Contacts of the strand formed by residues 705 - 712 (chain A) in PDB entry 5IJ7
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 ASP 705 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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118A GLN* 5.6 0.7 + - - -
288A ARG* 3.5 4.5 + - - -
296A LEU* 4.0 24.2 - - + +
297A HIS* 2.9 34.3 + - - -
519A ASN* 6.1 0.2 - - - -
700A MET 3.5 0.2 - - - +
701A MET* 3.6 5.0 - - - -
702A VAL* 2.7 43.4 + - - +
703A ASN 4.4 5.6 - - - +
704A GLY* 1.3 83.8 - - - +
706A HIS* 1.3 61.7 + - - +
707A ARG* 3.6 20.0 + - + +
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Residues in contact with HIS 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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119A ASN* 4.4 4.9 + - - -
517A VAL* 3.5 30.5 - - + +
518A TYR 3.3 19.1 + - - -
519A ASN* 4.0 14.5 + - - -
520A TYR 4.4 2.2 - - - -
541A ASN* 5.2 0.9 - - - -
669A LEU* 3.5 39.5 + - + +
670A ASN* 3.3 20.1 + - + +
699A VAL* 3.8 19.8 - - + +
700A MET 3.3 9.8 + - - -
701A MET* 3.4 30.4 - - + +
704A GLY 5.5 0.7 - - - -
705A ASP* 1.3 73.4 - - - +
707A ARG* 1.3 62.9 + - - +
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Residues in contact with ARG 707 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A GLN 4.7 2.4 + - - -
118A GLN* 3.8 37.7 - - - +
119A ASN* 5.1 5.4 - - - +
296A LEU* 6.3 0.4 - - - -
606A ILE* 3.5 35.4 + - + +
607A GLN* 3.6 27.1 + - - +
640A GLU* 2.9 39.3 + - - +
669A LEU* 4.3 2.5 - - - -
698A LYS 3.5 1.6 - - - +
699A VAL* 3.4 1.6 - - - -
700A MET* 2.8 34.0 + - - +
702A VAL* 3.9 21.5 + - + +
705A ASP* 4.0 22.1 + - + +
706A HIS* 1.3 79.7 - - - +
708A ILE* 1.3 61.1 + - - +
709A GLY 3.8 0.2 + - - -
627S ILE* 5.7 2.4 - - - +
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Residues in contact with ILE 708 (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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119A ASN* 5.6 1.2 - - - +
606A ILE* 4.4 0.4 - - - -
640A GLU* 3.1 13.7 + - - +
641A TYR* 2.8 62.5 + - + +
667A PHE* 4.5 12.1 - - + +
668A ASN 4.9 2.5 - - - +
669A LEU* 3.9 8.4 - - + +
675A VAL* 3.0 37.9 - - + -
697A ALA* 3.9 27.4 - - + -
698A LYS 3.6 6.1 - - - +
699A VAL* 3.7 22.4 - - + +
707A ARG* 1.3 70.3 - - - +
709A GLY* 1.3 59.0 + - - +
710A ILE* 3.9 4.0 - - + -
729A SER* 5.4 2.7 - - - +
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Residues in contact with GLY 709 (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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606A ILE* 3.9 14.0 - - - +
637A PHE* 4.3 3.4 - - - -
639A SER 3.9 4.0 - - - -
697A ALA* 3.3 5.2 - - - -
698A LYS 2.8 38.5 + - - -
707A ARG 3.8 1.2 + - - -
708A ILE* 1.3 74.3 - - - +
710A ILE* 1.3 61.9 + - - +
711A PHE* 3.6 19.1 - - - -
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Residues in contact with ILE 710 (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 PHE* 3.7 2.1 - - - -
638A ILE* 2.7 36.9 + - + -
639A SER 2.8 22.3 + - - +
641A TYR* 4.0 17.0 - - + -
684A ILE* 3.9 34.8 - - + -
695A CYS* 3.9 29.2 - - + -
696A TYR 3.4 2.9 - - - +
697A ALA* 3.5 29.8 - - + +
708A ILE* 3.9 10.1 - - + -
709A GLY* 1.3 70.8 - - - +
711A PHE* 1.3 56.5 + - - +
724A PHE* 4.4 24.5 - - + -
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Residues in contact with PHE 711 (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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579A GLU* 5.7 0.2 - - - -
605A SER* 5.8 0.9 - - - -
635A ASN 3.6 16.4 - - - +
636A GLU 3.4 5.2 - - - +
637A PHE* 3.5 42.0 - + + -
638A ILE* 3.7 4.5 - - - -
695A CYS* 3.2 4.9 - - - +
696A TYR* 2.8 63.2 + + + +
698A LYS* 3.7 33.2 - - + -
700A MET* 3.6 26.5 - - + -
709A GLY* 3.6 28.5 - - - -
710A ILE* 1.3 73.3 - - - +
712A ALA* 1.3 60.8 + - - +
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Residues in contact with ALA 712 (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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632A VAL* 3.4 33.7 - - + -
633A GLN 3.5 13.2 - - - +
635A ASN 2.8 22.9 + - - -
636A GLU 2.9 9.9 + - - +
638A ILE* 3.5 7.6 - - + +
694A ASN 3.7 5.8 - - - -
696A TYR* 3.2 10.3 - - - -
711A PHE* 1.3 69.4 - - - +
713A LYS* 1.3 58.6 + - - +
714A ARG 3.4 14.6 - - - +
716A ILE* 3.8 4.9 - - + -
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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