Contacts of the helix formed by residues 99 - 107 (chain B) in PDB entry 4O8M
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 VAL 99 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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95B LEU 2.9 5.9 + - - +
96B MET* 3.4 10.6 - - - -
98B ILE* 1.3 81.5 - - + +
100B PRO* 1.3 70.6 - - + +
101B ASP* 4.4 2.7 - - + +
102B LEU* 3.2 32.4 + - + +
129B LEU* 4.0 32.3 - - + +
132B LYS* 4.1 16.6 - - + +
133B LEU* 3.7 40.8 - - + +
136B HIS* 4.5 3.8 - - + -
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Residues in contact with PRO 100 (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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96B MET* 3.3 24.6 - - + +
97B ASP 5.3 1.3 - - - +
98B ILE 3.8 6.7 - - - +
99B VAL* 1.3 87.4 - - + +
101B ASP* 1.3 65.1 + - - +
102B LEU 3.0 1.6 + - - -
103B GLY 3.0 7.4 + - - -
312B GLU* 3.5 49.6 - - + +
313B TRP* 3.0 18.9 + - + -
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Residues in contact with ASP 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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99B VAL* 3.2 3.0 + - + +
100B PRO* 1.3 78.8 - - - +
102B LEU* 1.3 64.1 + - - +
103B GLY 3.0 1.1 + - - -
104B VAL* 3.3 23.1 + - - +
125B TRP* 3.9 6.6 + - + -
129B LEU* 3.9 29.7 - - + +
312B GLU 4.3 1.9 - - - +
313B TRP* 3.5 7.4 - - - -
314B SER* 2.7 46.9 + - - -
317B LEU* 3.6 25.1 - - + +
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Residues in contact with LEU 102 (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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92B TYR* 3.4 28.5 - - + +
95B LEU* 3.9 27.1 - - + +
99B VAL* 3.2 35.4 + - + +
100B PRO 3.0 1.2 + - - -
101B ASP* 1.3 76.7 - - - +
103B GLY* 1.3 62.6 + - - +
104B VAL 3.1 1.2 + - - -
105B ILE* 3.2 25.5 + - + +
126B PHE* 3.9 26.0 - - + -
129B LEU* 3.7 27.1 - - + +
133B LEU* 4.1 22.0 - - + -
140B ILE* 4.8 3.8 - - + -
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Residues in contact with GLY 103 (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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92B TYR* 3.7 18.0 + - - +
93B GLY* 4.4 0.8 + - - -
96B MET* 3.8 17.9 - - - +
100B PRO 3.0 10.8 + - - -
101B ASP 3.0 2.8 - - - -
102B LEU* 1.3 79.5 - - - +
104B VAL* 1.3 61.2 + - - +
105B ILE 3.1 1.3 + - - -
106B ASN* 3.7 2.1 + - - +
176B LEU* 3.4 27.4 - - - +
313B TRP* 3.8 7.0 - - - -
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Residues in contact with VAL 104 (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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101B ASP 3.3 16.7 + - - +
102B LEU 3.1 1.6 + - - -
103B GLY* 1.3 76.2 - - - +
105B ILE* 1.3 67.2 + - - +
107B ALA* 3.0 16.6 + - + +
110B ILE* 3.7 26.4 - - + +
125B TRP* 3.6 26.0 - - + -
313B TRP* 3.6 22.4 - - + -
317B LEU* 3.6 21.8 - - + +
318B TYR* 3.9 20.9 - - - -
321B VAL* 3.7 10.1 - - + -
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Residues in contact with ILE 105 (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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92B TYR* 3.6 42.0 - - + -
102B LEU* 3.4 22.4 - - + +
103B GLY 3.1 1.4 - - - -
104B VAL* 1.3 80.0 - - - +
106B ASN* 1.3 58.8 + - - +
110B ILE* 3.9 3.3 - - - +
117B LYS* 2.7 34.7 + - + +
120B LEU* 4.5 11.5 - - + +
121B LEU* 3.6 40.4 - - + -
125B TRP* 4.1 19.1 - - + -
126B PHE* 3.9 11.0 - - + -
236B MET* 4.5 5.4 - - + -
321B VAL* 5.7 1.1 - - - -
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Residues in contact with ASN 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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91B ASP* 4.3 5.6 + - - +
92B TYR* 4.1 15.5 - - + +
93B GLY 6.0 0.4 - - - +
103B GLY 3.7 3.2 + - - -
104B VAL 3.2 0.2 - - - -
105B ILE* 1.3 81.4 - - - +
107B ALA* 1.3 67.1 + - - +
108B PRO* 3.5 0.9 - - - +
117B LYS* 3.2 18.1 + - - +
176B LEU* 3.5 21.6 - - + +
177B PHE* 4.2 3.7 - - + -
233B THR* 3.4 31.6 + - + +
234B LYS 3.4 1.6 - - - +
235B HIS* 3.9 16.5 + - - +
236B MET* 3.0 44.2 + - - +
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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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103B GLY 3.8 1.0 + - - -
104B VAL* 3.0 25.9 + - + +
105B ILE 3.5 0.4 - - - -
106B ASN* 1.3 80.5 - - - +
108B PRO* 1.3 75.1 - - + +
109B TYR 3.4 0.5 + - - -
110B ILE* 3.3 17.6 + - + +
117B LYS* 4.9 0.9 + - - -
176B LEU* 3.9 7.6 - - + -
232B HIS 4.3 1.2 - - - +
233B THR* 5.3 0.9 - - - -
306B ILE* 4.8 0.7 - - + -
313B TRP* 4.2 11.4 - - + -
318B TYR* 3.6 28.0 - - + -
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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
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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