Contacts of the strand formed by residues 674 - 679 (chain A) in PDB entry 5JQY
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 674 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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620A ARG* 4.3 15.9 - - + -
622A LYS* 3.3 13.5 - - - +
623A GLY* 3.3 2.1 - - - -
624A ASP 3.0 26.2 + - - +
625A TRP* 4.6 0.2 - - + -
670A MET* 3.6 32.1 - - + -
671A HIS 2.6 23.3 + - - -
672A PRO 4.2 0.2 + - - -
673A GLY* 1.3 77.3 - - - +
675A HIS* 1.3 68.1 + - - +
676A VAL* 4.4 0.4 - - + -
728A TRP* 3.6 2.8 - - - +
729A GLN* 2.9 30.5 + - - +
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Residues in contact with HIS 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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620A ARG* 3.7 1.0 - - - -
621A GLU* 2.4 63.3 + - + +
622A LYS* 3.1 25.6 + - + +
674A THR* 1.3 75.2 - - - +
676A VAL* 1.3 74.4 + - - +
677A TRP* 4.0 24.4 - + - -
678A PRO* 4.8 0.2 - - + -
726A GLU* 2.7 27.2 + - - -
727A VAL 3.5 6.5 - - - -
728A TRP* 3.4 29.4 + + + -
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Residues in contact with VAL 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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619A LEU* 3.4 17.3 - - + +
620A ARG* 4.3 6.1 - - + +
625A TRP* 3.6 37.9 - - + -
670A MET* 3.6 22.0 - - + -
674A THR* 4.4 2.5 - - + -
675A HIS* 1.3 77.4 - - - +
677A TRP* 1.3 66.6 + - - +
679A HIS* 3.5 32.1 - - + +
726A GLU* 3.3 20.1 - - - +
727A VAL* 2.9 26.0 + - + +
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Residues in contact with TRP 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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536A GLN 4.8 3.4 - - - -
537A ARG* 3.4 85.5 - - + +
619A LEU* 2.8 25.8 + - - +
620A ARG 3.5 5.6 + - - -
621A GLU* 3.4 52.7 - - + +
675A HIS* 3.8 22.4 + + - -
676A VAL* 1.3 75.6 - - - +
678A PRO* 1.3 87.3 - - + +
679A HIS* 3.0 20.5 + - + -
725A HIS 3.7 1.2 - - - +
726A GLU* 4.4 0.2 - - - -
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Residues in contact with PRO 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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533A ASP* 3.3 19.2 - - - +
536A GLN* 4.0 22.6 - - + +
537A ARG* 5.4 0.6 + - + -
562A ARG* 5.6 0.8 + - - -
676A VAL 3.6 0.4 - - - -
677A TRP* 1.3 101.6 - - + +
679A HIS* 1.3 60.2 + - - +
703A ARG* 3.8 5.8 - - - +
724A GLU* 3.8 26.0 - - - +
725A HIS 3.3 9.6 - - - +
726A GLU* 3.6 33.0 - - + +
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Residues in contact with HIS 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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529A PHE* 5.8 2.2 - - + -
533A ASP* 4.9 4.5 - - - +
537A ARG* 5.8 0.9 - - - +
562A ARG* 5.1 2.7 - - - +
619A LEU* 3.8 34.4 - - + +
625A TRP* 4.9 0.4 - + - -
676A VAL* 3.5 21.6 - - + +
677A TRP* 3.0 18.8 + - + +
678A PRO* 1.3 76.3 - - - +
680A THR* 1.3 64.2 + - - +
724A GLU* 3.3 3.9 - - - +
725A HIS* 2.9 54.9 + + - +
726A GLU 5.1 0.7 - - - -
727A VAL* 5.3 1.1 - - + -
801A MN 2.3 36.4 + - - -
802A OGA 3.5 7.6 - - - -
103B ASP 3.4 20.2 - - - -
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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