Contacts of the helix formed by residues 96 - 103 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12C ASN* 3.6 23.4 + - - -
14C LYS* 4.1 7.5 + - - -
66C GLN 5.2 0.9 - - - +
93C VAL* 4.5 6.7 - - + -
94C LEU* 3.4 3.6 + - - +
95C GLY* 1.3 77.7 - - - +
97C SER* 1.3 68.5 + - - +
98C GLU* 3.0 56.4 + - + +
99C ARG* 2.8 34.7 + - + +
100C ARG 3.1 7.4 + - - -
127C CYS* 3.7 7.4 - - - +
168C GLU* 3.6 15.7 + - + +
233C LEU* 4.5 17.0 - - + +
76D THR* 3.4 25.9 + - + -
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Residues in contact with SER 97 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95C GLY 3.4 2.8 + - - -
96C HIS* 1.3 82.4 + - - +
98C GLU* 1.3 60.0 + - - +
100C ARG* 3.8 11.7 - - - +
101C ALA* 2.9 31.7 + - - +
168C GLU* 2.8 26.5 + - - +
170C VAL* 3.5 35.8 - - - +
173C ILE* 5.3 7.6 - - - +
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Residues in contact with GLU 98 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14C LYS* 2.6 27.9 + - - +
96C HIS* 3.0 20.5 + - + +
97C SER* 1.3 78.9 + - - +
99C ARG* 1.3 58.7 + - - +
101C ALA* 4.5 2.7 - - - -
102C TYR* 3.0 53.2 + - + +
103C TYR* 3.8 1.7 - - + -
173C ILE* 6.2 0.2 - - - +
74D ALA* 3.0 27.8 - - - +
75D PHE* 4.8 0.2 - - - -
76D THR* 2.6 43.8 + - - +
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Residues in contact with ARG 99 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66C GLN 4.6 4.0 - - - -
67C ASN* 3.2 39.3 - - - +
78C GLU* 4.5 11.9 + - - -
95C GLY 5.8 1.1 - - - +
96C HIS* 2.8 20.4 + - + +
98C GLU* 1.3 76.1 - - - +
100C ARG* 1.3 66.2 + - - +
101C ALA 3.1 1.1 - - - -
103C TYR* 3.0 50.0 + - + +
104C GLY 3.5 0.2 + - - -
105C GLU* 2.8 49.4 + - - +
76D THR* 3.0 36.9 + - - +
77D GLY* 3.6 10.5 + - - -
78D GLU* 2.8 29.5 + - - -
99D ARG* 5.7 0.6 - - - +
103D TYR* 5.9 3.0 - - - -
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Residues in contact with ARG 100 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95C GLY* 2.9 26.7 + - - +
96C HIS 3.1 2.9 + - - +
97C SER* 3.8 13.0 - - - +
99C ARG* 1.3 78.3 - - - +
101C ALA* 1.3 60.2 + - - +
104C GLY* 4.1 4.9 + - - -
105C GLU* 3.5 31.7 + - + +
106C THR 4.4 0.4 - - - -
107C ASN* 3.0 33.1 + - - +
110C VAL* 3.7 35.2 - - + +
126C VAL* 5.2 1.6 - - - +
127C CYS 3.0 22.8 + - - -
128C VAL* 4.6 3.0 - - - +
129C GLY 5.8 0.7 - - - +
147C GLN* 3.9 35.5 + - - +
151C VAL* 5.6 0.6 - - - +
168C GLU* 5.6 0.6 + - - -
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Residues in contact with ALA 101 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97C SER 2.9 19.1 + - - +
98C GLU* 4.0 4.0 - - - +
100C ARG* 1.3 79.8 - - - +
102C TYR* 1.3 76.8 + - + +
104C GLY 4.9 1.0 + - - -
170C VAL* 6.6 0.4 - - + -
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Residues in contact with TYR 102 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98C GLU* 3.0 31.1 + - + +
101C ALA* 1.3 90.8 - - + +
103C TYR* 1.3 97.8 + + + +
104C GLY 3.5 2.1 + - - -
74D ALA 4.0 11.5 + - - -
75D PHE* 3.8 26.9 - + - -
103D TYR 5.4 1.4 - - - +
104D GLY* 6.0 1.7 - - - -
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Residues in contact with TYR 103 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98C GLU 3.9 5.8 - - - -
99C ARG* 3.0 56.1 + - - +
102C TYR* 1.3 102.9 - + + +
104C GLY* 1.3 63.4 + - - +
105C GLU* 3.3 10.0 + - + +
69D ILE* 4.5 9.6 - - + +
75D PHE* 3.6 27.3 - - + +
76D THR 4.4 4.7 - - - -
78D GLU* 3.4 38.8 - - + +
99D ARG* 5.9 3.8 - - - -
102D TYR 5.0 2.6 - - - +
103D TYR* 4.8 33.4 - - + +
104D GLY* 6.2 0.7 - - - -
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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