Contacts of the strand formed by residues 674 - 680 (chain A) in PDB entry 4EJX
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 674 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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672A THR 3.7 2.6 + - - -
673A GLU* 1.3 75.5 - - - +
675A THR* 1.3 61.2 + - - -
676A PHE* 3.3 20.0 + - - -
695A THR* 4.5 1.6 - - - -
696A VAL 2.9 36.0 + - - -
825A SER* 4.1 9.6 - - - -
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Residues in contact with THR 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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674A GLY* 1.3 68.0 - - - -
676A PHE* 1.3 62.0 + - - +
677A ASN* 4.8 1.0 + - - -
693A LYS* 3.8 40.0 + - + +
694A TYR 3.8 3.1 - - - +
695A THR* 3.6 26.3 + - - +
825A SER* 3.5 24.2 + - - +
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Residues in contact with PHE 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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642A SER* 3.1 34.3 - - - +
643A GLY* 4.1 10.8 - - - -
644A ASN* 3.9 13.9 - - - -
672A THR* 3.4 53.2 - - + -
673A GLU 4.3 2.9 - - - -
674A GLY 3.3 27.8 + - - -
675A THR* 1.3 72.7 - - - +
677A ASN* 1.3 76.4 + - - +
693A LYS* 3.3 7.8 - - - +
694A TYR* 2.8 44.2 + + + +
696A VAL* 4.6 1.6 - - + -
822A THR* 5.4 1.8 - - - -
824A SER 3.9 17.0 - - - -
825A SER* 4.0 16.4 - - - -
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Residues in contact with ASN 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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374A PHE* 3.3 28.8 - - + -
640A TYR 3.1 13.2 - - - +
642A SER* 3.1 19.8 + - - +
675A THR 4.8 0.6 + - - -
676A PHE* 1.3 91.2 + - - +
678A VAL* 1.3 62.6 + - - +
679A GLU* 3.5 26.1 - - + +
692A GLN 3.3 4.3 - - - +
693A LYS* 3.3 25.7 - - - +
694A TYR* 3.3 13.8 - - - -
825A SER 5.5 2.4 - - - +
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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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561A LEU* 3.5 21.8 - - + -
604A MET* 3.4 41.0 - - + +
615A LEU* 4.2 11.2 - - + -
625A TRP* 5.0 0.4 - - + -
639A ILE* 3.9 11.2 - - + -
640A TYR 3.6 4.0 - - - +
641A PHE* 3.9 12.1 - - + -
677A ASN* 1.3 70.3 - - - +
679A GLU* 1.3 57.9 + - - +
691A LYS* 3.7 1.0 - - - -
692A GLN* 3.1 33.3 + - + -
694A TYR* 3.5 38.1 - - + +
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Residues in contact with GLU 679 (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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374A PHE* 4.1 4.3 - - - -
639A ILE* 4.7 0.7 - - - -
640A TYR* 2.9 63.5 + - + +
642A SER* 5.2 0.7 - - - -
677A ASN* 4.0 26.2 - - + +
678A VAL* 1.3 73.8 - - - +
680A CYS* 1.3 63.6 + - - +
681A LEU* 3.3 0.8 + - - -
686A TYR* 3.1 37.7 + - + -
690A MET 3.9 3.6 - - - -
691A LYS* 3.9 7.4 - - + +
861A TYR* 4.1 4.3 + - - -
866A GLN* 2.8 26.6 - - - +
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Residues in contact with CYS 680 (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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604A MET* 4.8 1.0 - - + +
638A GLY 3.4 19.5 - - - -
639A ILE* 3.7 17.9 - - + +
678A VAL 3.9 2.0 + - - -
679A GLU* 1.3 69.1 - - - +
681A LEU* 1.3 65.0 + - - +
682A THR* 3.1 22.8 + - - +
685A HIS* 3.9 1.6 - - + -
686A TYR* 3.4 23.3 - - - +
690A MET* 2.9 30.9 + - + +
1105A CU 1.9 34.8 - - - -
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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