Contacts of the strand formed by residues 672 - 678 (chain A) in PDB entry 1HKC
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 CYS 672 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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519A THR* 4.1 9.0 - - - +
662A MET* 3.8 15.7 - - - +
665A CYS* 3.5 38.1 - - - -
666A ALA* 3.8 16.5 - - - +
669A GLU 3.1 16.1 + - - +
670A PRO 3.1 5.0 - - - +
671A THR* 1.3 78.5 + - - +
673A GLU* 1.3 65.3 + - - +
674A VAL 3.7 16.6 - - - -
857A THR* 3.1 19.7 - - - +
859A GLY 3.8 1.8 - - - -
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Residues in contact with GLU 673 (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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519A THR* 6.2 0.2 - - + -
662A MET* 3.6 14.8 - - - -
670A PRO 5.3 1.6 - - - +
671A THR* 3.6 14.9 + - - +
672A CYS* 1.3 77.6 - - - +
674A VAL* 1.3 66.0 + - + +
686A TYR* 2.9 24.4 - - - +
687A MET* 2.9 24.3 + - + +
702A GLN* 4.6 2.8 + - - -
845A ILE* 4.6 8.8 - - + +
849A ARG* 2.5 49.3 + - - -
854A LEU* 4.9 6.2 - - - +
855A ASN 5.4 1.2 - - - +
856A VAL* 4.1 10.9 - - + +
857A THR 3.4 4.0 + - - -
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Residues in contact with VAL 674 (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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662A MET* 3.8 5.7 - - - -
672A CYS* 3.7 4.0 - - - -
673A GLU* 1.3 86.9 - - - +
675A GLY* 1.3 64.8 + - - +
684A ALA* 5.4 0.4 - - + -
685A CYS 3.1 11.9 - - - +
686A TYR* 3.7 4.7 - - + +
838A MET* 3.3 31.2 - - + -
841A VAL* 4.2 5.4 - - + -
842A VAL* 4.9 3.4 - - + -
845A ILE* 3.5 26.2 - - + -
856A VAL* 4.3 11.4 - - + -
857A THR 4.0 0.6 + - - +
858A VAL* 3.2 26.4 - - + +
859A GLY 2.8 24.3 + - - -
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Residues in contact with GLY 675 (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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658A THR* 4.1 7.2 - - - -
661A THR 5.1 0.2 - - - -
662A MET* 3.8 19.5 - - - +
674A VAL* 1.3 79.2 - - - +
676A LEU* 1.3 62.2 + - - +
684A ALA* 3.2 5.2 - - - +
685A CYS* 2.9 38.9 + - - +
858A VAL* 4.4 0.2 - - - -
859A GLY 3.2 8.5 - - - -
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Residues in contact with LEU 676 (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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658A THR* 4.4 1.2 - - - +
661A THR* 4.5 2.1 - - - +
675A GLY* 1.3 75.5 - - - +
677A ILE* 1.3 66.1 + - - +
678A VAL* 3.9 23.6 - - + +
683A ASN 3.5 10.8 - - - +
684A ALA* 4.2 1.6 - - + -
709A TRP* 3.4 40.2 - - + -
834A CYS* 4.2 3.8 - - - -
838A MET* 4.6 8.5 - - - -
858A VAL* 4.2 5.6 - - + -
859A GLY 2.8 9.3 + - - +
860A VAL* 3.1 30.8 - - + +
861A ASP 3.1 24.1 + - - -
865A TYR* 5.0 0.9 - - + -
875A MET* 3.5 28.3 - - + -
890A PHE* 4.7 4.3 - - + -
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Residues in contact with ILE 677 (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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657A ASP* 4.5 17.7 - - + +
658A THR* 3.6 28.5 - - - +
661A THR* 3.4 22.2 - - - +
676A LEU* 1.3 77.5 - - - +
678A VAL* 1.3 65.8 + - - +
679A GLY 4.3 3.8 - - - +
681A GLY 4.1 12.8 - - - +
682A SER* 3.0 32.7 + - - -
683A ASN* 2.9 16.7 + - + +
861A ASP* 3.4 26.5 - - + +
920A PO4 4.8 15.5 - - - +
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Residues in contact with VAL 678 (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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676A LEU* 3.9 29.4 - - + -
677A ILE* 1.3 79.2 - - - +
679A GLY* 1.3 57.9 + - - +
681A GLY 3.8 2.0 - - - -
682A SER* 4.2 5.6 - - - +
745A ILE* 4.3 9.6 - - + +
746A SER* 5.4 0.4 - - - -
834A CYS* 4.1 15.3 - - - -
861A ASP 2.9 8.1 + - - -
862A GLY* 2.9 23.2 - - - -
864A LEU* 3.4 36.3 + - + -
865A TYR* 3.4 15.4 + - + +
871A PHE* 4.0 18.4 - - + -
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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