Contacts of the strand formed by residues 673 - 681 (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 PHE 673 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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121B MET* 3.6 31.2 - - + -
298B PRO* 4.7 11.7 - - + -
299B PHE* 5.8 2.9 - + - -
519B ASN* 3.5 40.6 - - + -
521B GLN* 5.1 4.5 - - - -
645B ILE* 3.4 27.4 - - + -
646B ILE 3.4 13.0 - - - -
647B SER* 4.7 7.9 - - - +
648B GLN* 4.3 0.7 - - - +
669B LEU* 2.9 35.3 + - + +
670B ASN* 3.0 17.3 + - - +
672B ASP* 1.3 93.1 - - + +
674B VAL* 1.3 66.1 + - - +
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Residues in contact with VAL 674 (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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644B GLU 3.3 1.9 - - - +
645B ILE* 3.4 5.9 - - - +
646B ILE* 2.8 41.8 + - + +
648B GLN* 3.7 21.3 - - - +
651B ALA* 3.9 23.1 - - + -
666B LEU* 3.5 31.9 - - + -
667B PHE 3.5 16.2 - - - +
668B ASN* 3.5 23.8 - - - +
669B LEU* 4.8 0.4 - - - -
673B PHE* 1.3 76.3 - - - +
675B VAL* 1.3 62.4 + - - +
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Residues in contact with VAL 675 (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* 3.8 10.1 - - - +
641B TYR* 3.8 16.1 - - + +
642B CYS 3.9 1.8 - - - +
643B GLY* 3.5 32.1 - - - +
644B GLU 3.2 4.0 - - - -
645B ILE* 3.7 13.9 - - + -
665B PHE 4.1 1.2 - - - +
666B LEU* 3.4 1.6 - - - -
667B PHE* 2.8 41.3 + - + +
669B LEU* 4.2 11.4 - - + +
674B VAL* 1.3 70.6 - - - +
676B ASP* 1.3 60.0 + - - +
677B ALA 4.1 0.6 + - - -
708B ILE* 3.0 34.5 - - + -
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Residues in contact with ASP 676 (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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643B GLY* 4.0 1.3 - - - -
644B GLU* 2.8 38.7 + - - +
646B ILE* 3.8 20.5 - - + +
654B ARG* 2.8 27.6 + - - +
658B TYR* 2.7 32.9 + - - -
665B PHE 3.6 7.8 - - - +
666B LEU* 4.0 7.9 - - + +
675B VAL* 1.3 72.0 - - - +
677B ALA* 1.3 60.1 + - - +
678B THR* 2.6 28.8 + - - -
679B ARG 4.7 0.2 + - - -
680B LYS 3.3 4.3 + - - +
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Residues in contact with ALA 677 (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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641B TYR* 3.5 31.1 - - + +
642B CYS 3.6 19.5 - - - +
665B PHE* 3.1 12.3 + - + +
675B VAL 4.1 1.0 - - - -
676B ASP* 1.3 70.2 - - - +
678B THR* 1.4 52.6 + - - +
680B LYS 3.1 18.5 - - - +
681B GLY* 4.5 0.2 - - - -
685B ARG* 2.6 46.2 + - + -
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Residues in contact with THR 678 (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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112B SER 4.1 9.0 - - - +
658B TYR* 3.3 34.0 + - + +
663B CYS* 5.4 0.7 - - - -
665B PHE* 3.7 22.3 - - + +
676B ASP* 2.6 22.8 + - - -
677B ALA* 1.4 75.0 - - - +
679B ARG* 1.3 63.4 + - - +
685B ARG* 3.0 17.3 + - - +
9001B 6BN 3.8 44.3 - - + +
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Residues in contact with ARG 679 (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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112B SER 4.2 4.7 - - - +
113B TRP* 3.1 9.8 - - - -
114B SER* 2.9 22.2 + - - -
644B GLU* 3.3 29.9 + - - +
650B GLU* 5.5 0.6 + - - -
654B ARG* 3.8 31.6 - - - +
657B VAL* 6.1 0.8 - - - +
658B TYR* 2.9 40.7 + - - -
676B ASP* 4.7 1.0 + - - -
678B THR* 1.3 82.0 - - + +
680B LYS* 1.3 66.8 + - + +
9001B 6BN 3.8 17.8 + - - -
222F ARG* 5.9 7.4 - - - +
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Residues in contact with LYS 680 (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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113B TRP* 5.0 0.7 - - - -
114B SER* 3.3 17.9 - - - +
116B LEU* 3.6 16.8 - - + -
120B PHE* 3.7 32.6 - - + -
643B GLY* 3.4 4.0 - - - -
644B GLU* 3.1 36.6 + - + +
676B ASP 3.3 5.9 + - - +
677B ALA* 3.1 25.5 - - - -
679B ARG* 1.3 85.3 - - - +
681B GLY* 1.3 58.6 + - - +
218F VAL* 3.8 22.1 + - - +
591T TRP* 3.6 26.9 - - + -
595T LYS* 6.0 1.4 - - - +
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Residues in contact with GLY 681 (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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113B TRP* 3.1 20.0 - - - -
114B SER 3.0 6.1 + - - +
116B LEU* 3.0 30.7 + - - +
642B CYS 3.5 16.2 - - - -
677B ALA* 4.4 6.3 - - - -
680B LYS* 1.3 75.1 - - - +
682B ASN* 1.3 61.3 + - - -
685B ARG* 4.4 4.7 - - - -
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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