Contacts of the helix formed by residues 308 - 315 (chain A) 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 ASP 308 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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124A TYR* 3.5 2.4 + - - -
293A LYS* 3.2 19.7 + - - +
295A LEU* 5.9 0.5 - - - +
300A LEU* 3.5 38.4 - - - +
302A VAL 3.8 14.6 - - - +
303A THR* 3.7 3.1 + - - +
307A LEU* 1.3 76.4 - - - +
309A ILE* 1.3 69.3 + - + +
310A THR* 3.1 32.2 + - - -
311A GLU* 3.0 32.8 + - - +
312A LEU 3.4 6.4 + - - -
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Residues in contact with ILE 309 (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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120A LEU* 3.7 19.9 - - + +
121A ARG* 5.4 1.6 - - + -
124A TYR* 3.6 43.2 - - + -
142A PHE* 3.3 50.7 - - + +
295A LEU* 3.4 27.1 - - + -
299A ALA 5.0 4.3 - - - +
300A LEU* 6.1 0.4 - - - -
308A ASP* 1.3 73.3 - - + +
310A THR* 1.3 65.4 + - - +
312A LEU* 3.4 3.6 + - - +
313A SER* 2.9 31.2 + - - +
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Residues in contact with THR 310 (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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292A GLY 5.9 0.2 - - - -
293A LYS* 3.6 42.8 - - + +
294A ARG 5.0 0.9 + - - -
295A LEU* 4.3 11.6 - - - +
308A ASP* 3.2 14.2 + - - -
309A ILE* 1.3 80.7 - - - +
311A GLU* 1.3 65.0 + - + +
313A SER* 3.2 16.0 + - - -
314A ARG* 3.3 32.6 + - - +
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Residues in contact with GLU 311 (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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293A LYS* 3.4 16.1 + - - +
306A GLY 3.8 4.2 - - - +
307A LEU* 3.1 46.8 - - + +
308A ASP* 3.0 27.5 + - - +
310A THR* 1.3 76.5 - - + +
312A LEU* 1.3 65.3 + - - +
314A ARG* 3.4 20.3 + - - +
315A LEU* 3.5 16.9 - - - +
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Residues in contact with LEU 312 (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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120A LEU* 4.9 16.4 - - + -
123A LEU* 5.7 1.8 - - + -
124A TYR* 3.2 40.2 - - + +
304A PHE* 4.5 17.7 - - + +
305A ALA* 5.9 0.2 - - + -
307A LEU* 4.0 18.2 - - + +
308A ASP 3.4 3.8 + - - -
309A ILE* 3.7 7.9 - - - +
311A GLU* 1.3 77.6 - - - +
313A SER* 1.3 61.6 + - - +
315A LEU* 3.2 25.0 + - + +
320A VAL* 3.7 33.0 - - + +
323A LEU* 3.9 29.6 - - + -
324A LEU* 5.9 4.9 - - + -
373A LEU* 4.1 1.0 - - - +
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Residues in contact with SER 313 (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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117A SER* 5.6 1.6 + - - -
120A LEU* 4.8 11.4 - - - +
309A ILE* 2.9 22.4 + - - +
310A THR* 3.5 9.0 - - - -
311A GLU 3.2 0.6 - - - -
312A LEU* 1.3 74.9 - - - +
314A ARG* 1.3 62.3 + - - +
373A LEU* 3.4 28.0 + - - +
374A ASP* 3.3 34.7 + - - -
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Residues in contact with ARG 314 (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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292A GLY* 5.8 8.1 - - - -
310A THR* 3.3 30.4 + - - +
311A GLU* 3.4 15.7 + - - +
312A LEU 3.3 0.8 - - - -
313A SER* 1.3 78.6 - - - +
315A LEU* 1.3 66.0 + - + +
316A PRO* 3.9 1.9 - - - +
372A GLY* 4.3 7.4 - - - -
374A ASP* 3.3 23.4 + - - +
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Residues in contact with LEU 315 (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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307A LEU* 4.2 17.7 - - + -
311A GLU 3.5 16.4 - - - +
312A LEU* 3.2 14.6 + - + +
314A ARG* 1.3 82.3 - - + +
316A PRO* 1.3 82.9 - - + +
319A ARG* 4.3 11.9 - - + +
320A VAL* 4.2 3.6 - - + -
323A LEU* 3.8 29.8 - - + -
372A GLY* 3.5 11.9 - - - -
373A LEU* 3.7 12.8 - - - +
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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