Contacts of the strand formed by residues 637 - 641 (chain A) in PDB entry 3RFU
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 ILE 637 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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412A GLU* 3.8 3.1 - - + +
413A ALA* 3.5 25.8 - - + +
416A ARG* 3.4 35.7 - - + +
417A MET* 3.4 38.8 - - + +
420A VAL* 5.1 6.7 - - + -
619A VAL 3.8 2.8 + - - +
620A ALA* 3.3 11.5 - - + -
621A MET 3.0 22.9 + - - -
635A ALA* 3.7 7.9 - - - +
636A ASP* 1.3 98.6 - - + +
638A GLY* 1.3 69.1 + - - +
639A ILE* 4.3 2.2 - - + -
654A VAL* 4.5 10.5 - - + -
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Residues in contact with GLY 638 (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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621A MET* 3.7 6.7 - - - -
632A LEU* 3.8 23.7 + - - -
635A ALA 4.8 0.2 + - - -
637A ILE* 1.3 76.5 - - - +
639A ILE* 1.3 61.4 + - - -
652A ALA* 3.0 23.3 - - - +
653A GLY* 3.4 5.1 + - - +
654A VAL* 3.1 19.6 + - - +
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Residues in contact with ILE 639 (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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417A MET* 3.8 21.8 - - + -
423A LEU* 4.9 0.2 - - + -
620A ALA* 3.7 30.7 - - + -
621A MET 3.0 16.0 + - - +
622A ALA* 3.3 7.7 - - + +
623A GLY 3.0 26.2 + - - +
632A LEU* 3.8 2.0 - - - +
637A ILE* 4.3 2.7 - - + +
638A GLY* 1.3 76.5 - - - +
640A ALA* 1.3 63.5 + - - +
641A MET* 5.2 4.3 - - - +
652A ALA* 4.0 1.3 - - - -
654A VAL* 3.4 13.0 - - + +
656A LEU* 3.2 34.1 - - + -
664A ILE* 3.7 31.9 - - + -
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Residues in contact with ALA 640 (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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623A GLY 3.5 5.8 - - - +
632A LEU* 4.9 1.1 - - + -
639A ILE* 1.3 74.5 - - - +
641A MET* 1.3 62.8 + - - +
648A ALA* 3.2 30.5 - - + +
649A ILE* 3.5 17.7 - - + +
652A ALA* 3.5 9.6 - - + +
654A VAL 2.7 13.3 + - - +
655A THR* 3.3 7.7 - - + -
656A LEU* 2.7 31.7 + - - +
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Residues in contact with MET 641 (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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429A GLY 3.7 3.4 - - - +
430A THR* 3.4 50.7 - - + +
556A LYS* 3.5 14.1 - - - +
622A ALA* 5.8 3.4 - - - -
623A GLY 3.0 19.7 + - - +
624A ASP* 3.8 8.2 - - + +
639A ILE* 5.4 4.5 - - - +
640A ALA* 1.3 78.0 - - - +
642A GLY* 1.3 65.4 + - - +
643A THR* 2.9 27.8 - - - +
644A GLY 4.4 4.5 - - - +
648A ALA* 6.0 0.3 - - - +
649A ILE* 4.1 11.9 + - - +
656A LEU* 3.8 8.5 - - - -
659A GLY 2.9 27.4 - - - +
661A LEU* 4.0 14.6 - - - +
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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