Contacts of the strand formed by residues 556 - 560 (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 GLN 556 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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554A ASP 3.6 3.1 + - - +
555A LEU* 1.3 73.1 - - - +
557A ILE* 1.3 73.3 + - - +
558A LEU 3.8 0.2 - - - -
606A ARG 5.7 0.4 + - - -
608A ALA* 3.3 33.1 - - + +
623A TYR* 3.8 28.9 + - + -
628A ILE* 3.5 29.2 - - + +
629A ARG 2.9 9.3 + - - +
630A TRP* 3.1 6.9 - - + +
631A VAL* 3.0 24.0 + - - +
693A PRO 4.6 8.9 + - - -
694A VAL* 5.9 0.4 - - - +
696A LYS* 3.0 35.3 + - - +
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Residues in contact with ILE 557 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
555A LEU 3.9 0.2 + - - -
556A GLN* 1.3 87.2 + - - +
558A LEU* 1.4 65.7 + - - +
559A ILE* 3.9 20.6 - - - +
560A LYS* 4.2 5.8 - - + +
623A TYR* 5.0 1.6 + - - -
631A VAL* 3.7 18.8 - - + +
633A ILE* 3.9 18.2 - - + -
691A ILE* 3.5 31.4 - - + -
692A HIS 3.7 15.3 - - - +
693A PRO* 4.3 18.9 - - + +
695A ASP 3.7 19.7 + - - +
697A LEU* 4.0 17.0 - - + -
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Residues in contact with LEU 558 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
556A GLN 3.5 4.0 + - - -
557A ILE* 1.4 72.1 - - - +
559A ILE* 1.3 61.1 + - + +
590A LEU* 5.0 1.1 - - + -
591A LEU* 4.2 11.9 - - + -
605A VAL* 4.1 17.0 - - + +
606A ARG 5.5 1.7 - - - +
616A VAL* 3.9 31.4 - - + +
619A THR* 4.4 8.1 - - + -
620A ALA* 4.2 24.7 - - + +
623A TYR* 4.1 24.9 + - + -
630A TRP* 3.5 50.6 - - + +
631A VAL 2.8 12.5 + - - +
632A VAL* 4.4 1.8 - - + -
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Residues in contact with ILE 559 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
557A ILE* 3.4 7.6 - - - +
558A LEU* 1.3 84.0 - - + +
560A LYS* 1.3 73.3 + - - +
561A VAL* 4.0 20.6 - - + -
591A LEU* 4.3 14.1 - - + +
594A ALA* 4.5 13.5 - - + +
596A ASN* 3.9 27.6 - - + +
601A LYS 5.5 0.2 - - - +
603A ASN 6.3 0.4 - - - +
605A VAL* 3.8 24.2 - - + -
616A VAL* 4.9 11.0 - - + -
631A VAL 4.1 0.4 + - - -
632A VAL* 3.7 20.8 - - + -
633A ILE 3.0 22.5 + - - +
693A PRO* 6.6 0.2 - - - -
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Residues in contact with LYS 560 (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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557A ILE* 4.2 7.0 - - + +
559A ILE* 1.3 74.2 - - - +
561A VAL* 1.3 58.7 + - - +
596A ASN* 4.7 3.2 + - - -
597A ILE* 3.3 57.1 + - + +
633A ILE* 3.4 28.5 - - + -
688A TYR* 2.7 51.2 + - + +
689A ASN* 4.2 6.7 + - - +
691A ILE* 2.5 39.3 + - + +
692A HIS* 5.0 1.0 - - - +
693A PRO* 4.8 16.1 - - + +
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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