Contacts of the helix formed by residues 296 - 301 (chain B) in PDB entry 2VF7
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 296 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141B GLY 5.4 0.2 - - - +
147B PRO 2.5 30.4 + - - -
148B GLU* 3.0 23.8 + - - +
149B GLY* 3.1 14.8 + - - +
150B ALA 3.8 14.8 + - - +
151B CYS* 4.6 2.5 - - - +
152B PRO* 4.2 24.7 - - + +
295B LEU* 1.3 78.3 - - - +
297B GLN* 1.3 65.9 - - - +
298B GLU* 4.2 27.1 - - + +
299B ALA* 3.2 8.5 + - + +
300B LEU* 3.1 19.8 + - - +
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Residues in contact with GLN 297 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289B LEU* 3.9 31.0 + - + +
290B CYS* 5.0 0.8 - - - +
291B HIS* 5.6 2.0 - - - -
295B LEU 3.8 1.2 + - - -
296B ARG* 1.3 73.4 - - - +
298B GLU* 1.3 57.0 + - - +
300B LEU* 3.3 23.5 + - - +
301B ASN* 3.0 60.8 + - - +
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Residues in contact with GLU 298 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134B GLN* 2.9 47.0 + - - +
135B GLY 5.4 0.2 - - - +
136B ILE 5.1 1.7 - - - +
137B VAL* 3.6 23.8 - - + +
296B ARG* 4.2 23.8 - - + -
297B GLN* 1.3 75.6 - - - +
299B ALA* 1.3 64.7 + - + +
301B ASN* 3.8 10.3 + - - +
302B VAL* 3.6 11.6 - - - +
492C GLU* 4.9 4.3 - - - +
842C ARG* 5.6 0.7 - - - +
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Residues in contact with ALA 299 (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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137B VAL* 4.6 5.6 - - + -
141B GLY 3.2 28.7 - - - +
142B PHE* 3.4 36.5 - - + -
295B LEU* 4.2 13.4 - - + +
296B ARG* 3.2 12.2 + - + +
298B GLU* 1.3 79.1 - - + +
300B LEU* 1.3 66.1 + - - +
301B ASN 3.3 0.8 + - - -
302B VAL 3.4 12.1 + - - +
308B ASP* 5.1 1.2 - - - +
309B ILE* 5.2 2.8 + - - +
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Residues in contact with LEU 300 (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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290B CYS* 4.3 11.0 - - + +
293B LYS* 4.2 30.5 - - + -
295B LEU* 3.8 50.3 - - + +
296B ARG 3.1 6.6 + - - +
297B GLN* 3.3 33.4 + - - +
299B ALA* 1.3 79.4 - - - +
301B ASN* 1.3 60.1 + - - +
302B VAL 3.3 1.6 + - - +
303B THR* 5.3 1.0 + - - -
308B ASP* 3.4 32.5 - - + +
309B ILE* 5.5 0.7 - - + -
310B THR* 4.3 10.1 - - - +
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Residues in contact with ASN 301 (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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129B ASP 3.6 2.4 - - - +
131B PRO* 3.5 38.6 - - + +
134B GLN* 4.7 3.1 + - - +
297B GLN* 3.0 41.4 + - - +
298B GLU* 4.0 10.8 - - - +
299B ALA 3.3 0.6 - - - -
300B LEU* 1.3 75.0 - - - +
302B VAL* 1.3 64.0 + - - +
303B THR* 3.5 7.2 + - - -
492C GLU* 4.7 12.7 + - - +
493C PRO 5.2 5.3 + - - -
496C PRO* 4.8 4.9 - - - +
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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