Contacts of the helix formed by residues 95 - 111 (chain B) in PDB entry 1O2D
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 GLY 95 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94B GLY* 1.3 77.0 - - - +
96B GLY* 1.3 65.8 + - - -
97B SER 3.2 3.6 - - - -
98B PRO* 3.2 7.4 - - - +
99B MSE 3.1 24.5 + - - +
136B THR* 3.6 3.0 + - - -
137B THR* 3.7 15.7 - - - -
1801B NAP 3.3 27.7 + - - -
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Residues in contact with GLY 96 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95B GLY* 1.3 71.9 - - - -
97B SER* 1.3 56.9 + - - +
99B MSE 3.9 7.8 - - - +
100B ASP* 2.8 34.9 + - - -
140B THR* 3.6 17.0 + - - -
142B SER* 4.5 2.9 - - - -
1801B NAP 2.9 36.5 + - - -
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Residues in contact with SER 97 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66B VAL* 3.9 5.0 - - - +
67B GLU 3.6 21.1 - - - -
68B GLU* 4.0 2.5 - - - -
69B ASN 2.9 19.6 + - - -
70B PRO* 3.5 13.3 - - - +
96B GLY* 1.3 76.0 - - - +
98B PRO* 1.3 65.3 - - - +
100B ASP* 3.8 2.8 - - - +
101B PHE* 3.0 28.1 + - - +
1801B NAP 2.7 37.2 + - - -
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Residues in contact with PRO 98 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34B VAL* 3.5 12.3 - - - +
35B THR* 3.8 20.6 - - - +
36B GLY* 4.2 10.1 - - - +
66B VAL* 3.9 13.9 - - + -
92B GLY* 4.1 2.2 - - - -
93B LEU 3.4 26.5 - - - +
94B GLY* 3.7 2.2 - - - -
95B GLY 3.2 20.0 - - - +
97B SER* 1.3 95.2 - - - +
99B MSE 1.3 59.9 + - - -
101B PHE* 3.5 3.9 - - + +
102B ALA* 2.9 19.8 + - - +
1801B NAP 3.5 9.6 - - - +
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Residues in contact with MSE 99 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92B GLY* 4.3 10.3 - - - +
94B GLY 3.6 8.3 - - - +
95B GLY* 3.1 29.9 + - - +
96B GLY 3.9 0.4 - - - +
98B PRO* 1.3 76.1 - - - +
100B ASP* 1.3 63.0 + - - +
102B ALA* 3.4 7.6 + - - +
103B LYS* 3.4 6.9 + - - +
133B GLU* 2.7 50.0 - - - +
135B PRO* 3.6 40.6 - - + -
137B THR* 5.2 3.4 - - - +
140B THR* 3.6 24.9 - - - +
141B GLY 5.2 0.2 - - - +
142B SER* 3.6 13.2 - - - +
143B GLU* 3.7 23.3 - - - +
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Residues in contact with ASP 100 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70B PRO* 5.3 0.9 - - + -
96B GLY 2.8 19.9 + - - +
97B SER* 3.8 3.8 - - - +
99B MSE 1.3 73.2 - - - +
101B PHE* 1.3 66.3 + - - +
103B LYS* 3.2 3.8 + - - -
104B ALA* 3.2 11.4 + - - +
142B SER* 2.7 19.1 + - - -
147B TYR 3.5 2.6 - - - +
148B SER* 2.9 32.8 + - - +
149B ILE* 3.0 32.5 + - - +
150B LEU* 5.2 2.0 - - + -
1801B NAP 2.7 47.7 + - - -
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Residues in contact with PHE 101 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34B VAL* 4.0 13.2 - - + -
63B PHE* 3.6 22.9 - + - -
66B VAL* 3.7 22.4 - - + -
70B PRO* 3.9 10.4 - - + +
74B ASN* 3.4 36.3 - - + -
75B VAL* 3.6 32.1 - - + -
78B ALA* 3.7 15.7 - - + -
97B SER 3.0 17.3 + - - +
98B PRO* 3.5 10.5 - - + +
100B ASP* 1.3 78.2 - - - +
102B ALA* 1.3 61.2 + - - +
104B ALA* 3.2 6.9 + - - +
105B VAL* 3.0 45.8 + - + +
150B LEU* 5.0 4.3 - - - -
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Residues in contact with ALA 102 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34B VAL* 3.7 17.9 - - + +
90B VAL* 3.8 14.1 - - + +
92B GLY* 3.7 20.0 - - - +
98B PRO 2.9 13.3 + - - +
99B MSE 3.5 10.3 - - - +
100B ASP 3.2 0.2 - - - -
101B PHE* 1.3 78.1 - - - +
103B LYS* 1.3 62.7 + - - +
105B VAL* 3.4 3.9 - - - +
106B ALA* 3.0 25.6 + - - +
131B VAL* 4.0 7.4 - - + +
133B GLU* 4.1 4.9 - - - +
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Residues in contact with LYS 103 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99B MSE 3.4 4.2 + - - +
100B ASP* 3.2 7.4 + - - +
102B ALA* 1.3 75.4 - - - +
104B ALA* 1.3 64.5 + - - +
106B ALA 3.4 7.1 + - - -
107B VAL* 3.4 12.1 + - - +
131B VAL* 4.3 6.5 - - + -
