Contacts of the strand formed by residues 334 - 339 (chain A) in PDB entry 2HVI
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 GLY 334 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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320A VAL* 3.9 0.2 - - - -
321A GLU 3.0 25.3 + - - -
332A ILE* 3.4 4.6 - - - +
333A VAL* 1.3 84.0 - - - +
335A ILE* 1.3 65.6 + - - +
345A PHE* 4.1 5.8 - - - -
346A LEU 4.0 2.0 - - - -
348A PRO* 3.4 11.6 - - - +
447A LEU* 3.4 20.1 - - - +
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Residues in contact with ILE 335 (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 LEU* 4.2 10.8 - - + -
319A VAL 3.3 11.2 - - - +
320A VAL* 4.8 9.0 - - + -
332A ILE* 4.4 9.0 - - + -
334A GLY* 1.3 79.8 - - - +
336A ALA* 1.3 65.3 + - - +
337A VAL* 4.3 4.9 - - + -
345A PHE* 3.1 12.0 - - - -
346A LEU* 3.0 41.9 + - + +
348A PRO* 4.2 9.0 - - + -
351A ALA* 3.5 26.9 - - + -
352A LEU* 3.8 28.9 - - + -
357A PHE* 3.9 24.9 - - + -
447A LEU* 3.8 1.5 - - - +
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Residues in contact with ALA 336 (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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317A ALA 3.8 0.6 - - - +
318A LEU* 3.6 2.9 - - - +
319A VAL* 2.9 38.2 + - + +
335A ILE* 1.3 76.5 - - - +
337A VAL* 1.3 68.3 + - - +
344A PHE 3.3 9.6 - - - +
345A PHE* 5.1 0.2 - - + -
447A LEU* 3.3 42.8 - - + +
448A VAL* 3.8 8.7 - - + +
451A ALA* 4.3 3.5 - - + +
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Residues in contact with VAL 337 (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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311A MET* 3.8 23.6 - - + +
316A ALA* 4.1 14.6 - - + -
317A ALA 3.5 3.6 - - - +
318A LEU* 4.0 16.6 - - + -
335A ILE* 4.3 9.6 - - + -
336A ALA* 1.3 80.5 - - - +
338A VAL* 1.3 68.4 + - - +
339A ASN* 3.9 15.7 - - - +
343A ARG* 3.5 0.7 - - - -
344A PHE* 2.8 49.8 + - + +
346A LEU* 5.0 6.5 - - + -
357A PHE* 4.3 17.0 - - + -
360A TRP* 4.6 5.6 - - + -
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Residues in contact with VAL 338 (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 ALA* 3.4 3.2 - - - -
317A ALA* 2.9 36.7 + - + -
337A VAL* 1.3 79.1 - - - +
339A ASN* 1.3 67.7 + - - +
342A GLY 3.4 7.9 - - - +
343A ARG* 4.0 26.2 - - + +
448A VAL* 4.0 8.5 - - + +
451A ALA* 3.5 27.6 - - + +
452A ALA* 3.8 12.6 - - - +
455A TRP* 3.4 32.9 - - + -
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Residues in contact with ASN 339 (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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310A GLU 3.0 22.0 + - - +
311A MET* 3.7 20.4 + - - +
313A ALA* 3.9 11.4 - - + +
315A LYS 3.3 20.4 - - - +
316A ALA* 3.8 3.7 - - + +
337A VAL* 3.9 10.5 - - - +
338A VAL* 1.3 78.4 - - - +
340A GLU* 1.3 65.3 + - - +
341A HIS* 2.7 33.9 + - - +
342A GLY* 3.0 23.9 + - - +
344A PHE* 4.0 3.9 - - - -
455A TRP* 3.8 17.8 + - - -
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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