Contacts of the strand formed by residues 367 - 370 (chain D) in PDB entry 2HVH
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 LYS 367 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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459A ARG* 3.6 24.2 - - - +
463A ASP* 4.7 13.2 - - - +
314D ASP 3.2 8.9 + - - +
315D LYS* 3.2 19.7 + - + +
316D ALA* 3.1 24.1 + - - +
360D TRP* 5.1 1.2 - - - -
364D GLU* 2.7 31.3 + - - +
365D THR* 4.3 9.5 - - - +
366D LYS* 1.3 72.0 - - - +
368D LYS* 1.3 62.0 + - - +
389D GLY* 3.3 11.9 - - - +
391D SER* 3.4 26.7 - - - +
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Residues in contact with LYS 368 (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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315D LYS* 5.0 0.9 - - - -
316D ALA 3.3 5.2 - - - +
318D LEU* 4.1 13.7 - - + -
360D TRP* 2.8 63.8 + - + -
361D LEU* 3.3 11.7 + - - +
363D ASP 3.0 8.1 + - - -
366D LYS* 2.8 29.6 + - - +
367D LYS* 1.3 75.0 - - - +
369D SER* 1.3 60.6 + - - +
370D MET* 4.3 15.7 - - + -
387D LEU* 4.6 6.7 - - + -
388D CYS 2.8 27.6 + - - +
389D GLY 2.8 12.4 + - - +
390D VAL* 3.4 9.8 - - + +
391D SER* 3.0 24.1 + - - -
392D PHE 3.5 2.9 + - - -
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Residues in contact with SER 369 (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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315D LYS* 3.7 8.2 - - - +
316D ALA 2.7 15.8 + - - -
317D ALA* 3.3 6.0 - - - -
318D LEU 2.7 32.1 + - - -
368D LYS* 1.3 69.6 - - - +
370D MET* 1.3 63.0 + - - +
391D SER* 5.1 0.3 + - - -
392D PHE* 3.5 15.1 - - - +
454D ILE* 3.6 21.6 - - - +
455D TRP* 5.3 2.5 - - - -
458D GLU* 2.6 35.2 + - - -
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Residues in contact with MET 370 (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* 3.5 48.9 - - + +
319D VAL* 4.8 0.2 - - - -
320D VAL* 4.4 7.6 - - + +
368D LYS* 4.3 9.4 - - + +
369D SER* 1.3 80.6 - - - +
371D PHE* 1.3 60.4 + - - +
372D ASP 4.2 1.3 - - - +
373D SER* 4.0 19.3 - - - -
376D ALA* 3.8 27.6 - - + -
387D LEU* 4.2 8.1 - - + -
390D VAL* 3.9 25.8 - - + -
392D PHE* 2.9 11.4 + - - +
393D ASP* 4.3 1.3 - - - -
394D LEU* 2.8 33.8 + - - +
454D ILE* 3.7 11.3 - - - +
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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