Contacts of the helix formed by residues 296 - 301 (chain A) in PDB entry 2YEV
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 VAL 296 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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250A HIS* 3.6 37.7 - - + +
254A TYR* 4.8 1.6 - - + +
292A LEU 3.4 18.2 - - - +
293A GLY* 4.0 2.7 - - - +
294A THR 3.5 0.4 - - - -
295A MET* 1.3 84.5 - - - +
297A TRP* 1.3 69.7 + - - +
298A ALA 2.9 4.9 + - - -
299A HIS* 2.9 29.1 + - + +
314A PHE* 3.5 8.3 - - - -
317A PHE* 3.6 11.4 - - + +
318A THR* 3.4 39.9 + - + +
321A ILE* 4.4 5.2 - - + -
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Residues in contact with TRP 297 (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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243A GLN* 3.0 41.8 + - + +
246A TRP* 3.1 35.8 - - + +
247A PHE* 3.7 31.9 - + - +
250A HIS* 4.2 11.4 - - + +
251A PRO* 5.2 1.6 - - + -
293A GLY 5.4 0.4 + - - +
294A THR 3.5 28.0 - - - -
295A MET* 4.4 0.4 - - - -
296A VAL* 1.3 79.8 - - - +
298A ALA* 1.3 72.8 + - - +
299A HIS 3.1 5.0 + - - -
300A HIS* 3.2 24.4 + - - +
301A MET* 3.6 10.5 - - + +
310A PHE* 5.5 0.2 - + - -
314A PHE* 3.6 28.5 - + - -
7C PHE* 4.1 24.5 - + - -
53C VAL* 4.4 22.0 - - + -
56C MET* 4.4 9.4 - - + -
57C LEU* 4.7 5.2 - - + -
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Residues in contact with ALA 298 (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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296A VAL 2.9 2.4 + - - -
297A TRP* 1.3 76.7 - - - +
299A HIS* 1.3 56.5 + - - +
300A HIS 2.8 5.6 - - - -
301A MET* 2.8 54.2 + - + +
302A PHE* 3.8 5.5 + - - -
310A PHE* 3.4 10.3 - - + -
314A PHE* 3.3 41.4 - - + -
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Residues in contact with HIS 299 (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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250A HIS* 3.2 31.0 + + - -
296A VAL* 2.9 22.1 + - + +
298A ALA* 1.3 75.4 - - - +
300A HIS* 1.3 93.1 + + - +
301A MET 3.2 2.0 - - - -
302A PHE* 3.6 43.4 - - + -
314A PHE* 4.1 3.9 - - - +
318A THR* 2.8 42.3 + - + +
367A LEU 5.2 1.2 - - - +
368A SER* 5.2 1.8 - - - -
373A ASP* 4.4 6.1 - - - +
377A HIS* 5.9 0.3 + - - -
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Residues in contact with HIS 300 (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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142A TYR* 4.1 11.1 + - - -
242A GLN* 4.9 0.2 - - - +
246A TRP* 3.2 63.6 - + + -
249A SER 4.9 0.9 + - - -
250A HIS* 4.1 16.0 + - + +
253A VAL* 6.4 1.1 - - + -
297A TRP 3.2 16.8 + - - +
298A ALA 2.8 1.2 - - - -
299A HIS* 1.3 115.8 + + - +
301A MET* 1.3 59.5 + - - +
302A PHE 3.7 1.6 - - - -
304A VAL* 5.4 0.7 - - - +
373A ASP* 6.0 0.2 - - - -
377A HIS* 4.2 20.0 - - - -
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Residues in contact with MET 301 (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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239A VAL* 4.9 3.8 - - - +
242A GLN* 3.7 23.1 - - - +
243A GLN* 3.0 56.8 - - - +
246A TRP* 4.0 11.4 - - + -
297A TRP* 3.6 6.1 - - + +
298A ALA* 2.8 42.9 + - + +
300A HIS* 1.3 86.6 - - + +
302A PHE* 1.3 63.2 + - - +
303A THR 3.2 3.6 - - - -
304A VAL* 3.2 35.5 - - + +
305A GLY 4.9 0.3 + - - -
306A GLU* 4.9 5.6 - - + +
310A PHE* 3.9 9.8 - - + -
311A GLN* 5.5 0.9 - - - +
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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