Contacts of the strand formed by residues 614 - 618 (chain A) in PDB entry 1XR2
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 GLN 614 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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395A GLN* 3.0 29.7 + - + +
396A ARG* 5.6 4.2 - - - +
399A LEU* 3.9 18.6 - - + +
401A LEU* 5.1 1.8 - - - +
572A LYS 3.1 15.7 + - - +
573A ILE* 3.4 18.4 - - + +
574A VAL 3.0 25.3 + - - -
612A GLU 3.7 2.2 + - - -
613A THR* 1.3 69.8 - - - +
615A ILE* 1.3 61.1 + - - +
616A HIS* 2.8 24.2 + - - +
637A ASP* 3.4 5.8 - - + -
638A VAL* 3.9 16.6 - - + -
663A GLN* 4.0 16.8 + - - +
699A TRP* 3.4 23.4 - - - -
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Residues in contact with ILE 615 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384A ARG* 3.5 28.0 - - - +
563A VAL* 4.9 3.4 - - + -
574A VAL* 3.4 25.4 - - + +
576A ILE* 4.7 7.0 - - + -
603A PHE* 4.6 5.2 - - + -
607A ALA* 4.0 31.4 - - + +
609A ALA* 3.9 21.1 - - + -
613A THR* 3.9 5.4 - - + +
614A GLN* 1.3 76.3 - - - +
616A HIS* 1.3 68.8 + - - +
636A PHE* 3.8 18.7 - - + +
637A ASP* 2.8 36.4 + - - +
638A VAL* 3.2 9.5 + - - +
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Residues in contact with HIS 616 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
407A THR* 5.4 0.6 - - + +
409A ILE* 5.3 3.6 - - + +
457A VAL* 5.9 0.2 - - + -
527A LYS* 3.7 19.4 + - - -
573A ILE* 3.5 24.7 - - + +
574A VAL 2.9 6.9 + - - -
575A GLN* 3.3 24.0 + - + +
576A ILE* 2.8 31.7 + - - +
614A GLN* 2.8 26.2 + - + -
615A ILE* 1.3 78.4 - - - +
617A ALA* 1.3 60.7 + - - +
638A VAL* 3.1 41.5 - - + +
640A SER* 6.0 1.8 - - - +
699A TRP* 3.6 28.6 - + - -
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Residues in contact with ALA 617 (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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575A GLN* 5.2 0.2 - - - -
576A ILE 3.8 6.5 - - - +
603A PHE* 4.2 13.7 - - + -
616A HIS* 1.3 75.2 - - - +
618A HIS* 1.3 60.1 + - - +
619A MET* 4.3 14.1 - - + -
636A PHE* 3.8 33.2 - - + +
638A VAL 2.9 7.8 + - - +
639A ILE* 3.3 11.0 - - + +
640A SER* 3.0 26.0 + - - -
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Residues in contact with HIS 618 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
409A ILE* 4.0 23.6 + - + +
468A MET* 6.5 1.3 - - + -
575A GLN* 4.0 10.5 - - - +
576A ILE 3.7 7.3 + - - -
577A ASP* 3.1 30.8 + - + +
578A GLU 3.6 17.8 + - - -
579A PRO* 4.6 1.6 - - - +
616A HIS 4.2 0.6 + - - -
617A ALA* 1.3 74.8 - - - +
619A MET* 1.3 78.9 + - - +
620A CYS* 2.9 11.8 - - - -
640A SER* 2.5 30.7 + - - +
703A ASP 3.5 9.9 - - - -
704A CYS* 2.9 42.6 - - - +
705A GLY 4.9 0.6 + - - -
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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
------------------------------------------------------------
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