Contacts of the helix formed by residues 98 - 103 (chain A) in PDB entry 1VHQ
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 PHE 98 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16A VAL* 2.7 27.4 + - + +
17A TYR* 3.4 45.8 - + + +
97A GLY* 1.3 72.2 - - - -
99A GLY* 1.3 55.0 + - - +
100A ALA 3.1 0.2 - - - -
101A ALA* 2.9 26.7 + - + +
102A LYS* 3.0 31.9 + - + +
139A ILE* 4.9 5.2 - - + -
231A ACT 4.0 31.4 - - + -
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Residues in contact with GLY 99 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A SER* 3.1 23.0 - - - -
18A ASP 4.1 1.1 - - - -
19A GLY* 2.9 25.5 + - - +
98A PHE* 1.3 77.1 - - - +
100A ALA* 1.3 56.6 + - - +
102A LYS* 3.7 1.8 - - - -
103A ASN* 2.8 36.2 + - - -
104A LEU 3.1 6.4 + - - -
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Residues in contact with ALA 100 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A SER* 3.5 4.4 + - - -
95A PRO 4.5 9.2 - - - +
96A GLY 4.6 1.8 + - - -
97A GLY 3.0 14.9 + - - +
99A GLY* 1.3 77.3 - - - +
101A ALA* 1.3 54.4 + - - +
102A LYS 3.4 0.9 - - - -
104A LEU* 3.7 20.0 - - + +
105A SER* 2.9 24.3 + - - -
139A ILE* 4.1 12.6 - - + -
140A ALA* 4.1 13.5 - - + +
143A MSE 3.8 22.4 - - + +
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Residues in contact with ALA 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 GLY 4.2 0.2 + - - -
98A PHE* 2.9 12.3 + - + +
100A ALA* 1.3 74.2 - - - +
102A LYS* 1.3 59.0 + - + +
105A SER* 3.1 18.9 - - - +
106A ASN* 3.5 1.6 - - - -
107A PHE* 3.2 18.3 + - + -
108A ALA* 2.8 46.1 + - + +
139A ILE* 4.3 17.5 - - + -
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Residues in contact with LYS 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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17A TYR 2.9 26.9 + - - +
18A ASP* 4.7 2.7 - - - -
49A VAL* 3.3 37.1 - - + +
50A ASP* 2.7 38.9 + - - +
52A ILE* 4.1 7.7 - - - +
98A PHE* 3.0 29.4 + - + +
99A GLY* 3.3 3.6 + - - +
101A ALA* 1.3 81.7 - - - +
103A ASN* 1.3 61.1 + - - +
105A SER 3.0 13.6 + - - +
106A ASN* 4.8 3.9 - - - +
108A ALA* 3.8 18.8 - - + -
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Residues in contact with ASN 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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12A SER* 3.0 30.7 + - - +
18A ASP* 3.1 20.8 + - - +
44A PRO* 5.4 0.2 - - + -
46A LYS* 2.9 37.8 + - - +
47A GLN 4.4 1.4 - - - +
48A GLN* 3.6 6.6 - - - +
49A VAL* 3.0 29.1 + - - +
50A ASP* 5.9 0.6 + - - +
66A VAL* 3.7 23.2 - - + +
99A GLY* 2.8 19.0 + - - +
102A LYS* 1.3 78.4 - - - +
104A LEU* 1.3 64.2 + - + +
105A SER 3.4 1.3 - - - -
117A ASP* 4.3 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