Contacts of the helix formed by residues 94 - 109 (chain B) in PDB entry 1OJ7
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 94 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93B GLY* 1.3 74.2 - - - -
95B GLY* 1.3 65.0 + - - -
96B SER 3.3 3.1 - - - -
97B VAL* 3.1 16.0 + - - +
98B LEU* 3.1 14.6 + - - +
137B LEU* 4.3 2.0 - - - -
138B THR* 3.3 4.2 + - - -
139B LEU* 3.9 25.8 - - - -
1388B NZQ 3.4 17.3 + - - -
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Residues in contact with GLY 95 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94B GLY* 1.3 70.3 - - - -
96B SER* 1.3 55.0 + - - +
98B LEU* 3.8 7.6 - - - -
99B ASP* 2.8 35.7 + - - +
137B LEU* 4.5 2.3 - - - +
139B LEU 4.4 2.8 + - - -
142B THR* 3.7 20.6 - - - -
144B SER* 4.6 1.3 - - - -
1388B NZQ 2.8 32.1 + - - -
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Residues in contact with SER 96 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65B ILE* 3.4 12.3 - - - +
66B GLU 3.5 20.9 - - - -
67B PRO* 3.8 2.0 - - - -
68B ASN 3.1 18.5 + - - -
69B PRO* 3.4 12.3 - - - +
95B GLY* 1.3 70.4 - - - -
97B VAL* 1.3 58.6 + - - +
99B ASP* 4.6 0.2 - - - -
100B GLY 2.9 23.6 + - - -
1388B NZQ 2.6 50.9 + - - -
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Residues in contact with VAL 97 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35B THR* 3.6 34.3 - - - +
36B TYR* 3.8 7.9 - - - +
37B GLY* 3.5 31.6 - - - +
65B ILE* 4.0 14.7 - - + +
91B ALA* 4.0 1.8 - - + -
92B VAL 3.9 13.0 - - - +
93B GLY* 4.1 16.4 - - - -
94B GLY 3.1 9.9 + - - +
96B SER* 1.3 75.6 - - - +
98B LEU* 1.3 64.2 + - - +
100B GLY* 3.4 0.7 + - - -
101B THR* 2.7 30.4 + - - +
1388B NZQ 5.4 2.7 - - - +
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Residues in contact with LEU 98 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91B ALA* 3.8 23.3 - - + +
93B GLY 3.6 18.4 - - - +
94B GLY 3.1 19.0 + - - +
95B GLY* 3.8 4.7 - - - +
97B VAL* 1.3 76.9 - - - +
99B ASP* 1.3 57.3 + - - +
101B THR* 3.2 3.1 + - - -
102B LYS* 2.8 32.4 + - - +
133B MET* 3.7 6.1 - - + +
135B CYS* 3.8 26.5 - - + -
136B VAL 4.8 0.9 - - - +
137B LEU* 3.9 11.9 - - + -
144B SER* 3.6 17.5 - - - +
145B GLU* 3.4 42.0 - - + +
170B PRO* 5.6 0.7 - - + -
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Residues in contact with ASP 99 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69B PRO* 4.2 2.5 - - + -
95B GLY 2.8 23.5 + - - +
96B SER* 3.9 3.1 - - - +
98B LEU* 1.3 68.4 - - - +
100B GLY* 1.3 65.7 + - - +
102B LYS* 3.2 5.2 + - - +
103B PHE 3.1 18.2 + - - -
144B SER* 2.6 29.6 + - - -
149B GLY 3.6 2.1 - - - +
150B ALA* 3.5 17.8 - - + +
151B VAL 3.0 29.0 + - - +
152B ILE* 3.5 9.5 - - - +
1388B NZQ 2.8 37.3 + - - -
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Residues in contact with GLY 100 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65B ILE* 4.4 2.0 - - - -
69B PRO* 4.0 5.1 - - - +
74B LEU* 3.6 35.0 - - - +
96B SER 2.9 17.9 + - - -
97B VAL 3.9 0.7 - - - -
99B ASP* 1.3 75.2 - - - +
101B THR* 1.3 56.4 + - - +
103B PHE* 3.2 5.5 + - - +
104B ILE* 3.0 31.4 + - - +
152B ILE* 4.1 0.4 - - - -
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Residues in contact with THR 101 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35B THR* 2.5 38.6 + - + +
65B ILE* 4.1 1.2 - - - +
89B LEU* 3.8 28.5 - - + -
91B ALA* 3.5 8.3 - - + +
97B VAL 2.7 20.1 + - - -
98B LEU 3.5 4.5 - - - -
100B GLY* 1.3 74.5 - - - +
102B LYS* 1.3 58.4 + - - +
104B ILE* 3.2 9.0 + - - +
105B ALA* 2.9 28.1 + - - +
133B MET* 3.7 20.4 - - + -
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Residues in contact with LYS 102 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98B LEU* 2.8 16.6 + - - +
