Contacts of the helix formed by residues 100 - 105 (chain A) in PDB entry 1QV6
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 CYS 100 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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97A CYS* 3.2 10.0 - - - -
99A LYS* 1.3 81.0 - - - +
101A ARG* 1.3 67.4 + - - +
102A VAL* 3.2 8.0 + - - -
103A CYS* 3.2 16.6 + - - -
104A LYS* 3.0 22.0 + - - +
112A LEU* 3.5 37.0 - - + -
113A LYS* 5.9 0.9 - - + -
376A ZN 2.4 34.7 - - - -
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Residues in contact with ARG 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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100A CYS* 1.3 75.2 - - - +
102A VAL* 1.3 62.1 + - + +
104A LYS* 3.4 7.2 + - + +
105A HIS* 3.2 22.0 + - - +
112A LEU* 4.4 11.3 - - + +
258B SER 2.9 18.6 + - - -
259B ASN* 3.3 18.7 + - - +
260B GLY* 3.3 23.2 + - - -
261B GLY 2.9 25.3 + - - -
263B ASP* 6.6 0.2 - - - -
283B GLN* 3.8 11.3 - - - +
286B TYR* 2.9 22.8 + - + +
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Residues in contact with VAL 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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100A CYS* 3.2 7.5 - - - -
101A ARG* 1.3 75.0 - - + +
103A CYS* 1.3 67.6 + - - +
105A HIS* 3.0 14.6 + - - +
108A GLY* 3.7 4.0 - - - +
109A ASN* 3.7 11.4 - - - +
110A PHE 3.4 47.8 - - - +
111A CYS 4.0 0.9 - - - +
112A LEU* 4.0 13.9 - - + -
323A LYS* 3.2 10.2 + - - -
283B GLN* 3.4 32.8 - - - +
285B ALA* 3.7 11.9 - - + -
286B TYR* 3.9 8.7 - - + -
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Residues in contact with CYS 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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96A GLN* 3.9 17.1 + - + +
97A CYS 3.4 7.2 - - - -
98A GLY* 3.4 35.1 - - - +
100A CYS* 3.2 10.6 + - - +
102A VAL* 1.3 80.3 - - - +
104A LYS* 1.3 57.7 + - - +
108A GLY 5.1 0.2 - - - -
109A ASN* 5.7 2.2 - - - +
111A CYS* 3.6 12.6 - - - -
323A LYS* 2.9 26.4 + - - +
376A ZN 2.3 36.1 - - - -
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Residues in contact with LYS 104 (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 GLY 3.9 17.9 - - - +
99A LYS* 2.9 31.1 + - - +
100A CYS 3.0 15.7 + - - +
101A ARG* 3.8 7.6 - - - +
102A VAL 3.1 0.4 - - - -
103A CYS* 1.3 77.1 - - - +
105A HIS* 1.3 61.8 + - - +
106A PRO* 3.7 5.0 - - - +
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Residues in contact with HIS 105 (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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101A ARG* 3.2 11.8 + - + +
102A VAL 3.0 11.0 + - - +
104A LYS* 1.3 78.5 - - - +
106A PRO* 1.3 73.7 - - + +
107A GLU* 2.9 40.0 + - + -
108A GLY 3.3 7.6 + - - +
323A LYS* 2.5 31.4 + - - -
263B ASP* 4.8 5.0 + - - -
286B TYR* 3.5 58.0 + + + -
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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