Contacts of the helix formed by residues 308 - 315 (chain B) in PDB entry 2VF8
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 ASP 308 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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124B TYR* 3.2 1.8 + - - -
293B LYS* 3.0 19.6 + - - -
300B LEU* 3.6 33.4 - - + +
302B VAL 3.8 9.9 - - - +
303B THR* 4.4 2.4 + - - +
306B GLY 4.0 0.8 + - - -
307B LEU* 1.3 77.2 - - - +
309B ILE* 1.3 64.5 + - - +
310B THR* 2.8 34.8 + - - -
311B GLU* 2.8 53.6 + - - +
312B LEU 3.0 8.3 + - - -
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Residues in contact with ILE 309 (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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120B LEU* 3.6 31.0 - - + +
121B ARG* 4.0 17.5 - - + +
124B TYR* 3.4 43.1 - - + -
142B PHE* 4.0 27.1 - - + +
295B LEU* 3.9 26.7 - - + -
299B ALA 5.7 2.3 + - - +
300B LEU* 5.3 1.8 - - + -
302B VAL 4.4 1.0 + - - -
308B ASP* 1.3 73.6 - - - +
310B THR* 1.3 61.9 + - - +
312B LEU* 3.3 1.9 + - - +
313B SER* 2.8 36.8 + - - +
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Residues in contact with THR 310 (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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293B LYS* 3.4 39.7 - - + +
294B ARG 4.7 2.3 + - - -
295B LEU* 4.2 15.4 - - - +
300B LEU* 4.7 0.2 - - - +
308B ASP* 2.8 15.3 + - - -
309B ILE* 1.3 76.8 - - - +
311B GLU* 1.3 65.1 + - + +
313B SER* 3.0 16.9 + - - -
314B ARG* 3.3 23.7 + - + +
374B ASP* 5.0 1.9 - - - +
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Residues in contact with GLU 311 (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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293B LYS* 3.0 18.1 + - - +
306B GLY 4.3 2.8 - - - +
307B LEU* 3.3 29.2 - - + +
308B ASP* 2.8 56.8 + - - +
310B THR* 1.3 78.7 - - + +
312B LEU* 1.3 64.8 + - - +
313B SER 3.1 0.5 + - - -
314B ARG* 3.2 26.2 + - + +
315B LEU* 3.8 7.6 + - - +
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Residues in contact with LEU 312 (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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120B LEU* 4.2 21.3 - - + -
124B TYR* 3.5 35.9 - - + +
304B PHE* 4.6 11.7 - - + +
307B LEU* 3.8 13.7 - - + +
308B ASP 3.0 6.9 + - - -
309B ILE* 3.6 5.6 - - + +
311B GLU* 1.3 73.9 - - - +
313B SER* 1.3 58.0 + - - +
314B ARG 3.1 5.5 + - - -
315B LEU* 3.1 24.7 + - + +
320B VAL* 3.8 21.1 - - + -
323B LEU* 3.8 39.9 - - + -
324B LEU* 5.5 3.1 - - + -
373B LEU* 3.5 8.0 - - + +
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Residues in contact with SER 313 (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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117B SER* 5.7 0.7 + - - -
120B LEU* 4.9 6.2 - - - +
309B ILE* 2.8 28.4 + - - +
310B THR* 3.0 11.6 + - - -
312B LEU* 1.3 76.9 - - - +
314B ARG* 1.3 58.7 + - - +
373B LEU* 3.6 21.3 + - - +
374B ASP* 3.0 42.3 + - - -
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Residues in contact with ARG 314 (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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310B THR* 3.3 17.3 + - + +
311B GLU* 3.2 21.5 + - - +
312B LEU 3.1 0.2 + - - -
313B SER* 1.3 77.7 - - - +
315B LEU* 1.3 67.4 + - + +
316B PRO* 4.0 0.9 - - - +
372B GLY* 4.2 7.5 - - - -
374B ASP* 3.4 22.9 + - - +
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Residues in contact with LEU 315 (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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307B LEU* 3.8 28.3 - - + -
311B GLU 3.8 5.7 + - - +
312B LEU* 3.1 21.4 + - + +
314B ARG* 1.3 79.4 - - + +
316B PRO* 1.3 80.1 - - + +
319B ARG* 4.0 17.7 - - + -
320B VAL* 4.0 9.2 - - + -
323B LEU* 4.0 11.9 - - + -
372B GLY* 3.2 17.9 - - - -
373B LEU* 3.6 10.7 - - - +
811B GLU* 5.2 2.0 - - - +
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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