99B ASP 3.2 7.2 + - - +
101B THR* 1.3 76.8 - - - +
103B PHE* 1.3 62.8 + - - +
105B ALA* 3.3 1.8 + - - +
106B ALA* 3.2 18.2 + - - +
133B MET* 3.6 13.4 - - - -
144B SER* 2.8 41.2 + - - +
147B ASN* 2.9 29.2 + - - -
149B GLY 2.8 29.7 + - - +
150B ALA* 4.1 9.0 - - + -
163B PHE* 4.0 2.5 - - + -
168B VAL* 3.4 50.7 - - + +
170B PRO* 4.0 7.2 - - - -
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Residues in contact with PHE 103 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71B TYR* 3.7 25.4 - + + -
74B LEU* 3.8 29.8 - - + -
75B MET* 4.0 13.9 - - - -
78B VAL* 4.5 1.6 - - + -
99B ASP 3.1 5.7 + - - -
100B GLY 3.2 6.5 + - - +
102B LYS* 1.3 77.0 - - - +
104B ILE* 1.3 59.7 + - - +
106B ALA* 3.2 1.7 + - - +
107B ALA* 2.8 50.8 + - + +
116B PRO* 3.5 28.5 - - + -
119B ILE* 4.1 11.0 - - + -
120B LEU* 3.7 26.9 - - + -
152B ILE* 3.7 25.1 - - + -
163B PHE* 3.8 15.0 - + + -
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Residues in contact with ILE 104 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35B THR* 4.4 9.4 - - + -
65B ILE* 4.3 10.3 - - + -
74B LEU* 3.8 36.3 - - + +
77B ALA* 3.5 20.9 - - + -
78B VAL* 4.0 19.0 - - + +
81B VAL* 3.9 28.0 - - + -
89B LEU* 4.2 11.9 - - + -
100B GLY 3.0 23.5 + - - +
101B THR* 3.2 11.6 + - - +
103B PHE* 1.3 75.0 - - - +
105B ALA* 1.3 64.6 + - - +
107B ALA* 4.0 0.2 - - - +
108B ALA* 3.0 25.1 + - - +
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Residues in contact with ALA 105 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89B LEU* 3.5 16.8 - - + +
101B THR 2.9 16.8 + - - +
102B LYS* 3.6 8.5 - - - +
104B ILE* 1.3 78.8 - - - +
106B ALA* 1.3 58.9 + - - +
108B ALA* 4.0 4.9 + - - +
109B ASN* 4.2 5.0 + - - -
130B ALA* 3.3 11.0 - - + -
131B ILE* 3.1 47.2 + - - +
133B MET* 4.7 7.6 - - + -
168B VAL* 4.7 2.5 - - + -
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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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102B LYS 3.2 15.5 + - - +
103B PHE 3.9 2.5 - - - +
105B ALA* 1.3 75.0 - - - +
107B ALA* 1.3 66.7 + - - +
108B ALA 3.3 0.4 - - - -
109B ASN* 3.3 6.1 + - - +
110B TYR* 3.3 23.9 + - - +
119B ILE* 4.0 8.1 - - + -
127B ILE* 3.6 37.5 - - + -
129B SER 4.2 4.6 - - - +
130B ALA* 4.0 6.7 - - - +
163B PHE* 4.7 2.2 - - + -
168B VAL* 3.9 9.0 - - + -
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Residues in contact with ALA 107 (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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78B VAL* 3.6 24.5 - - + -
82B ARG* 2.8 23.6 + - - -
103B PHE* 2.8 32.1 + - + +
106B ALA* 1.3 73.1 - - - +
108B ALA* 1.3 59.3 + - - +
110B TYR* 3.2 12.1 + - - +
116B PRO* 3.8 22.5 - - + +
119B ILE* 4.0 8.9 - - + +
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Residues in contact with ALA 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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78B VAL* 4.1 7.5 - - + +
81B VAL* 3.5 18.2 - - + -
82B ARG* 3.1 34.7 + - + +
104B ILE 3.0 17.7 + - - +
105B ALA 4.2 0.9 - - - +
106B ALA 3.3 0.2 - - - -
107B ALA* 1.3 77.0 - - - +
109B ASN* 1.3 62.3 + - - +
110B TYR 4.6 0.2 - - - +
131B ILE* 3.4 28.9 - - + -
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Residues in contact with ASN 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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105B ALA 4.2 2.7 + - - +
106B ALA 3.3 4.5 + - - +
107B ALA 3.2 0.4 - - - -
108B ALA* 1.3 79.5 + - - +
110B TYR* 1.3 66.4 + - - +
111B PRO* 3.7 2.6 - - - +
129B SER* 3.1 39.0 + - - +
130B ALA* 3.6 21.9 + - - +
131B ILE* 3.8 18.9 + - - +
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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