Contacts of the strand formed by residues 361 - 363 (chain A) in PDB entry 3RSG
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 ALA 361 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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338A PRO* 5.9 0.2 - - - -
339A ALA* 3.2 12.3 - - + +
341A ILE* 4.1 12.3 - - + -
354A LEU* 4.0 26.7 - - + -
357A ARG* 4.4 7.0 - - - +
359A SER 5.1 0.4 - - - +
360A PRO* 1.3 79.2 - - - +
362A VAL* 1.3 64.1 + - - +
363A LEU* 4.3 4.3 - - + -
396A ASP 4.9 4.6 + - - +
397A CYS* 3.5 8.6 - - + +
398A VAL* 3.1 24.3 + - - +
447A PRO* 4.7 1.9 - - - +
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Residues in contact with VAL 362 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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339A ALA 2.9 8.5 + - - +
340A VAL* 3.4 5.8 - - + +
341A ILE* 2.8 32.1 + - - +
361A ALA* 1.3 73.7 - - - +
363A LEU* 1.3 61.0 + - - +
364A THR* 4.0 11.4 - - + -
398A VAL* 3.3 11.7 - - + +
400A VAL* 3.8 18.8 - - + -
437A ILE* 4.3 9.0 - - + -
441A ILE* 4.1 14.6 - - + -
447A PRO* 3.5 33.7 - - + +
451A SER* 3.4 25.6 - - - +
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Residues in contact with LEU 363 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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341A ILE* 3.4 30.7 - - + +
346A ILE* 4.7 8.1 - - + -
349A LEU* 3.7 23.6 - - + -
354A LEU* 3.9 27.8 - - + -
361A ALA* 4.3 3.8 - - + -
362A VAL* 1.3 77.4 - - - +
364A THR* 1.3 62.3 + - - +
365A PRO* 3.4 5.1 - - + +
373A LEU* 3.8 24.5 - - + -
391A PHE* 4.1 7.2 - - + -
397A CYS* 4.1 11.9 - - - -
398A VAL 2.9 7.6 + - - +
399A LEU* 3.8 14.4 - - + -
400A VAL* 2.8 27.4 + - - +
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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