Contacts of the helix formed by residues 96 - 103 (chain A) in PDB entry 3Q37
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 HIS 96 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12A ASN* 3.5 25.8 + - - -
14A LYS* 4.2 6.8 + - - -
66A GLN 5.4 0.9 - - - +
93A VAL* 4.5 5.8 - - + -
94A LEU 3.3 3.2 + - - -
95A GLY* 1.3 80.3 - - - +
97A SER* 1.3 60.7 + - - +
98A GLU* 3.1 55.3 + - + +
99A ARG* 2.8 29.5 + - + +
100A ARG 3.1 7.4 + - - -
127A CYS* 3.7 15.3 - - - -
168A GLU* 3.3 30.8 + - - -
233A LEU* 4.4 8.5 - - + +
76B THR* 3.5 25.5 + - + -
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Residues in contact with SER 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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95A GLY 3.4 2.4 + - - -
96A HIS* 1.3 76.7 + - - +
98A GLU* 1.3 61.6 + - - +
99A ARG 3.3 0.2 - - - -
100A ARG* 3.5 11.8 + - - +
101A ALA* 3.0 28.9 + - - +
128A VAL 6.6 0.2 - - - -
168A GLU* 2.7 36.3 + - - -
170A VAL* 3.5 30.1 - - - +
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Residues in contact with GLU 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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14A LYS* 2.8 27.8 + - - +
96A HIS* 3.0 21.8 + - + +
97A SER* 1.3 79.7 - - - +
99A ARG* 1.3 59.5 + - - +
101A ALA* 4.4 2.5 - - - -
102A TYR* 2.9 53.0 + - + +
103A TYR* 3.8 1.9 - - + -
74B ALA* 3.1 29.6 - - + +
75B PHE* 4.8 0.2 - - - -
76B THR* 2.7 42.2 + - - +
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Residues in contact with ARG 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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66A GLN 4.4 4.3 - - - -
67A ASN* 3.4 36.7 - - - +
78A GLU* 4.9 9.1 + - - -
94A LEU* 6.5 0.2 - - - +
95A GLY 5.6 1.8 - - - +
96A HIS* 2.8 20.9 + - + +
98A GLU* 1.3 75.0 - - - +
100A ARG* 1.3 64.3 + - - +
101A ALA 3.1 1.1 - - - -
103A TYR* 3.0 51.3 + - + +
105A GLU* 2.9 51.1 + - + +
113A LYS* 5.3 0.6 - - - +
76B THR* 2.8 44.2 + - - +
77B GLY* 3.6 8.9 - - - -
78B GLU* 2.9 29.1 + - - -
99B ARG* 5.9 0.6 - - - +
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Residues in contact with ARG 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 GLY* 2.8 27.0 + - - +
96A HIS 3.1 2.9 + - - +
97A SER* 3.7 14.1 - - - +
99A ARG* 1.3 79.1 - - - +
101A ALA* 1.3 59.6 + - - +
104A GLY* 4.3 4.3 + - - -
105A GLU* 3.5 32.0 + - + +
106A THR 4.5 0.4 - - - -
107A ASN* 2.9 33.1 + - - +
110A VAL* 3.7 33.3 - - + +
126A VAL* 5.1 1.6 - - - +
127A CYS 2.9 22.8 + - - -
128A VAL* 4.5 3.4 - - - +
129A GLY 5.9 1.3 - - - +
147A GLN* 3.9 33.8 + - - +
151A VAL* 5.3 1.2 - - - +
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Residues in contact with ALA 101 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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97A SER 3.0 18.3 + - - +
98A GLU* 3.8 6.1 - - - +
100A ARG* 1.3 80.5 - - - +
102A TYR* 1.3 77.0 + - + +
103A TYR 3.6 0.2 - - - -
104A GLY* 4.8 1.8 + - - -
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Residues in contact with TYR 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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98A GLU* 2.9 39.1 + - + +
101A ALA* 1.3 87.1 - - + +
103A TYR* 1.3 93.8 + + + +
104A GLY 3.5 1.5 + - - -
74B ALA* 3.9 11.6 + - - +
75B PHE* 3.9 31.8 - + - -
103B TYR 5.8 0.2 - - - +
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Residues in contact with TYR 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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98A GLU 4.0 2.0 - - - -
99A ARG* 3.0 58.6 + - - +
102A TYR* 1.3 108.4 - + + +
104A GLY* 1.3 63.7 + - - +
105A GLU* 3.2 10.9 + - + +
69B ILE* 4.3 9.6 - - + +
75B PHE* 3.6 27.9 - - + +
76B THR 4.3 5.2 - - - -
78B GLU* 3.4 38.5 - - + +
99B ARG* 6.2 1.6 - - - -
103B TYR* 5.7 15.4 - - - +
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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