Contacts of the strand formed by residues 334 - 339 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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320D VAL* 3.9 0.2 - - - -
321D GLU 3.0 25.1 + - - -
332D ILE* 3.5 4.0 - - - +
333D VAL* 1.3 83.7 - - - +
335D ILE* 1.3 67.1 + - - +
345D PHE* 4.1 7.2 - - - -
346D LEU 4.1 1.8 - - - -
348D PRO* 3.5 11.6 - - - +
443D LEU* 4.7 0.2 - - - -
447D LEU* 3.5 19.0 - - - +
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Residues in contact with ILE 335 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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318D LEU* 4.1 6.7 - - + -
319D VAL 3.2 13.2 - - - +
320D VAL* 4.4 10.5 - - + -
332D ILE* 4.4 10.1 - - + -
334D GLY* 1.3 81.0 - - - +
336D ALA* 1.3 71.2 + - - +
337D VAL* 4.4 3.1 - - + -
345D PHE* 3.2 10.0 - - - -
346D LEU* 2.8 45.3 + - + +
348D PRO* 4.6 7.0 - - + -
351D ALA* 4.0 17.0 - - + -
352D LEU* 3.8 34.3 - - + -
357D PHE* 4.1 24.5 - - + -
361D LEU* 6.0 0.2 - - + -
447D LEU* 3.8 2.6 - - - +
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Residues in contact with ALA 336 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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317D ALA 3.9 0.4 - - - +
318D LEU* 3.7 2.6 - - - +
319D VAL* 3.0 34.3 + - + +
335D ILE* 1.3 77.6 - - - +
337D VAL* 1.3 69.1 + - - +
344D PHE 3.1 10.8 - - - +
345D PHE* 5.0 0.2 - - + -
346D LEU 4.9 0.2 - - - +
447D LEU* 3.6 39.7 - - + +
448D VAL* 3.9 10.5 - - + +
451D ALA* 4.2 4.9 - - + +
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Residues in contact with VAL 337 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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311D MET* 3.8 22.7 - - + +
316D ALA* 4.1 14.4 - - + -
317D ALA 3.5 4.5 - - - +
318D LEU* 3.9 17.5 - - + -
335D ILE* 4.4 4.3 - - + -
336D ALA* 1.3 80.1 - - - +
338D VAL* 1.3 66.1 + - - +
339D ASN* 3.9 16.8 - - - +
343D ARG* 3.4 1.9 - - - -
344D PHE* 2.6 54.4 + - + +
346D LEU* 4.7 7.2 - - + -
357D PHE* 4.2 22.0 - - + -
360D TRP* 4.8 4.5 - - + -
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Residues in contact with VAL 338 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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316D ALA* 3.4 1.7 - - - -
317D ALA* 2.9 32.3 + - + -
337D VAL* 1.3 78.4 - - - +
339D ASN* 1.3 69.5 + - - +
342D GLY 3.5 6.7 - - - +
343D ARG* 3.9 27.8 - - + +
448D VAL* 4.1 7.4 - - + +
451D ALA* 3.4 32.5 - - + +
452D ALA* 3.7 13.5 - - + +
455D TRP* 3.6 33.8 - - + -
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Residues in contact with ASN 339 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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310D GLU 2.9 23.9 + - - +
311D MET* 3.8 16.6 + - - +
313D ALA* 3.8 15.2 - - + +
315D LYS 3.4 20.2 - - - +
316D ALA* 3.8 3.3 - - + +
337D VAL* 3.9 9.3 - - - +
338D VAL* 1.3 79.8 - - - +
340D GLU* 1.3 64.5 + - - +
341D HIS* 2.7 32.0 + - - +
342D GLY* 3.0 27.4 + - - +
344D PHE* 3.9 2.5 - - - -
455D TRP* 3.9 18.0 + - - -
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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