Contacts of the strand formed by residues 477 - 481 (chain B) in PDB entry 3H44
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 ARG 477 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205B GLU* 4.0 1.8 - - - +
208B THR* 2.9 37.6 + - - -
293B PHE* 3.4 54.3 - - - -
297B HIS* 3.0 32.6 + - - +
298B LEU* 4.3 6.3 - - + -
300B GLN* 3.9 8.1 - - + +
302B TYR* 2.7 32.1 + - + -
315B VAL* 3.6 2.1 - - - -
316B THR* 2.9 52.4 + - + +
318B PRO* 5.6 0.9 - - - -
475B ASN 4.1 0.2 + - - -
476B VAL* 1.3 75.9 - - - +
478B VAL* 1.3 65.1 + - - +
2002B DIO 3.4 22.6 + - - -
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Residues in contact with VAL 478 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300B GLN 3.0 10.5 + - - +
301B LEU* 3.2 20.7 - - + -
302B TYR* 2.7 35.7 + - - -
313B LEU* 3.6 25.1 - - + -
314B TYR 3.5 2.9 - - - +
315B VAL* 4.5 2.7 - - + -
387B VAL* 5.1 0.9 - - + -
391B ILE* 3.6 24.5 - - + -
476B VAL* 4.1 18.8 - - + -
477B ARG* 1.3 80.0 - - - +
479B ALA* 1.3 58.4 + - - +
480B ILE* 4.6 3.1 - - + -
505B ILE* 4.0 19.3 - - + -
513B TRP* 4.7 4.9 - - + -
2002B DIO 5.2 0.2 - - - -
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Residues in contact with ALA 479 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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302B TYR* 3.3 7.2 - - + +
304B ILE* 4.0 13.7 - - + -
312B ASN 3.8 0.3 - - - +
313B LEU* 3.3 7.1 - - - +
314B TYR* 2.7 50.1 + - + +
478B VAL* 1.3 76.2 - - - +
480B ILE* 1.3 64.4 + - - +
2002B DIO 3.7 36.3 - - - -
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Residues in contact with ILE 480 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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301B LEU* 3.9 25.6 - - + -
302B TYR 2.6 11.9 + - - +
303B LYS* 3.5 4.5 - - + -
304B ILE* 2.9 26.7 + - - +
312B ASN 3.3 9.0 - - - +
313B LEU* 4.0 12.6 - - + -
379B LEU* 4.2 16.2 - - + -
384B LEU* 4.5 12.8 - - + -
387B VAL* 3.8 25.8 - - + -
478B VAL* 4.6 0.4 - - + -
479B ALA* 1.3 79.0 - - - +
481B VAL* 1.3 71.3 + - - +
482B SER* 4.9 0.7 - - - -
485B PHE* 3.7 27.2 - - + -
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Residues in contact with VAL 481 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197B ASP* 5.5 0.2 - - - +
201B LEU* 4.0 15.3 - - + -
304B ILE* 3.4 26.0 - - + +
306B PRO* 3.5 34.3 - - + -
310B ILE* 3.1 22.7 - - + +
311B ARG* 3.2 2.9 - - - -
312B ASN* 2.8 40.3 + - + +
314B TYR* 3.9 26.0 - - + -
379B LEU* 5.5 0.3 - - - +
480B ILE* 1.3 80.2 - - - +
482B SER* 1.3 61.3 + - - +
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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
------------------------------------------------------------
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