Contacts of the strand formed by residues 705 - 712 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118B GLN* 5.7 0.7 + - - -
288B ARG* 3.5 8.8 + - - -
296B LEU* 4.1 23.9 - - + +
297B HIS* 2.9 33.7 + - - -
519B ASN* 6.1 0.4 - - - -
700B MET 3.5 0.2 - - - +
701B MET* 3.6 4.9 - - - -
702B VAL* 2.7 42.8 + - - +
703B ASN 4.4 5.7 - - - +
704B GLY* 1.3 77.8 - - - +
706B HIS* 1.3 61.8 + - - +
707B ARG* 3.6 19.2 + - + +
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Residues in contact with HIS 706 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119B ASN* 4.4 4.9 + - - -
517B VAL* 3.4 30.7 - - + +
518B TYR 3.3 19.7 + - - -
519B ASN* 4.0 13.9 + - - +
520B TYR* 4.4 2.2 - - + -
541B ASN* 5.2 0.7 - - - -
669B LEU* 3.4 42.2 + - + +
670B ASN* 3.3 20.1 + - + +
699B VAL* 3.8 18.7 - - + +
700B MET 3.3 9.5 + - - -
701B MET* 3.4 30.4 - - + +
704B GLY 5.4 0.4 - - - -
705B ASP* 1.3 74.0 - - - +
707B ARG* 1.3 62.9 + - - +
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Residues in contact with ARG 707 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117B GLN 4.8 2.2 + - - -
118B GLN* 3.8 36.8 - - - +
119B ASN* 5.1 5.8 - - - +
606B ILE* 3.5 34.6 + - + +
607B GLN* 3.6 27.5 + - - +
640B GLU* 2.9 38.4 + - - +
669B LEU* 4.3 2.0 - - - -
698B LYS 3.5 0.5 - - - +
699B VAL* 3.4 1.3 - - - -
700B MET* 2.8 34.1 + - - +
702B VAL* 3.9 21.8 + - + +
703B ASN* 6.1 0.2 - - - +
705B ASP* 4.0 21.6 + - + +
706B HIS* 1.3 80.3 - - - +
708B ILE* 1.4 63.7 + - - +
709B GLY 3.7 0.7 + - - -
627T ILE* 5.7 2.6 - - - +
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Residues in contact with ILE 708 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119B ASN* 5.7 0.8 - - - +
606B ILE* 4.4 0.4 - - - -
640B GLU* 3.1 12.8 + - - +
641B TYR* 2.8 65.9 + - + +
667B PHE* 4.5 11.9 - - + +
668B ASN 4.9 2.5 - - - +
669B LEU* 3.9 8.0 - - + +
675B VAL* 3.0 37.2 - - + -
697B ALA* 3.9 27.8 - - + -
698B LYS 3.6 6.3 - - - +
699B VAL* 3.6 23.3 - - + +
707B ARG* 1.4 70.3 - - - +
709B GLY* 1.3 58.7 + - - +
710B ILE* 3.9 4.0 - - + -
724B PHE* 6.1 0.2 - - + -
729B SER* 5.4 3.6 - - - +
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Residues in contact with GLY 709 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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606B ILE* 3.9 14.5 - - - +
637B PHE* 4.3 3.4 - - - -
639B SER 3.9 3.6 - - - -
697B ALA* 3.2 4.7 - - - -
698B LYS 2.8 37.9 + - - -
707B ARG 3.7 1.6 + - - -
708B ILE* 1.3 73.7 - - - +
710B ILE* 1.3 61.8 + - - +
711B PHE* 3.6 19.5 - - - -
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Residues in contact with ILE 710 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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637B PHE* 3.7 2.1 - - - -
638B ILE* 2.7 36.6 + - + +
639B SER 2.8 21.0 + - - +
641B TYR* 4.0 16.6 - - + +
684B ILE* 3.9 35.9 - - + -
695B CYS* 4.0 26.2 - - + -
696B TYR 3.4 5.4 - - - +
697B ALA* 3.6 29.8 - - + -
708B ILE* 3.9 10.3 - - + -
709B GLY* 1.3 72.8 - - - +
711B PHE* 1.3 56.6 + - - +
724B PHE* 4.3 24.2 - - + -
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Residues in contact with PHE 711 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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579B GLU* 5.6 0.2 - - - -
605B SER* 5.7 0.9 - - - -
606B ILE* 4.8 0.2 - - + -
635B ASN 3.6 16.4 - - - +
636B GLU 3.4 5.6 - - - +
637B PHE* 3.5 42.2 - + + -
638B ILE* 3.7 4.3 - - - -
695B CYS* 3.2 5.0 - - - +
696B TYR* 2.8 64.0 + + + +
698B LYS* 3.7 33.9 - - + -
700B MET* 3.6 27.4 - - + -
709B GLY* 3.6 28.0 - - - -
710B ILE* 1.3 73.2 - - - +
712B ALA* 1.3 60.0 + - - +
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Residues in contact with ALA 712 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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632B VAL* 3.4 33.4 - - + -
633B GLN 3.5 13.2 - - - +
635B ASN* 2.8 23.7 + - - -
636B GLU 2.9 11.0 + - - +
638B ILE* 3.5 7.1 - - + +
694B ASN 3.7 5.6 - - - -
696B TYR* 3.2 9.4 - - - -
711B PHE* 1.3 69.5 - - - +
713B LYS* 1.3 59.2 + - - +
714B ARG 3.3 14.6 - - - +
716B 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