Contacts of the strand formed by residues 656 - 661 (chain A) in PDB entry 1B0K
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 GLY 656 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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630A TRP* 3.3 32.5 - - - -
651A PRO 2.8 24.6 + - - +
652A ARG* 4.4 11.8 + - - -
655A GLY* 1.4 73.9 - - - +
657A ARG* 1.3 64.3 + - - -
659A ILE* 6.4 0.4 - - - -
677A LEU* 3.8 14.0 - - - +
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Residues in contact with ARG 657 (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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545A ASP* 2.9 28.1 + - - -
546A LYS 5.2 3.4 + - - -
547A TRP* 5.8 5.1 - - - +
548A ASP* 6.1 1.2 - - - +
552A LEU* 4.0 27.6 - - + +
555A LEU* 4.4 16.4 - - + -
629A ARG* 4.1 43.6 - - + +
630A TRP 2.8 18.7 + - - +
652A ARG* 4.0 19.1 - - - +
655A GLY* 4.0 14.6 + - - -
656A GLY* 1.3 79.9 + - - -
658A ALA* 1.3 62.0 + - + +
676A GLY 4.9 1.7 - - - +
677A LEU* 3.9 11.5 - - - +
678A LEU* 3.5 22.0 + - - +
739A PHE* 5.7 1.2 - - - -
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Residues in contact with ALA 658 (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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552A LEU* 5.0 6.5 - - + -
630A TRP* 4.0 1.3 + - - +
631A VAL* 3.3 23.3 - - + -
632A VAL 3.2 19.8 + - - -
657A ARG* 1.3 79.9 + - + +
659A ILE* 1.3 68.8 + - - +
660A ILE* 4.7 8.3 - - + -
677A LEU* 4.1 2.5 - - - +
678A LEU* 3.4 29.2 - - + +
680A LEU* 4.7 5.2 - - + -
699A ILE* 5.1 3.8 - - + -
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Residues in contact with ILE 659 (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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630A TRP* 5.2 2.2 - - + -
632A VAL* 3.5 36.3 - - + +
638A TYR* 3.7 35.0 - - + +
651A PRO* 4.7 22.0 - - + -
657A ARG 6.2 0.2 - - - +
658A ALA* 1.3 80.6 - - - +
660A ILE* 1.3 62.2 + - - +
661A THR* 4.1 11.2 - - + -
664A PHE* 3.7 3.9 - - + -
672A LEU* 4.1 33.4 - - + -
677A LEU* 4.8 8.1 - - + -
678A LEU 3.2 5.9 + - - +
680A LEU 3.0 24.8 + - - +
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Residues in contact with ILE 660 (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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631A VAL* 4.4 12.6 - - + -
632A VAL 2.9 7.8 + - - +
633A ILE* 3.3 26.2 - - + +
634A GLY 2.7 31.4 + - - +
658A ALA* 4.7 1.3 - - + -
659A ILE* 1.3 79.3 - - - +
661A THR* 1.3 57.3 + - - +
680A LEU* 3.3 22.4 - - + +
682A PHE* 3.6 34.1 - - + -
691A ILE* 5.5 0.9 - - + -
697A LEU* 4.3 12.8 - - + -
699A ILE* 4.0 25.8 - - + -
713A CYS* 5.2 1.6 - - - -
727A LEU* 4.0 20.4 - - + -
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Residues in contact with THR 661 (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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634A GLY* 3.2 19.1 - - - +
635A ASP 3.4 9.0 - - - -
638A TYR* 3.4 36.8 - - + -
659A ILE* 4.1 5.2 - - + -
660A ILE* 1.3 78.7 - - - +
662A LYS* 1.3 60.4 + - - +
663A SER* 3.1 17.2 + - - -
664A PHE* 3.1 26.6 - - + -
680A LEU 3.0 4.0 + - - -
681A THR* 3.0 25.1 - - - -
682A PHE* 3.1 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