Contacts of the strand formed by residues 694 - 706 (chain A) in PDB entry 6EJ9
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 ARG 694 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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690A PHE* 3.5 3.6 - - - -
691A LEU 3.0 32.4 + - - +
692A ALA* 3.7 11.7 - - + +
693A ASP* 1.3 86.4 - - - +
695A PHE* 1.3 65.3 + - - +
696A GLN* 3.2 15.0 + - - +
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Residues in contact with PHE 695 (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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688A LEU* 4.0 23.6 - - + -
689A TYR 3.8 6.5 - - - -
690A PHE* 3.7 31.7 - + + -
693A ASP 4.3 0.2 + - - -
694A ARG* 1.3 72.6 - - - +
696A GLN* 1.3 64.8 + - - +
697A GLY* 3.4 40.8 - - - -
698A PHE* 4.5 4.9 - + - -
720A MET* 5.2 2.4 - - - +
721A PRO* 4.8 17.2 - - + +
756A PHE* 3.7 39.9 - + + -
757A GLY* 4.2 10.3 - - - -
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Residues in contact with GLN 696 (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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689A TYR* 2.8 38.0 + - + +
691A LEU* 3.7 38.5 + - + +
694A ARG* 3.2 36.4 + - - +
695A PHE* 1.3 76.3 + - - +
697A GLY* 1.3 58.4 + - - +
718A TRP* 3.1 25.4 + - - +
720A MET* 3.2 44.0 - - + +
721A PRO* 4.6 1.3 - - - -
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Residues in contact with GLY 697 (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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688A LEU* 3.9 1.4 - - - -
689A TYR* 3.1 27.3 + - - +
695A PHE* 3.4 32.6 - - - -
696A GLN* 1.3 79.1 - - - +
698A PHE* 1.3 62.5 + - - -
718A TRP* 5.0 0.9 - - - -
719A VAL 3.3 8.5 - - - -
721A PRO* 4.3 7.6 - - - -
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Residues in contact with PHE 698 (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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634A VAL* 4.7 2.5 - - + -
652A TYR* 4.3 14.6 - + - -
655A PHE* 3.9 20.0 - + + -
686A VAL* 3.8 21.5 - - + -
687A HIS 3.4 6.3 - - - +
688A LEU* 3.5 26.0 - - + -
695A PHE* 4.5 4.3 - + - -
697A GLY* 1.3 75.9 - - - -
699A LEU* 1.3 64.6 + - - +
700A ILE* 4.0 9.4 - - + -
717A THR 3.5 0.9 - - - +
718A TRP* 3.5 4.0 - - - -
719A VAL* 3.0 44.3 + - + +
755A ASN* 5.8 0.4 - - - -
757A GLY* 3.7 35.7 - - - -
759A LEU* 4.0 27.4 - - + -
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Residues in contact with LEU 699 (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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631A TRP* 3.6 35.7 - - + +
685A SER 3.9 0.3 - - - +
686A VAL* 3.2 5.9 - - - +
687A HIS* 2.9 48.5 + - + +
689A TYR* 4.0 21.5 - - + -
698A PHE* 1.3 81.0 - - - +
700A ILE* 1.3 62.9 + - - +
701A LYS 4.1 0.3 + - - -
716A GLU* 3.9 29.7 - - - +
717A THR 3.2 3.8 - - - +
718A TRP* 3.6 33.0 - - + +
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Residues in contact with ILE 700 (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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652A TYR* 4.2 14.6 - - + +
655A PHE* 3.6 35.2 - - + -
656A ALA* 4.4 6.5 - - + -
683A PRO* 4.1 20.0 - - + -
685A SER 3.6 4.9 - - - +
686A VAL* 4.4 13.0 - - + +
698A PHE* 3.9 11.4 - - + +
699A LEU* 1.3 76.6 - - - +
701A LYS* 1.3 69.6 + - - +
702A HIS* 3.2 16.6 - - + -
716A GLU* 3.1 5.4 - - - -
717A THR* 2.7 48.5 + - - +
719A VAL* 3.7 21.8 - - + -
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Residues in contact with LYS 701 (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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683A PRO* 3.7 2.6 - - - +
684A ALA* 2.9 48.1 + - + +
685A SER* 2.9 34.9 + - - +
699A LEU 4.1 1.0 + - - -
700A ILE* 1.3 71.8 - - - +
702A HIS* 1.3 66.3 + - - +
703A HIS* 5.8 1.1 - - - -
714A THR* 4.0 20.8 - - + +
715A LEU 3.2 13.5 - - - +
716A GLU* 4.1 15.2 + - + +
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Residues in contact with HIS 702 (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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656A ALA* 3.7 38.0 - - + +
660A LEU* 3.7 33.0 - - + +
679A PRO* 6.0 1.8 - - - +
680A MET 5.8 0.4 - - - +
682A HIS 5.2 1.6 - - - +
683A PRO* 4.6 11.2 - - + -
684A ALA* 4.5 4.7 - - - +
700A ILE* 3.2 22.9 - - + -
701A LYS* 1.3 77.5 - - - +
703A HIS* 1.3 75.6 + - - +
713A GLU 4.1 0.2 - - - +
714A THR* 3.6 2.5 - - - -
715A LEU* 2.8 50.8 + - + +
717A THR* 3.0 25.5 + - - -
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Residues in contact with HIS 703 (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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637A GLU* 4.8 10.2 + - - -
679A PRO* 4.0 2.1 - - - +
680A MET* 3.1 36.3 + - + +
681A GLY* 6.1 0.4 - - - -
682A HIS 4.6 14.5 + - - -
684A ALA* 4.0 20.7 - - + +
701A LYS* 5.8 1.3 - - - -
702A HIS* 1.3 80.0 + - - +
704A ALA* 1.3 64.9 + - - +
712A LEU* 4.5 11.7 - - + -
713A GLU 3.4 6.7 - - - +
714A THR* 3.1 36.6 + - + +
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Residues in contact with ALA 704 (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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660A LEU* 4.1 15.7 - - + -
677A TYR* 3.9 25.6 - - + -
678A TYR 3.3 15.9 - - - +
679A PRO* 4.2 2.5 - - + -
680A MET* 4.1 1.3 - - - -
702A HIS* 5.0 1.3 - - - +
703A HIS* 1.3 78.3 - - - +
705A THR* 1.3 59.4 + - - +
706A ASN 3.7 0.9 + - - -
712A LEU* 3.2 7.7 - - - +
713A GLU* 2.8 36.7 + - - +
715A LEU* 4.5 5.8 - - + -
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Residues in contact with THR 705 (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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677A TYR* 3.2 6.0 - - - -
678A TYR* 2.9 40.2 + - - -
680A MET* 3.6 17.8 - - - +
704A ALA* 1.3 71.6 - - - +
706A ASN* 1.3 75.0 + - - +
707A LEU* 3.3 13.5 + - + +
710A SER* 4.2 9.2 - - - -
711A LYS 3.5 15.9 - - - +
712A LEU* 3.5 17.5 - - - +
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Residues in contact with ASN 706 (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 SER* 3.1 24.6 + - - +
676A ARG 3.8 2.9 - - - -
677A TYR* 3.4 33.1 + - + -
704A ALA 3.7 2.8 + - - -
705A THR* 1.3 70.3 - - - +
707A LEU* 1.3 52.6 + - - +
708A ALA* 3.2 19.8 + - - +
709A VAL* 3.4 20.4 + - + +
710A SER* 2.7 36.9 + - - -
711A LYS 2.8 15.1 + - - +
713A GLU* 3.4 23.0 + - - +
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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