Contacts of the strand formed by residues 628 - 632 (chain A) in PDB entry 2R8O
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 628 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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608A ARG 2.9 6.8 + - - +
609A VAL* 3.3 17.1 - - + -
610A ALA 3.0 22.6 + - - -
623A VAL* 3.9 3.3 - - - +
627A GLY* 1.3 74.9 - - - +
629A ILE* 1.3 68.4 + - - +
658A LYS* 4.3 20.2 - - + +
661A GLU* 6.2 0.2 - - - +
662A LEU* 4.1 18.6 - - + -
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Residues in contact with ILE 629 (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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610A ALA* 3.5 8.5 - - + +
612A GLU 6.1 0.4 - - - +
616A ALA* 3.4 50.5 - - + +
619A TRP* 4.0 20.9 - - + -
620A TYR* 3.8 32.1 - - + +
623A VAL* 3.7 24.7 - - + -
628A ALA* 1.3 82.6 - - - +
630A VAL* 1.3 64.7 + - - +
631A GLY* 3.7 9.2 + - - +
658A LYS* 5.6 3.2 - - - +
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Residues in contact with VAL 630 (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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609A VAL* 4.2 15.5 - - + -
610A ALA 2.8 15.5 + - - +
611A VAL* 3.5 8.3 - - + -
612A GLU 3.1 25.8 + - - +
629A ILE* 1.3 73.8 - - - +
631A GLY* 1.3 57.8 + - - +
648A PHE 5.6 0.7 - - - +
649A GLY 3.7 24.5 - - - +
650A PHE* 3.4 16.8 - - + -
654A ASN* 4.0 6.5 - - - +
655A VAL* 4.0 25.1 - - + -
658A LYS* 4.1 27.1 - - + -
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Residues in contact with GLY 631 (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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612A GLU 3.2 13.7 - - - -
614A GLY 3.6 4.0 - - - -
616A ALA* 4.4 5.7 - - - +
619A TRP* 6.4 0.7 - - - -
629A ILE* 3.6 15.2 + - - +
630A VAL* 1.3 77.1 - - - +
632A MET* 1.3 62.0 + - - +
633A THR* 4.2 2.8 + - - +
648A PHE 4.3 7.8 - - - +
650A PHE* 3.7 14.6 - - - -
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Residues in contact with MET 632 (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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464A ILE* 3.9 27.8 - - + -
476A VAL* 3.6 28.3 - - + -
612A GLU 4.2 0.2 + - - -
613A ALA* 4.0 8.7 - - + +
614A GLY* 2.8 24.1 + - - +
615A ILE* 3.4 7.4 - - - +
616A ALA 2.9 23.6 + - - -
631A GLY* 1.3 75.0 - - - +
633A THR* 1.3 63.8 + - - +
634A THR* 3.5 19.1 - - - +
635A PHE 4.0 6.5 - - - +
648A PHE* 3.6 49.6 - - + -
650A PHE* 3.9 10.5 - - + -
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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