Contacts of the strand formed by residues 402 - 406 (chain D) in PDB entry 3HN3
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 402 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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288D TRP* 4.1 13.0 - - + -
290D PRO* 3.7 33.4 - - + -
338D ILE* 4.3 2.2 - - + -
343D PHE* 3.7 15.0 - - + -
345D PHE* 3.8 14.4 - - + -
379D ASN 3.0 19.5 + - - +
380D ALA* 3.2 18.9 - - + -
381D PHE 2.9 26.0 + - - +
401D ILE* 1.3 74.8 - - - +
403D VAL* 1.3 61.3 + - - +
442D ALA* 3.2 9.4 - - - +
444D VAL* 4.0 21.5 - - + -
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Residues in contact with VAL 403 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
381D PHE* 3.2 11.0 - - + +
383D THR* 3.9 16.2 - - + -
393D MET* 4.0 16.2 - - + -
396D CYS* 3.4 35.2 - - + -
401D ILE 3.6 2.9 - - - +
402D VAL* 1.3 81.0 - - - +
404D ILE* 1.3 67.8 + - - +
405D ASP* 3.5 28.0 + - + +
442D ALA* 2.8 15.6 + - + +
443D VAL* 3.6 7.7 - - + -
444D VAL* 3.1 25.0 + - - +
445D MET 3.6 4.7 + - - -
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Residues in contact with ILE 404 (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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345D PHE* 4.1 25.1 - - + -
381D PHE 3.1 7.5 + - - +
382D ARG* 3.3 19.2 - - + +
383D THR 3.1 24.3 + - - -
403D VAL* 1.3 73.9 - - - +
405D ASP* 1.3 60.1 + - - +
445D MET* 3.4 43.1 - - + +
447D SER* 3.9 25.8 - - - +
480D THR* 4.6 2.9 - - + -
482D VAL* 5.8 0.7 - - + -
500D CYS* 5.2 5.8 - - - -
537D ILE* 4.4 8.3 - - + -
585D LEU* 4.0 26.7 - - + -
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Residues in contact with ASP 405 (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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383D THR* 3.6 11.7 + - - +
387D PRO* 4.2 14.2 - - - +
388D TYR 5.2 0.2 + - - -
393D MET* 4.5 3.8 - - - +
403D VAL* 3.5 11.1 - - + +
404D ILE* 1.3 70.4 - - - +
406D GLU* 1.3 62.6 + - - +
407D CYS 4.2 0.3 + - - -
430D MET* 5.7 0.3 - - - +
433D VAL* 4.3 6.4 - - - +
437D ASP* 2.6 41.1 - - - +
443D VAL* 3.8 26.3 - - + +
445D MET 3.0 6.5 + - - -
446D TRP* 3.4 22.5 - - + -
447D SER 3.0 20.9 + - - +
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Residues in contact with GLU 406 (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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382D ARG* 3.0 30.9 + - + -
383D THR* 2.9 22.1 + - - +
385D HIS* 2.8 40.4 + - - +
386D TYR 3.1 26.2 - - - -
387D PRO* 3.2 3.8 - - - +
404D ILE 4.4 3.6 - - - +
405D ASP* 1.3 75.6 + - - +
407D CYS* 1.3 71.3 + - - +
410D VAL* 5.4 0.3 - - - +
433D VAL* 5.3 1.1 - - - -
447D SER* 2.8 34.0 + - - +
449D ALA 3.8 7.2 - - - +
450D ASN* 3.6 9.6 - - - +
482D VAL* 3.8 0.3 - - - +
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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