9 + - - -
154O SER* 4.0 7.2 - - - +
84P ASP* 4.6 2.2 - - - +
130P ARG* 2.9 42.0 + - - +
----------------------------------------------------------
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