Contacts of the strand formed by residues 293 - 297 (chain A) in PDB entry 4HXG
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 293 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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256A ILE* 4.4 12.6 - - + +
257A LEU* 5.9 0.4 - - - -
260A ILE* 4.4 23.8 - - + -
276A PHE* 4.2 22.4 - - + -
278A LEU* 6.1 0.7 - - + -
287A TYR* 4.1 23.8 - - + -
288A LEU 3.5 3.8 - - - +
289A TRP* 3.9 18.6 - - + -
292A GLU* 1.3 73.4 - - - +
294A ARG* 1.3 62.6 + - - +
295A GLU 4.3 0.2 + - - -
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Residues in contact with ARG 294 (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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287A TYR* 3.6 6.4 - - - -
288A LEU* 2.8 53.2 + - + +
290A ASP* 3.0 40.5 + - - +
292A GLU* 3.3 28.7 - - - +
293A VAL* 1.3 74.3 + - - +
295A GLU* 1.3 62.7 + - - +
296A ILE* 5.0 2.7 - - + -
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Residues in contact with GLU 295 (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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286A LEU 4.9 0.4 - - - +
287A TYR* 3.4 26.3 + - + -
293A VAL 4.3 0.4 + - - -
294A ARG* 1.3 74.2 - - - +
296A ILE* 1.3 68.8 + - - +
298A LYS* 3.6 40.8 + - + +
328A TRP* 5.1 5.2 - - - -
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Residues in contact with ILE 296 (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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275A TYR* 5.3 1.1 - - + -
286A LEU* 3.1 25.0 + - + +
287A TYR 4.0 2.9 - - - +
288A LEU* 3.8 41.1 - - + +
294A ARG* 4.9 2.7 - - + +
295A GLU* 1.3 81.7 - - - +
297A ALA* 1.3 65.4 + - + +
298A LYS 4.1 1.1 + - - -
312A LEU* 3.6 28.5 - - + -
314A TYR* 4.7 1.3 - - + -
328A TRP* 3.7 63.8 + - + +
332A GLU* 6.1 0.3 - - - +
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Residues in contact with ALA 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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285A ASN* 3.4 4.9 - - - +
286A LEU* 2.8 45.5 + - + +
296A ILE* 1.3 80.4 - - + +
298A LYS* 1.3 59.6 + - - +
301A HIS* 3.6 8.1 + - + -
303A ILE* 4.2 8.7 - - + +
314A TYR* 4.0 33.2 - - + +
332A GLU* 4.2 7.4 - - - +
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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