Contacts of the helix formed by residues 96 - 108 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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79A ALA 3.2 21.8 - - - -
80A MET 3.5 7.2 - - - -
82A ALA* 2.5 37.8 + - - -
85A ILE* 3.8 1.4 - - - +
95A VAL* 1.3 74.9 - - - +
97A CYS* 1.3 64.5 + - - +
98A VAL 3.4 2.6 + - - -
99A SER* 2.7 26.5 + - - -
100A CYS* 3.1 15.4 + - - +
1294A HEC 4.1 7.4 - - - -
1295A HEC 3.6 12.2 - - - +
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Residues in contact with CYS 97 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79A ALA 4.4 0.4 + - - -
80A MET* 3.2 28.1 + - - +
96A SER* 1.3 75.2 - - - +
98A VAL* 1.3 63.8 + - - +
100A CYS* 4.3 0.3 - - - -
101A HIS* 3.2 30.3 + - - -
1294A HEC 5.4 1.2 - - - +
1295A HEC 1.8 87.1 - - + +
1297A HEC 3.6 20.6 - - + -
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Residues in contact with VAL 98 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80A MET 3.5 3.1 + - - +
81A HIS* 3.7 35.0 - - + +
83A THR* 3.6 27.1 - - + -
96A SER* 3.2 1.9 + - - +
97A CYS* 1.3 76.9 - - - +
99A SER* 1.3 65.4 + - - +
100A CYS 3.2 0.2 + - - -
101A HIS* 3.3 5.3 + - - +
102A GLU* 3.0 31.5 + - + +
122A ARG* 5.7 2.0 - - - +
126A TRP* 3.9 37.2 - - + -
1296A HEC 5.8 0.4 - - - +
1297A HEC 4.2 14.6 - - + -
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Residues in contact with SER 99 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82A ALA 3.4 10.5 + - - -
83A THR* 4.5 12.1 - - - +
85A ILE* 3.4 14.2 - - - +
95A VAL* 3.7 6.9 - - - +
96A SER* 2.7 43.9 + - - -
98A VAL* 1.3 74.3 - - - +
100A CYS* 1.3 62.4 + - - +
102A GLU* 3.7 5.8 - - - +
103A GLN* 3.0 31.7 + - - +
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Residues in contact with CYS 100 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95A VAL* 4.6 4.5 - - + -
96A SER 3.1 5.3 + - - +
99A SER* 1.3 78.9 + - - +
101A HIS* 1.3 66.6 + - - +
103A GLN* 3.2 18.4 + - - +
104A GLN* 3.0 33.2 + - - +
1295A HEC 1.8 88.4 - - + -
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Residues in contact with HIS 101 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97A CYS 3.2 15.0 + - - +
98A VAL* 3.3 5.0 + - - +
100A CYS* 1.3 75.6 - - - +
102A GLU* 1.3 66.2 + - - +
104A GLN* 3.1 23.2 + - - +
105A THR* 3.3 10.9 + - - +
213A LEU* 3.6 24.2 - - + +
217A PHE* 4.0 9.2 - + - -
1295A HEC 2.0 90.7 + + + -
1296A HEC 4.4 11.2 - - + +
1297A HEC 3.7 16.6 - - + +
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Residues in contact with GLU 102 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83A THR* 5.6 4.0 - - + -
98A VAL* 3.0 30.3 + - + +
99A SER* 3.7 7.2 - - - +
101A HIS* 1.3 78.1 - - - +
103A GLN* 1.3 59.9 + - - +
105A THR* 2.6 31.2 + - - +
106A LYS* 3.2 29.6 + - - +
120A PRO* 4.9 6.6 - - - +
126A TRP* 6.4 0.2 - - + -
1296A HEC 2.5 41.9 - - - +
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Residues in contact with GLN 103 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95A VAL* 4.5 15.5 - - - +
99A SER* 3.0 21.5 + - - +
100A CYS* 3.2 21.9 + - - +
102A GLU* 1.3 72.3 - - - +
104A GLN* 1.3 61.6 + - - +
106A LYS* 3.1 7.0 + - - +
107A GLU* 2.8 61.6 + - - +
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Residues in contact with GLN 104 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44A ILE* 4.9 5.3 - - - +
100A CYS* 3.0 35.3 + - - +
101A HIS* 3.1 9.6 + - - +
103A GLN* 1.3 77.7 - - - +
105A THR* 1.3 57.8 + - - +
107A GLU* 4.9 9.3 + - - -
108A ARG* 3.0 67.9 + - - +
111A CYS* 4.0 2.6 - - - -
213A LEU* 3.8 22.9 - - + -
1295A HEC 3.6 21.3 - - + +
1296A HEC 4.4 6.1 - - + -
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Residues in contact with THR 105 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101A HIS 3.5 13.9 - - - +
102A GLU* 2.6 29.4 + - - +
104A GLN* 1.3 76.7 - - - +
106A LYS* 1.3 81.1 + - - +
111A CYS* 3.6 9.2 - - - -
112A ALA* 3.2 29.8 + - - -
115A HIS* 3.6 24.3 + - - +
1296A HEC 3.7 37.5 - - + -
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Residues in contact with LYS 106 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102A GLU* 3.2 26.5 + - - +
103A GLN* 3.1 10.8 + - - +
105A THR* 1.3 105.4 + - - +
107A GLU* 1.3 63.1 + - + +
108A ARG 3.6 0.2 - - - -
112A ALA* 3.7 16.6 - - + +
115A HIS* 4.0 26.7 + - + +
116A ALA* 5.6 2.0 - - - +
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Residues in contact with GLU 107 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103A GLN* 2.8 49.7 + - + +
104A GLN* 4.4 8.1 + - - +
106A LYS* 1.3 84.1 - - + +
108A ARG* 1.3 67.2 + - + +
109A ARG 3.6 3.0 + - - -
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Residues in contact with ARG 108 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43A LYS* 6.1 3.9 - - - +
104A GLN* 3.0 49.2 + - - +
107A GLU* 1.3 84.2 - - + +
109A ARG* 1.3 55.1 + - - +
110A GLU* 3.0 31.2 + - - +
111A CYS* 2.7 30.5 + - - +
112A ALA* 2.8 13.6 + - - +
211A ASP* 2.6 32.3 + - - +
213A LEU* 5.0 3.0 - - - +
1295A HEC 5.1 4.8 + - - +
1296A HEC 3.4 25.7 - - - +
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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