Contacts of the strand formed by residues 667 - 671 (chain A) in PDB entry 1ZJK
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 667 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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618A CYS* 3.4 6.2 - - - +
619A ALA 2.9 36.1 + - - -
620A GLY* 4.8 0.6 - - - -
630A ARG* 3.5 31.4 - - - +
665A GLN 4.3 0.2 + - - -
666A TYR* 1.3 73.6 - - - +
668A VAL* 1.3 62.2 + - - +
669A TYR* 3.4 12.1 - - - -
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Residues in contact with VAL 668 (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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598A CYS* 4.6 0.2 - - - -
602A TYR* 3.9 20.4 - - + -
612A VAL* 4.6 1.8 - - + -
616A MET* 3.7 26.9 - - + -
617A LEU 3.6 5.6 - - - +
618A CYS* 4.4 13.0 - - - -
630A ARG* 4.6 0.9 + - - -
654A SER* 3.2 8.4 + - - -
655A TRP* 2.8 88.2 + - + +
666A TYR 4.1 1.6 - - - +
667A GLY* 1.3 77.0 - - - +
669A TYR* 1.3 66.3 + - - +
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Residues in contact with TYR 669 (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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590A ILE* 3.4 14.8 - - + +
616A MET* 3.2 8.5 - - - -
617A LEU* 2.9 44.3 + - + +
619A ALA* 4.0 19.2 + - + -
630A ARG* 2.7 34.9 + - + -
637A LEU* 3.8 34.3 - - + -
651A GLY* 4.0 7.4 - - - -
652A ILE 3.2 13.5 - - - +
653A VAL* 3.6 43.3 - - + -
654A SER* 4.2 2.0 - - - -
667A GLY* 3.4 26.9 - - - -
668A VAL* 1.3 78.0 - - - +
670A THR* 1.3 61.6 + - - +
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Residues in contact with THR 670 (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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529A PHE 4.9 0.7 + - - -
531A ASN* 5.2 0.4 - - - +
532A ASP* 2.6 48.5 + - - +
533A ILE* 4.2 7.2 - - + -
615A ASN 3.8 6.7 - - - +
616A MET* 4.6 2.2 - - - +
617A LEU* 4.3 0.2 - - - -
651A GLY* 3.2 5.9 - - - -
652A ILE* 2.9 38.6 + - + -
654A SER* 3.9 7.8 + - - -
669A TYR* 1.3 70.0 - - - +
671A LYS* 1.3 61.5 + - - +
672A VAL* 3.0 9.2 + - - +
675A TYR* 3.6 30.3 - - + +
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Residues in contact with LYS 671 (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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559A GLU* 2.9 35.5 + - - -
562A MET* 5.3 4.7 - - + -
614A ALA 3.9 16.2 + - - +
615A ASN* 2.9 26.6 + - - +
616A MET 3.9 9.9 - - - +
617A LEU* 3.7 24.7 - - + -
650A GLY 4.9 0.9 - - - +
669A TYR 3.3 2.2 + - - -
670A THR* 1.3 67.3 - - - +
672A VAL* 1.3 66.1 + - - +
673A ILE* 3.2 17.1 + - + +
674A ASN* 3.2 31.6 + - - +
675A TYR* 3.2 15.3 - - - -
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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