Contacts of the helix formed by residues 99 - 104 (chain B) in PDB entry 3DVA
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 ARG 99 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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347A MET* 6.0 0.7 - - - -
94B CYS 2.8 22.4 + - - +
95B GLY* 3.7 12.9 - - - -
96B GLN 2.8 8.1 + - - +
98B ALA* 1.3 81.4 - - - +
100B ILE* 1.3 52.8 + - - +
101B ARG 3.5 2.2 - - - -
102B TYR* 3.3 16.3 + - + +
103B ARG* 2.6 52.6 + - + +
139B GLN* 3.4 21.2 + - - +
140B PRO 5.2 0.2 - - - +
87D TYR* 3.2 25.7 + - - -
126D GLU* 4.7 6.8 + - - +
127D LEU* 3.1 28.8 - - - +
130D ASP* 2.6 30.3 + - - -
132D LEU* 4.6 4.4 - - - +
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Residues in contact with ILE 100 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138A LEU* 5.5 7.0 - - + -
150A GLN* 5.3 3.6 - - - +
67B ILE* 3.7 19.7 - - + -
71B LEU* 4.9 5.2 - - + -
96B GLN* 3.0 20.9 + - + +
97B MET* 3.7 3.0 + - - -
98B ALA 3.6 1.2 - - - -
99B ARG* 1.3 76.9 - - - +
101B ARG* 1.3 53.3 + - - +
103B ARG* 4.1 19.1 - - - +
104B THR* 2.7 44.7 + - + -
108B TYR* 3.8 30.1 - - + -
109B HIS 4.4 0.2 - - - +
110B MET* 3.5 46.9 - - + -
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Residues in contact with ARG 101 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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346A ILE* 3.1 18.5 - - - +
347A MET 4.0 6.3 - - - +
348A PHE* 3.5 22.9 + - - +
349A GLU* 3.5 33.6 + - - +
97B MET 5.0 1.6 + - - -
98B ALA 5.3 1.7 + - - +
99B ARG 3.5 0.4 - - - -
100B ILE* 1.3 77.3 - - - +
102B TYR* 1.3 58.2 + - - +
105B GLY* 3.0 6.9 + - - -
106B GLY* 2.7 49.3 + - - -
108B TYR 3.3 14.3 + - - +
109B HIS* 3.2 35.5 + - - +
110B MET 5.5 0.8 - - - +
164B ASN* 3.5 13.3 + - - +
165B ASP* 2.6 31.5 + - - +
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Residues in contact with TYR 102 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126A PHE* 4.7 5.6 - - + +
343A LEU* 3.8 54.0 - - + +
346A ILE* 3.2 28.3 + - + +
347A MET* 3.6 35.8 + - + +
98B ALA 5.4 0.8 + - - +
99B ARG* 3.3 19.1 + - + +
101B ARG* 1.3 77.7 - - - +
103B ARG* 1.3 73.9 + - + +
105B GLY* 3.0 10.9 + - - -
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Residues in contact with ARG 103 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126A PHE* 4.8 2.4 - - - +
129A ASN* 2.8 45.5 + - - +
139A PRO* 4.4 19.5 - - + -
140A PRO 5.9 1.8 - - - -
141A GLN* 4.2 11.6 + - - +
150A GLN* 5.1 0.6 + - - +
95B GLY 2.7 27.9 + - - -
96B GLN* 2.8 27.0 + - - +
99B ARG* 2.6 32.0 + - + +
100B ILE* 3.7 24.7 - - - +
102B TYR* 1.3 82.2 - - + +
104B THR* 1.3 60.6 + - + +
105B GLY 3.4 0.2 - - - -
126D GLU* 2.7 42.3 + - - +
127D LEU* 4.4 4.4 - - - +
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Residues in contact with THR 104 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129A ASN* 3.6 18.2 - - - +
130A GLN* 3.6 6.4 - - - +
138A LEU* 4.9 2.0 - - + -
139A PRO* 4.0 22.2 - - + -
100B ILE* 2.7 33.5 + - + +
101B ARG 3.6 1.7 + - - -
103B ARG* 1.3 78.3 - - + +
105B GLY* 1.3 61.5 + - - +
107B ARG* 3.0 21.8 + - - +
108B TYR* 3.0 53.8 + - + -
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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