Contacts of the helix formed by residues 96 - 108 (chain B) in PDB entry 1OFY
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 SER 96 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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79B ALA 3.2 22.4 - - - -
80B MET 3.6 7.0 - - - -
82B ALA* 2.4 37.4 + - - -
85B ILE* 3.9 1.0 - - - +
95B VAL* 1.3 75.2 - - - +
97B CYS* 1.3 65.3 + - - +
98B VAL 3.5 1.9 + - - -
99B SER* 2.8 25.3 + - - -
100B CYS 3.0 17.5 + - - -
1294B HEC 4.1 7.9 - - - -
1295B HEC 3.6 11.6 - - - +
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Residues in contact with CYS 97 (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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80B MET* 3.1 23.1 + - - +
96B SER* 1.3 75.2 - - - +
98B VAL* 1.3 63.9 + - - +
100B CYS* 4.2 0.3 - - - +
101B HIS* 3.3 28.1 + - - -
1294B HEC 5.5 2.1 - - - +
1295B HEC 1.8 72.6 - - + +
1297B HEC 3.6 30.5 - - + -
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Residues in contact with VAL 98 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80B MET 3.4 3.8 + - - +
81B HIS* 3.6 35.0 - - + +
83B THR* 3.6 26.0 - - + -
96B SER* 3.2 0.4 + - - -
97B CYS* 1.3 77.9 - - - +
99B SER* 1.3 61.8 + - - +
101B HIS* 3.3 6.5 + - - +
102B GLU* 2.9 27.5 + - + +
122B ARG* 4.3 18.6 - - - +
126B TRP* 3.9 26.5 - - + -
1296B HEC 5.5 0.7 - - - +
1297B HEC 4.1 16.4 - - + -
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Residues in contact with SER 99 (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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82B ALA 3.4 11.2 + - - -
83B THR* 4.5 9.0 - - - +
85B ILE* 3.4 15.5 - - - +
95B VAL* 3.8 7.1 - - - +
96B SER* 2.8 43.0 + - - -
98B VAL* 1.3 74.4 - - - +
100B CYS* 1.3 58.7 + - - +
102B GLU* 3.3 7.8 + - - +
103B GLN* 2.9 33.9 + - - +
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Residues in contact with CYS 100 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95B VAL* 4.7 4.3 - - + -
96B SER 3.0 3.7 + - - +
99B SER* 1.3 80.8 + - - +
101B HIS* 1.3 64.4 + - - +
103B GLN* 3.0 18.9 + - - +
104B GLN* 3.0 43.7 + - - +
1295B HEC 1.8 87.9 - - + -
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Residues in contact with HIS 101 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97B CYS 3.3 16.2 + - - +
98B VAL* 3.7 4.5 - - - +
100B CYS* 1.3 75.4 - - - +
102B GLU* 1.3 65.5 + - - +
104B GLN* 3.2 17.1 + - - +
105B THR* 3.3 17.0 + - - +
213B LEU* 3.7 23.3 - - + +
217B PHE* 3.8 10.7 - + + -
1295B HEC 2.1 90.8 + + + -
1296B HEC 4.4 14.1 - - + +
1297B HEC 4.0 12.7 - - + +
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Residues in contact with GLU 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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83B THR* 5.1 6.5 - - + -
98B VAL* 2.9 30.9 + - + +
99B SER* 3.6 7.4 - - - +
101B HIS* 1.3 78.3 - - - +
103B GLN* 1.3 63.3 + - - +
105B THR* 2.8 26.8 + - - -
106B LYS* 3.2 32.8 + - - +
120B PRO* 4.8 2.8 - - - +
122B ARG* 3.5 22.1 + - - +
1296B HEC 2.3 41.9 - - - +
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Residues in contact with GLN 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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95B VAL* 4.4 15.1 - - - +
99B SER* 2.9 15.5 + - - +
100B CYS* 3.0 25.1 + - - +
102B GLU* 1.3 75.1 - - - +
104B GLN* 1.3 61.9 + - - +
106B LYS* 2.9 9.8 + - - +
107B GLU* 2.8 63.0 + - - +
1295B HEC 5.7 0.2 - - - +
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Residues in contact with GLN 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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44B ILE* 4.8 6.5 - - - +
100B CYS* 3.0 40.3 + - - +
101B HIS* 3.2 9.4 + - - +
103B GLN* 1.3 79.2 - - - +
105B THR* 1.3 63.2 + - - +
106B LYS 3.0 1.0 + - - -
107B GLU* 4.5 6.2 + - - +
108B ARG* 3.1 58.2 + - - +
111B CYS* 4.1 1.5 - - - +
213B LEU* 3.9 23.3 - - + -
1295B HEC 3.7 23.7 - - + +
1296B HEC 4.4 4.5 - - + -
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Residues in contact with THR 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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101B HIS 3.6 12.6 - - - +
102B GLU* 2.8 22.6 + - - -
104B GLN* 1.3 75.8 - - - +
106B LYS* 1.3 62.0 + - - +
111B CYS* 3.6 11.1 - - - -
112B ALA* 3.2 29.3 + - - -
115B HIS* 3.6 30.6 + - - +
1296B HEC 3.5 48.4 - - + +
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Residues in contact with LYS 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 GLU* 3.2 36.3 + - - +
103B GLN* 2.9 11.6 + - - +
105B THR* 1.3 86.8 + - - +
107B GLU* 1.3 64.4 + - + +
108B ARG 3.6 0.4 - - - -
112B ALA* 3.7 15.7 - - - +
115B HIS* 6.0 3.1 - - + +
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Residues in contact with GLU 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 GLN* 2.8 49.7 + - - +
104B GLN* 4.4 5.5 + - - +
106B LYS* 1.3 85.7 - - + +
108B ARG* 1.3 64.7 + - + +
109B ARG 3.8 2.5 + - - -
112B ALA* 5.3 0.2 - - - -
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Residues in contact with ARG 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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43B LYS* 6.2 3.7 - - - +
104B GLN* 3.1 44.6 + - - +
107B GLU* 1.3 82.3 - - + +
109B ARG* 1.3 56.3 + - - +
110B GLU* 2.9 32.2 + - - +
111B CYS* 2.7 32.8 + - - +
112B ALA* 2.8 13.9 + - - -
211B ASP* 2.5 33.7 + - - +
213B LEU* 5.3 1.8 - - - +
1295B HEC 5.2 7.5 + - - +
1296B HEC 3.6 22.6 - - - +
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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