Contacts of the strand formed by residues 398 - 401 (chain A) in PDB entry 3RSS
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 398 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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361A ALA 3.0 6.2 + - - +
362A VAL* 3.3 12.6 - - + -
363A LEU* 2.8 27.5 + - - +
397A CYS* 1.3 81.7 - - - +
399A LEU* 1.3 70.1 + - - +
400A VAL* 4.3 0.4 - - + -
408A VAL* 4.3 1.6 - - + -
409A THR 3.3 10.3 - - - +
410A ASP* 4.2 10.8 - - + -
447A PRO* 3.9 11.7 - - + -
448A LEU* 3.7 40.2 - - + +
451A SER* 3.7 27.8 - - - +
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Residues in contact with LEU 399 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363A LEU* 3.9 16.2 - - + -
365A PRO* 3.8 31.4 - - + -
370A MET* 3.6 27.1 - - + -
373A LEU* 5.1 0.2 - - + -
388A ALA* 3.6 36.3 - - + +
391A PHE* 4.1 22.9 - - + -
392A ALA* 4.3 11.2 - - + -
397A CYS* 4.1 1.0 - - - -
398A VAL* 1.3 74.3 - - - +
400A VAL* 1.3 63.1 + - - +
401A LEU* 3.8 4.9 - - + +
407A ILE 3.5 2.1 - - - +
408A VAL* 3.4 3.5 - - - -
409A THR* 2.8 39.1 + - + +
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Residues in contact with VAL 400 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362A VAL* 3.8 13.2 - - + -
363A LEU 2.9 11.2 + - - +
364A THR* 3.4 12.8 - - + -
365A PRO* 3.3 25.1 - - - +
398A VAL* 4.3 2.0 - - + -
399A LEU* 1.3 75.1 - - - +
401A LEU* 1.3 57.2 + - - +
402A LYS* 3.5 11.8 + - + +
406A THR* 3.7 23.6 - - + -
407A ILE 3.4 3.4 - - - -
408A VAL* 4.3 6.1 - - + -
433A LEU* 4.5 6.5 - - + -
437A ILE* 4.5 2.5 - - + -
451A SER* 3.7 34.1 - - - +
455A VAL* 3.7 16.4 - - + -
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Residues in contact with LEU 401 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365A PRO* 3.6 14.6 - - + +
367A PRO* 4.1 19.3 - - + -
370A MET* 3.7 36.8 - - + -
381A VAL 3.6 23.8 - - - +
382A LYS* 5.0 1.1 - - - -
383A TYR* 4.3 11.4 - - + +
384A ASN 4.6 2.9 - - - +
388A ALA* 4.7 14.6 - - + -
399A LEU* 3.8 9.5 - - + -
400A VAL* 1.3 70.1 - - - +
402A LYS* 1.3 64.2 + - - +
403A SER* 3.7 1.6 + - - +
405A THR 4.3 1.6 - - - +
406A THR* 3.4 3.5 - - - +
407A ILE* 2.8 52.5 + - + +
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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