Contacts of the helix formed by residues 92 - 101 (chain E) in PDB entry 1S9D
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 THR 92 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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90E GLN* 3.0 28.2 + - + +
91E ASN* 1.3 80.4 - - - +
93E PRO* 1.3 75.1 - - + +
94E GLU* 3.7 12.7 + - - +
95E GLU* 3.2 28.4 + - - +
96E ILE* 2.9 26.8 + - - +
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Residues in contact with PRO 93 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91E ASN 4.5 1.1 - - - +
92E THR* 1.3 88.9 - - + +
94E GLU* 1.3 75.0 + - - +
96E ILE* 4.0 0.7 - - - +
97E ALA* 3.0 26.0 + - - +
121E LEU* 4.1 14.8 - - + -
124E ALA* 3.7 45.1 - - + +
125E VAL* 3.7 19.3 - - + +
128E ALA* 4.0 3.6 - - + +
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Residues in contact with GLU 94 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92E THR* 3.7 16.9 - - - +
93E PRO* 1.3 87.5 - - - +
95E GLU* 1.3 64.6 + - + +
97E ALA* 3.5 2.3 + - - +
98E ARG* 3.1 36.6 + - - +
128E ALA* 4.0 17.7 - - + +
132E LEU* 5.3 0.2 - - - +
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Residues in contact with GLU 95 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89E LEU* 3.6 11.1 - - + +
90E GLN* 3.6 40.7 - - + +
92E THR* 3.0 20.2 + - - +
94E GLU* 1.3 82.7 - - + +
96E ILE* 1.3 63.7 + - - +
98E ARG* 3.4 29.2 + - - +
99E PHE* 3.0 22.3 + - - +
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Residues in contact with ILE 96 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80E ILE* 4.1 24.7 - - + -
89E LEU* 4.1 18.6 - - + -
90E GLN 4.1 5.4 - - - +
91E ASN* 3.7 23.6 - - - +
92E THR 2.9 25.6 + - - +
93E PRO 4.0 4.0 - - - +
95E GLU* 1.3 77.7 - - - +
97E ALA* 1.3 62.3 + - - +
99E PHE* 3.0 17.5 + - - +
100E LEU* 3.1 16.5 + - + +
114E TYR* 3.9 35.9 - - + +
121E LEU* 4.5 13.9 - - + -
125E VAL* 3.9 9.4 - - + -
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Residues in contact with ALA 97 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93E PRO 3.0 18.1 + - - +
94E GLU 3.8 4.3 - - - +
96E ILE* 1.3 76.0 - - - +
98E ARG* 1.4 57.6 + - - +
100E LEU* 3.2 7.7 + - - +
101E TYR* 2.9 30.5 + - - +
125E VAL* 3.8 15.2 - - + +
128E ALA* 3.8 7.6 - - + +
129E PHE* 3.6 36.7 - - + +
132E LEU* 3.8 3.7 - - + +
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Residues in contact with ARG 98 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94E GLU* 3.1 25.1 + - - +
95E GLU* 3.6 33.6 + - - +
97E ALA* 1.4 76.2 - - - +
99E PHE* 1.3 62.3 + - - +
101E TYR* 3.6 15.5 - - - +
132E LEU* 3.8 33.1 - - + +
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Residues in contact with PHE 99 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65E MET* 4.2 13.5 - - - -
69E ARG* 3.7 39.6 + - + -
72E PHE* 5.0 2.2 - + + -
80E ILE* 4.3 9.0 - - + -
83E LEU* 3.4 30.7 - - + -
88E LEU 5.7 2.2 - - - -
89E LEU* 4.0 27.8 - - + -
95E GLU 3.0 14.1 + - - +
96E ILE* 3.0 8.3 + - - +
98E ARG* 1.3 78.2 - - - +
100E LEU* 1.3 74.3 + - + +
101E TYR 4.2 0.2 - - - +
103E GLY* 3.6 17.5 - - - -
106E LEU* 3.7 26.4 - - + +
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Residues in contact with LEU 100 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72E PHE* 3.4 35.7 - - + -
80E ILE* 4.9 2.0 - - + -
96E ILE* 3.1 14.8 + - + +
97E ALA* 3.2 7.2 + - - +
99E PHE* 1.3 84.9 - - + +
101E TYR* 1.3 64.3 + - - +
102E LYS 3.0 4.3 + - - -
103E GLY* 3.1 9.0 + - - -
106E LEU* 3.8 15.3 - - + -
111E ILE* 3.8 28.1 - - + +
114E TYR* 3.9 26.5 - - + -
115E LEU* 4.1 11.4 - - + -
125E VAL* 4.0 16.6 - - + -
129E PHE* 3.9 12.0 - - + -
150E SER 5.2 0.3 - - - +
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Residues in contact with TYR 101 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97E ALA 2.9 16.2 + - - +
98E ARG* 3.6 13.1 + - - +
99E PHE 3.4 0.8 - - - -
100E LEU* 1.3 71.2 - - - +
102E LYS* 1.3 105.9 + - + +
103E GLY* 3.2 2.1 + - - -
129E PHE* 3.8 13.9 - + + -
132E LEU* 3.8 44.7 + - + -
133E HIS* 3.6 38.1 - + - -
146E GLN* 4.6 11.4 + - - -
150E SER* 3.9 9.9 - - - -
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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