Contacts of the helix formed by residues 99 - 108 (chain B) in PDB entry 1VDV
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 99 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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91B ILE* 3.2 36.5 + - + +
97B ARG 3.7 2.0 + - - -
98B LEU* 1.3 73.6 - - - +
100B PRO* 1.3 93.0 - - + +
101B VAL* 3.0 32.5 + - + +
102B GLN* 2.9 28.2 + - - +
103B GLU* 2.9 10.3 + - - +
125B TYR* 3.4 23.6 - + - -
128B LEU* 4.9 0.7 - - + -
204B LEU* 3.6 18.9 - - + +
209B GLU* 2.7 31.0 + - - -
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Residues in contact with PRO 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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99B HIS* 1.3 102.2 - - + +
101B VAL* 1.3 55.8 + - - +
103B GLU* 4.2 9.6 - - + +
104B ARG* 2.8 36.8 + - - +
163B PHE* 3.9 21.3 - - + -
202B MET* 3.6 48.0 - - + +
203B PRO 3.9 10.1 - - - +
204B LEU* 4.3 8.1 - - + -
205B ASP 5.6 0.4 - - - +
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Residues in contact with VAL 101 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91B ILE* 4.8 2.0 - - + -
99B HIS* 3.0 19.9 + - + +
100B PRO* 1.3 75.5 - - - +
102B GLN* 1.3 62.5 + - - +
105B ILE* 3.2 22.7 + - - +
121B VAL* 3.5 36.6 - - + +
124B MET* 3.9 10.5 - - + -
125B TYR* 4.1 11.4 - - + -
128B LEU* 3.6 30.5 - - + -
160B PHE* 3.5 24.1 - - + -
163B PHE* 3.8 9.6 - - + -
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Residues in contact with GLN 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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88B VAL* 3.4 19.6 + - - +
91B ILE* 3.7 13.4 - - + +
92B GLY* 3.4 33.3 + - - -
98B LEU* 3.6 17.6 - - + +
99B HIS* 2.9 28.9 + - - +
101B VAL* 1.3 73.6 - - - +
103B GLU* 1.3 66.6 + - - +
105B ILE* 3.4 6.0 - - - +
106B ALA* 3.2 24.8 + - - +
121B VAL* 3.9 13.7 - - + -
586B ALA* 3.2 40.4 + - + +
587B SER* 3.5 6.7 - - - +
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Residues in contact with GLU 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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98B LEU* 4.0 21.9 - - + +
99B HIS 2.9 12.7 + - - +
100B PRO* 3.6 9.8 - - + +
102B GLN* 1.3 78.2 - - - +
104B ARG* 1.3 59.7 + - - +
106B ALA* 3.7 1.7 - - - +
107B LYS* 2.9 69.0 + - + +
200B GLU 4.2 2.6 - - - +
201B PHE* 3.6 7.8 - - + +
202B MET* 3.0 42.1 + - + +
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Residues in contact with ARG 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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100B PRO* 2.8 20.4 + - - +
101B VAL 4.2 2.5 - - - +
103B GLU* 1.3 74.8 - - - +
105B ILE* 1.3 59.3 + - - +
108B SER* 2.7 35.3 + - - -
159B GLY* 4.3 7.9 - - - +
160B PHE* 4.7 3.4 - - + -
162B THR* 2.8 56.6 + - - -
163B PHE* 3.5 43.3 - - + +
201B PHE* 3.5 44.6 + - + +
202B MET 2.9 31.1 + - - -
203B PRO* 3.7 10.3 - - - +
204B LEU 4.3 0.8 - - - +
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Residues in contact with ILE 105 (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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101B VAL 3.2 16.0 + - - +
102B GLN 3.4 11.9 - - - +
104B ARG* 1.3 77.0 - - - +
106B ALA* 1.3 61.3 + - - +
108B SER* 3.5 5.4 + - - -
110B GLY* 2.8 58.9 + - - +
111B SER* 3.8 1.7 + - - +
116B CYS* 6.4 0.2 - - - -
117B THR* 4.0 19.1 - - + -
120B ILE* 3.8 29.8 - - + -
121B VAL* 4.0 9.4 - - + -
156B ILE* 4.1 13.9 - - + +
160B PHE* 3.8 16.9 - - + -
586B ALA* 3.8 18.4 - - + -
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Residues in contact with ALA 106 (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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98B LEU* 5.1 1.1 - - + -
102B GLN 3.2 15.1 + - - +
103B GLU* 3.7 5.2 - - - +
104B ARG 3.2 0.4 - - - -
105B ILE* 1.3 82.1 - - - +
107B LYS* 1.3 64.3 + - + +
109B HIS* 3.3 11.6 + - - -
111B SER* 5.1 1.6 - - - -
578B PRO* 3.8 15.8 - - - +
582B ALA* 4.0 20.3 - - + +
583B ALA* 3.9 32.8 - - + +
586B ALA* 4.5 1.6 - - + -
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Residues in contact with LYS 107 (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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103B GLU* 2.9 55.3 + - + +
106B ALA* 1.3 78.2 - - + +
108B SER* 1.3 59.0 + - - +
109B HIS* 3.2 14.0 + - - -
195B LEU 4.5 0.2 - - - +
196B PHE* 3.3 18.1 - - + +
200B GLU* 3.8 39.8 + - - +
201B PHE* 3.8 22.4 - - + -
578B PRO* 4.7 12.0 - - + +
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Residues in contact with SER 108 (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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104B ARG 2.7 24.2 + - - -
105B ILE* 3.5 11.1 + - - +
107B LYS* 1.3 75.5 - - - +
109B HIS* 1.3 73.4 + - - +
110B GLY* 3.8 1.9 + - - -
154B ARG* 4.3 2.8 + - - -
155B PRO* 3.4 25.9 + - - +
156B ILE* 4.9 0.3 - - - -
159B GLY* 3.7 17.8 - - - -
196B PHE* 3.5 35.1 - - - -
201B PHE* 4.8 1.3 - - - -
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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