Contacts of the helix formed by residues 95 - 102 (chain A) in PDB entry 4M92
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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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28A ASN* 4.6 1.5 - - - +
29A GLY 4.5 4.7 - - - -
90A VAL* 4.0 12.9 - - - +
91A ASP 2.8 13.1 + - - -
92A TYR 3.7 3.1 - - - -
94A GLU* 1.3 77.1 - - - +
96A THR* 1.3 61.9 + - - -
97A ASP* 3.2 12.3 - - - -
98A VAL* 2.9 21.5 + - - +
99A PHE* 3.2 13.8 + - - -
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Residues in contact with THR 96 (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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92A TYR* 2.5 52.7 + - + +
93A ASP* 4.1 6.9 + - - -
94A GLU 3.7 1.4 - - - -
95A GLY* 1.3 73.9 - - - +
97A ASP* 1.3 62.5 + - - +
99A PHE* 3.2 3.8 + - - +
100A GLN* 3.1 39.0 + - - +
14B TYR* 5.5 0.4 - - - -
15B GLY* 3.6 22.8 - - - +
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Residues in contact with ASP 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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29A GLY* 3.7 12.3 + - - -
33A ARG* 2.8 37.8 + - - +
94A GLU 4.8 1.0 - - - +
95A GLY* 3.5 14.6 - - - -
96A THR* 1.3 72.3 + - - +
98A VAL* 1.3 66.9 + - - -
100A GLN* 3.9 12.2 - - - +
101A GLN* 3.1 22.3 + - - +
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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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29A GLY* 3.6 32.3 - - - +
32A PHE* 3.8 42.4 - - + -
33A ARG* 4.9 2.9 - - - +
49A PHE* 3.9 24.9 - - + -
90A VAL* 4.2 11.2 - - + -
95A GLY* 2.9 11.5 + - - +
97A ASP* 1.3 77.0 + - - +
99A PHE* 1.3 64.6 + - - +
101A GLN* 3.2 6.3 + - + +
102A LEU* 3.1 25.6 + - + +
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Residues in contact with PHE 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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49A PHE* 3.7 28.0 - + + -
50A THR 3.6 20.4 - - - -
90A VAL* 3.6 21.5 - - + -
91A ASP 4.0 1.3 - - - -
92A TYR* 3.5 37.2 - + + -
95A GLY 3.2 13.3 + - - -
96A THR 3.2 8.4 + - - +
98A VAL* 1.3 78.2 - - - +
100A GLN* 1.3 59.2 + - + +
102A LEU 3.3 1.7 + - - -
103A ASN 2.9 8.1 + - - -
104A MET* 2.8 66.0 + - + +
106A SER 3.7 19.3 - - - -
107A ALA* 4.4 2.0 - - + -
12B LEU* 3.8 13.2 - - + -
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Residues in contact with GLN 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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92A TYR* 5.1 3.1 + - + +
96A THR* 3.1 30.9 + - + +
97A ASP* 3.9 11.2 - - - +
99A PHE* 1.3 75.6 - - + +
101A GLN* 1.3 63.9 + - - +
103A ASN* 3.1 22.8 + - - +
104A MET 5.4 1.3 - - - +
13B LYS 4.9 9.9 + - - -
14B TYR* 6.0 3.0 - - - +
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Residues in contact with GLN 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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32A PHE* 6.5 0.9 - - + -
37A LYS* 4.4 20.3 - - - +
97A ASP 3.1 17.0 + - - +
98A VAL* 3.2 9.1 + - + +
100A GLN* 1.3 77.3 - - - +
102A LEU* 1.3 62.5 + - + +
103A ASN* 3.3 9.6 + - - -
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Residues in contact with LEU 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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32A PHE* 4.4 5.8 - - + -
37A LYS* 4.3 22.7 - - - +
49A PHE* 3.4 39.7 - - + -
98A VAL* 3.1 24.8 + - + +
99A PHE 4.0 2.0 - - - +
101A GLN* 1.3 80.6 - - + +
103A ASN* 1.3 73.7 + - - +
104A MET* 3.2 23.3 + - + +
111A MET* 4.6 8.1 - - + -
113A PHE* 4.5 10.8 - - + -
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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
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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