133B GLU* 3.3 26.0 - - - +
142B SER* 2.8 38.3 + - - -
145B THR* 2.8 22.3 + - - +
146B PRO 4.2 2.5 - - - +
147B TYR 2.8 30.8 + - - +
148B SER* 4.4 0.7 - - - -
162B LEU* 3.7 11.7 - - + -
163B MSE 3.5 45.7 - - - +
165B PRO* 4.3 4.5 - - + -
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Residues in contact with ALA 104 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75B VAL* 4.4 14.4 - - + -
100B ASP 3.2 10.0 + - - +
101B PHE* 3.2 10.1 + - - +
103B LYS* 1.3 79.4 - - - +
105B VAL* 1.3 62.2 + - - +
107B VAL* 3.3 5.4 + - - +
108B LEU* 3.1 26.8 + - - +
119B LEU* 3.9 20.1 - - + +
148B SER* 4.1 8.3 - - - +
150B LEU* 4.3 11.4 - - + -
162B LEU* 3.8 10.4 - - + +
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Residues in contact with VAL 105 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32B LEU* 4.4 13.5 - - + -
34B VAL* 4.4 4.7 - - + -
75B VAL* 4.3 9.4 - - + -
78B ALA* 4.6 4.9 - - + -
79B VAL* 4.0 20.6 - - + -
90B VAL* 3.8 21.8 - - + -
101B PHE* 3.0 39.1 + - + +
102B ALA* 3.4 12.6 - - - +
104B ALA* 1.3 75.6 - - - +
106B ALA* 1.3 59.6 + - - +
108B LEU* 4.4 6.3 - - - +
109B LEU* 2.8 39.8 + - + +
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Residues in contact with ALA 106 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90B VAL* 3.9 17.7 - - + -
102B ALA 3.0 19.2 + - - +
103B LYS 3.7 4.0 - - - +
104B ALA 3.2 0.2 - - - -
105B VAL* 1.3 78.0 - - - +
107B VAL* 1.3 62.5 + - - +
110B LYS* 3.6 6.8 + - - +
128B TRP* 3.5 1.7 - - - -
129B LEU* 3.0 41.1 + - + +
131B VAL* 3.4 26.2 - - + -
163B MSE 3.9 2.5 - - + -
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Residues in contact with VAL 107 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103B LYS 3.6 13.7 - - - +
104B ALA 3.3 6.6 + - - +
105B VAL 3.2 0.4 - - - -
106B ALA* 1.3 77.1 - - - +
108B LEU* 1.3 63.3 + - - +
110B LYS* 3.1 13.7 + - - +
111B GLU* 3.2 13.7 + - - +
114B LEU* 3.9 17.0 - - + -
119B LEU* 3.5 22.2 - - + -
125B VAL* 4.1 26.5 - - + -
127B HIS 4.0 10.5 - - - +
128B TRP* 4.0 11.0 - - + -
162B LEU* 4.2 12.3 - - + -
163B MSE 3.6 16.8 - - + -
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Residues in contact with LEU 108 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75B VAL* 3.7 30.3 - - + -
79B VAL* 3.9 22.7 - - + -
83B ARG* 3.0 20.1 + - - +
104B ALA 3.1 16.3 + - - +
105B VAL 4.1 0.2 - - - +
107B VAL* 1.3 75.8 - - - +
109B LEU* 1.3 60.3 + - - +
111B GLU 3.2 15.5 - - - +
114B LEU* 3.7 27.4 - - + +
115B SER 3.5 23.3 - - - +
116B VAL* 3.9 17.0 - - + +
119B LEU* 3.8 21.3 - - + -
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Residues in contact with LEU 109 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32B LEU* 3.9 27.4 - - + -
79B VAL* 4.3 22.4 - - + +
82B TYR* 3.8 31.6 - - + +
83B ARG* 4.0 12.5 + - - +
87B PHE* 4.3 15.9 - - + -
90B VAL* 4.5 4.0 - - + -
105B VAL* 2.8 28.9 + - + +
108B LEU* 1.3 77.1 - - - +
110B LYS* 1.3 60.9 + - - +
112B LYS* 4.5 12.6 + - - +
129B LEU* 4.1 22.7 - - + -
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Residues in contact with LYS 110 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106B ALA 3.6 14.6 + - - +
107B VAL 3.1 9.1 + - - +
109B LEU* 1.3 80.6 - - - +
111B GLU* 1.3 58.5 + - + +
112B LYS* 3.9 5.2 + - - +
127B HIS* 3.9 24.0 - - + +
128B TRP* 3.7 26.7 - - - +
129B LEU* 4.0 22.9 - - + +
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Residues in contact with GLU 111 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107B VAL 3.2 7.2 + - - +
108B LEU* 3.2 12.0 - - - +
110B LYS* 1.3 78.5 - - + +
112B LYS* 1.3 64.3 + - - +
113B ASP* 3.1 4.7 + - + +
114B LEU* 3.2 42.7 + - + +
124B LYS 5.7 0.2 - - - +
127B HIS* 5.6 5.8 - - + +
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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
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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