Contacts of the helix formed by residues 315 - 325 (chain A) in PDB entry 2V40
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 ASN 315 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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313A GLN* 3.0 37.0 + - - +
314A ASP* 1.3 78.0 + - - +
316A GLU* 1.3 72.2 + - - +
317A ILE* 2.9 20.2 + - - +
318A GLY 3.1 11.1 + - - -
319A GLU* 2.8 45.2 + - - +
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Residues in contact with GLU 316 (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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315A ASN* 1.3 89.5 + - - +
317A ILE* 1.3 82.3 + - + +
319A GLU* 3.7 17.7 + - - +
320A LEU* 3.0 28.4 + - - +
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Residues in contact with ILE 317 (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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313A GLN* 4.1 21.5 - - + +
315A ASN* 2.9 8.3 + - - +
316A GLU* 1.3 93.7 - - + +
318A GLY* 1.3 64.7 + - - +
320A LEU* 3.2 8.6 + - - +
321A LEU* 3.0 29.1 + - + +
340A TRP* 3.5 50.5 - - + +
369A PHE* 4.0 12.1 - - + -
373A LYS* 5.8 5.4 - - - +
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Residues in contact with GLY 318 (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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313A GLN* 3.1 26.8 + - - +
315A ASN* 3.1 8.6 + - - -
317A ILE* 1.3 82.1 - - - +
319A GLU* 1.3 55.4 + - - +
321A LEU* 3.5 4.9 + - - +
322A GLN* 3.0 29.7 + - - +
338A CYS* 3.8 15.5 - - - +
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Residues in contact with GLU 319 (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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315A ASN* 2.8 27.5 + - - +
316A GLU* 3.7 15.4 + - - +
317A ILE 3.2 0.4 - - - -
318A GLY* 1.3 76.4 - - - +
320A LEU* 1.3 56.4 + - - +
322A GLN* 3.3 7.1 + - - +
323A THR* 2.9 36.5 + - - +
335A LYS* 6.1 3.4 - - - +
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Residues in contact with LEU 320 (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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316A GLU 3.0 17.8 + - - +
317A ILE* 3.2 6.5 + - - +
319A GLU* 1.3 75.0 - - - +
321A LEU* 1.3 63.9 + - - +
323A THR* 3.4 5.7 + - + -
324A ARG* 2.9 55.6 + - + +
368A MET* 5.0 11.9 - - + +
369A PHE* 3.6 38.8 - - + -
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Residues in contact with LEU 321 (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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300A TYR* 3.6 35.0 + - + -
317A ILE* 3.0 30.3 + - + +
318A GLY* 3.8 7.0 - - - +
320A LEU* 1.3 76.3 - - - +
322A GLN* 1.3 55.8 + - - +
325A GLY* 2.8 31.5 + - - -
327A GLU* 4.1 2.8 - - - +
338A CYS* 3.9 12.8 - - + -
339A GLY* 3.6 37.9 - - - +
340A TRP* 5.0 4.9 - - + -
365A ILE* 3.8 16.3 - - + +
366A LEU* 3.9 7.9 - - + -
369A PHE* 3.5 21.8 - - + -
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Residues in contact with GLN 322 (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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318A GLY 3.0 18.4 + - - +
319A GLU* 3.7 7.0 - - - +
320A LEU 3.3 0.2 - - - -
321A LEU* 1.3 74.9 - - - +
323A THR* 1.3 72.8 + - - +
326A ARG* 3.1 3.6 + - - -
327A GLU* 3.0 59.1 + - + +
328A PHE* 3.6 14.6 - - - -
335A LYS* 3.5 43.2 + - + +
336A ARG 4.1 12.8 - - - +
338A CYS* 3.8 12.5 - - - -
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Residues in contact with THR 323 (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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319A GLU* 2.9 20.0 + - - +
320A LEU* 3.8 7.0 - - + -
322A GLN* 1.3 86.3 + - - +
324A ARG* 1.3 67.7 + - + +
326A ARG* 3.3 21.5 + - - +
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Residues in contact with ARG 324 (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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320A LEU* 2.9 43.4 + - + +
323A THR* 1.3 80.7 - - + +
325A GLY* 1.3 59.8 + - - +
326A ARG* 3.3 7.6 + - - +
364A ASP* 2.9 27.5 + - - +
365A ILE* 2.7 44.7 + - + +
367A ASP* 3.6 15.2 + - - +
368A MET* 3.2 37.4 - - - +
369A PHE* 4.8 0.7 - - - -
1457A GDP 5.2 1.7 + - - -
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Residues in contact with GLY 325 (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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300A TYR* 3.3 22.9 - - - -
321A LEU 2.8 15.7 + - - -
324A ARG* 1.3 72.0 - - - +
326A ARG* 1.3 72.0 + - - +
327A GLU* 3.2 6.6 + - - -
362A LYS* 3.0 24.8 + - - -
365A ILE* 3.5 11.8 - - - +
1457A GDP 5.9 0.2 - - - -
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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