Contacts of the strand formed by residues 402 - 406 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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288B TRP* 3.9 15.9 - - + -
290B PRO* 3.7 35.0 - - + -
338B ILE* 4.4 1.1 - - + -
343B PHE* 3.8 11.7 - - + -
345B PHE* 3.7 21.1 - - + -
379B ASN 3.0 9.2 + - - +
380B ALA* 3.1 23.5 - - + +
381B PHE 2.9 25.8 + - - -
401B ILE* 1.3 74.2 - - - +
403B VAL* 1.3 62.1 + - - +
442B ALA 3.2 12.1 - - - +
444B VAL* 4.0 15.3 - - + -
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Residues in contact with VAL 403 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
381B PHE* 3.2 11.0 - - + +
383B THR* 3.7 23.6 - - + -
393B MET* 4.1 15.7 - - + -
396B CYS* 3.4 36.8 - - + -
401B ILE 3.7 2.2 - - - +
402B VAL* 1.3 81.6 - - - +
404B ILE* 1.3 76.3 + - - +
405B ASP* 3.7 11.7 - - + +
442B ALA* 2.8 14.6 + - + +
443B VAL* 3.6 8.8 - - + +
444B VAL* 3.0 27.6 + - - +
445B MET 3.5 5.5 + - - +
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Residues in contact with ILE 404 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345B PHE* 4.0 25.8 - - + -
381B PHE 3.0 8.9 + - - +
382B ARG* 3.3 19.8 - - + +
383B THR 3.0 25.5 + - - -
403B VAL* 1.3 71.4 - - - +
405B ASP* 1.3 60.3 + - - +
406B GLU 3.6 0.7 + - - -
445B MET* 3.4 41.7 - - + +
447B SER* 3.9 25.4 - - - +
480B THR* 4.6 2.7 - - + -
482B VAL* 5.8 1.1 - - + -
500B CYS* 5.1 4.9 - - - -
537B ILE* 4.3 9.6 - - + -
539B SER* 6.3 0.2 - - - -
585B LEU* 4.0 26.0 - - + -
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Residues in contact with ASP 405 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383B THR* 3.6 12.8 + - - +
387B PRO* 4.2 11.3 - - - +
393B MET* 4.3 3.5 - - - +
403B VAL* 3.6 9.3 - - + -
404B ILE* 1.3 70.2 - - - +
406B GLU* 1.3 61.8 + - - +
407B CYS 4.2 0.2 + - - -
430B MET* 5.6 0.9 - - - +
433B VAL* 4.2 8.0 - - - +
437B ASP* 2.6 42.8 - - - +
443B VAL* 3.7 26.6 - - + +
445B MET 2.9 8.3 + - - -
446B TRP* 3.4 22.0 - - + +
447B SER 2.9 23.4 + - - +
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Residues in contact with GLU 406 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
382B ARG* 2.9 31.1 + - + -
383B THR* 2.9 22.8 + - - +
384B SER* 4.0 0.2 - - - -
385B HIS* 2.8 39.2 + - - +
386B TYR* 3.0 28.1 - - - -
387B PRO* 3.1 4.6 - - - +
404B ILE 4.4 3.8 - - - +
405B ASP* 1.3 74.9 + - - +
407B CYS* 1.3 72.7 + - - +
410B VAL* 5.5 0.2 - - - +
433B VAL* 5.3 1.3 - - - -
447B SER* 2.8 34.1 + - - +
449B ALA 3.7 5.6 - - - +
450B ASN* 3.6 10.8 - - - +
482B VAL* 3.6 1.9 - - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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