Contacts of the strand formed by residues 636 - 641 (chain A) in PDB entry 1CJY
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 THR 636 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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569A ASP* 2.7 21.2 + - + +
570A LEU* 3.6 22.9 - - + +
571A ILE* 2.9 25.6 + - - +
622A VAL* 4.6 2.9 - - - +
623A PHE 3.8 10.3 + - - -
624A LYS* 4.5 13.5 - - - +
625A PRO* 4.4 15.5 - - + -
634A CYS 5.5 0.4 - - - +
635A PRO* 1.3 74.7 - - - +
637A ILE* 1.3 65.9 + - - +
711A ALA* 4.6 9.2 - - + +
715A SER* 3.8 15.7 - - - +
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Residues in contact with ILE 637 (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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558A TYR* 3.0 39.0 - - + +
571A ILE* 3.4 21.8 - - + +
573A SER* 4.6 1.8 - - - -
590A LEU* 5.3 3.1 - - + -
604A PHE* 3.5 30.1 - - + -
605A PRO* 3.6 29.2 - - + -
607A ILE* 5.0 2.9 - - + -
621A TYR 3.9 0.2 - - - +
622A VAL* 3.5 2.4 - - - +
623A PHE* 2.8 43.6 + - + +
635A PRO 4.8 0.7 - - - +
636A THR* 1.3 78.9 + - - +
638A ILE* 1.3 73.9 + - - +
639A HIS* 3.8 11.9 + - + +
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Residues in contact with ILE 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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570A LEU* 4.4 11.0 - - + -
571A ILE 2.9 10.2 + - - +
572A ILE* 3.6 8.0 - - + -
573A SER* 2.9 29.8 + - - +
620A CYS* 4.5 9.4 - - - -
621A TYR 3.5 8.3 - - - +
622A VAL* 4.4 10.3 - - + -
636A THR* 4.2 1.1 + - - +
637A ILE* 1.3 75.1 - - - +
639A HIS* 1.3 60.2 + - - +
640A PHE* 3.4 30.5 - - + -
707A VAL* 3.8 21.3 - - + +
708A ILE* 3.8 20.4 - - + -
711A ALA* 3.5 32.3 - - + -
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Residues in contact with HIS 639 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
556A LEU* 4.4 6.4 - - + +
558A TYR* 5.1 1.8 + - - -
573A SER* 4.0 15.8 + - - -
575A ASP* 3.8 20.2 + - + +
586A PRO 3.3 18.8 + - - -
587A PHE* 3.9 19.5 - + - -
589A GLU* 3.5 18.6 + - - -
590A LEU* 3.3 27.5 - - + +
620A CYS* 3.2 3.5 - - - -
621A TYR* 2.8 38.8 + + - +
623A PHE* 4.1 16.2 - - + -
637A ILE* 3.8 5.1 - - + -
638A ILE* 1.3 69.8 - - - +
640A PHE* 1.3 65.3 + - - +
641A VAL* 3.8 6.1 + - + +
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Residues in contact with PHE 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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572A ILE* 4.1 7.9 - - + -
573A SER 2.9 21.6 + - - +
574A PHE* 3.6 38.6 - + + -
575A ASP* 3.0 28.6 + - - +
619A GLU 3.6 9.6 - - - +
620A CYS* 3.6 12.8 - - + -
638A ILE* 3.4 31.0 - - + -
639A HIS* 1.3 75.5 - - - +
641A VAL* 1.3 60.1 + - - +
697A MET* 4.9 5.6 - - + -
700A ASN* 3.5 30.5 - - + -
701A THR* 3.8 13.0 - - - -
704A ASN* 4.0 20.9 - - + -
707A VAL* 6.0 0.2 - - + -
708A ILE* 4.1 17.5 - - + -
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Residues in contact with VAL 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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575A ASP* 3.8 10.8 - - + +
579A ARG* 3.8 15.7 - - - +
586A PRO* 3.2 38.4 - - + +
617A LEU* 4.9 1.8 - - + -
618A LYS 2.9 29.2 - - - +
619A GLU* 3.1 14.3 + - - +
621A TYR* 4.1 10.8 - - + -
639A HIS* 4.7 8.1 - - + +
640A PHE* 1.3 75.7 - - - +
642A LEU* 1.3 66.1 + - - +
643A ALA* 3.2 10.3 + - + +
697A MET* 4.4 7.4 - - - +
700A ASN* 4.2 8.8 + - - -
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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