Contacts of the helix formed by residues 95 - 101 (chain A) in PDB entry 1HTI
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 95 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11A ASN* 3.3 22.1 + - - -
13A LYS* 4.4 4.8 - - - -
64A GLN 5.3 0.7 - - - +
92A VAL* 4.0 22.0 - - + -
93A LEU* 3.2 2.5 - - - +
94A GLY* 1.3 77.8 - - - +
96A SER* 1.3 70.5 + - - +
97A GLU* 3.1 23.2 + - - -
98A ARG* 2.8 40.3 + - + +
99A ARG* 3.1 4.6 + - - -
126A CYS* 3.8 16.2 - - - -
165A GLU* 3.1 23.7 + - - -
230A LEU* 4.4 8.3 - - + +
75B THR* 3.5 36.2 + - + -
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Residues in contact with SER 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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94A GLY 3.6 0.6 + - - -
95A HIS* 1.3 76.5 + - - +
97A GLU* 1.3 61.1 + - - +
99A ARG* 3.7 8.7 - - - +
100A HIS* 2.8 51.9 + - - +
165A GLU* 2.8 35.7 + - - +
167A VAL* 4.2 17.8 - - - +
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Residues in contact with GLU 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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13A LYS* 3.0 23.1 + - - -
95A HIS* 2.9 19.9 + - + +
96A SER* 1.3 80.6 + - - +
98A ARG* 1.3 56.6 - - - +
101A VAL* 2.8 46.7 + - + +
102A PHE* 3.0 8.9 - - + -
170A ILE* 5.1 7.6 - - - +
73B ALA* 3.1 32.1 - - - +
74B PHE* 4.5 3.1 - - - -
75B THR* 2.5 40.9 + - - +
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Residues in contact with ARG 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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64A GLN 5.1 0.9 - - - +
65A ASN* 3.7 26.2 - - + +
77A GLU* 5.9 1.0 + - - -
93A LEU* 6.0 0.9 - - - -
94A GLY 5.2 1.8 - - - +
95A HIS* 2.8 29.0 + - + +
97A GLU* 1.3 77.8 - - - +
99A ARG* 1.3 56.9 + - + +
100A HIS 3.2 1.1 - - - -
102A PHE* 2.9 66.5 + - - +
103A GLY 3.0 0.3 + - - -
104A GLU* 2.9 46.0 + - + +
75B THR* 2.6 44.4 + - + -
76B GLY* 3.8 4.1 + - - -
77B GLU* 2.9 28.1 + - - -
98B ARG* 6.1 1.4 - - - +
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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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94A GLY* 2.8 29.3 + - - +
95A HIS 3.1 4.9 + - - +
96A SER* 3.9 11.9 - - - +
98A ARG* 1.3 78.4 - - - +
100A HIS* 1.3 77.6 + - + +
103A GLY* 4.5 5.1 - - - -
104A GLU* 3.5 20.4 + - + +
106A ASP* 3.1 36.6 + - - +
109A ILE* 3.4 32.5 - - + +
126A CYS 2.8 23.0 + - - -
127A ILE* 4.1 9.2 - - - +
128A GLY 6.0 1.8 - - - +
146A GLN* 4.0 20.3 - - - +
150A ILE* 4.1 17.8 - - - +
165A GLU* 5.7 0.7 - - - -
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Residues in contact with HIS 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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96A SER* 2.8 33.5 + - - +
99A ARG* 1.3 100.2 + - + +
101A VAL* 1.3 68.3 + - + +
102A PHE 3.4 0.2 - - - -
103A GLY* 4.4 3.4 + - - +
128A GLY 4.6 6.4 + - - -
130A LYS* 3.4 51.0 + - + +
146A GLN* 5.9 3.0 + - - -
167A VAL* 3.8 20.2 - - + +
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Residues in contact with VAL 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 GLU* 2.8 32.8 + - + +
100A HIS* 1.3 83.3 - - + +
102A PHE* 1.3 83.5 + - + +
103A GLY 3.6 1.6 + - - -
67B TYR* 4.3 9.4 - - - +
74B PHE* 4.3 20.4 - - + -
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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