Contacts of the strand formed by residues 673 - 681 (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 PHE 673 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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121A MET* 3.6 31.4 - - + -
298A PRO* 4.8 11.4 - - + -
299A PHE* 5.9 2.5 - + - -
519A ASN* 3.5 39.7 - - + -
521A GLN* 5.2 4.0 - - - -
645A ILE* 3.5 28.3 - - + -
646A ILE 3.4 13.5 - - - -
647A SER* 4.3 7.6 - - - -
648A GLN* 4.3 0.2 - - - -
669A LEU* 2.9 33.3 + - + +
670A ASN* 3.0 18.5 + - - +
672A ASP* 1.3 93.8 - - + +
674A VAL* 1.3 67.6 + - - +
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Residues in contact with VAL 674 (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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644A GLU 3.3 1.9 - - - +
645A ILE* 3.5 5.7 - - - -
646A ILE* 2.8 42.5 + - + +
648A GLN* 3.7 21.1 - - - +
651A ALA* 3.9 23.3 - - + -
666A LEU* 3.6 31.4 - - + -
667A PHE 3.5 15.9 - - - +
668A ASN* 3.5 24.0 - - - +
669A LEU* 4.2 0.4 - - - +
673A PHE* 1.3 75.7 - - - +
675A VAL* 1.3 61.4 + - - +
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Residues in contact with VAL 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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119A ASN* 3.8 9.2 - - - +
641A TYR* 3.8 16.8 - - + +
642A CYS 3.9 2.0 - - - +
643A GLY* 3.5 32.1 - - - +
644A GLU 3.2 4.3 - - - -
645A ILE* 3.7 13.5 - - + -
665A PHE 4.1 1.2 - - - +
666A LEU* 3.4 1.6 - - - -
667A PHE* 2.8 41.2 + - + +
669A LEU* 4.2 12.1 - - + +
674A VAL* 1.3 71.3 - - - +
676A ASP* 1.3 60.5 + - - +
677A ALA 4.2 0.2 + - - -
708A ILE* 3.0 34.8 - - + -
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Residues in contact with ASP 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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643A GLY* 4.0 1.1 - - - -
644A GLU* 2.8 39.3 + - - +
646A ILE* 3.9 19.5 - - + +
654A ARG* 2.8 27.7 + - - +
658A TYR* 2.7 32.8 + - - -
665A PHE 3.6 7.2 - - - +
666A LEU* 4.0 9.0 - - + +
675A VAL* 1.3 73.1 - - - +
677A ALA* 1.3 60.3 + - - +
678A THR* 2.6 28.6 + - - -
680A LYS 3.3 4.5 + - - +
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Residues in contact with ALA 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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641A TYR* 3.5 29.8 - - + +
642A CYS 3.6 20.2 - - - +
665A PHE* 3.1 12.8 + - + +
675A VAL 4.1 1.8 - - - -
676A ASP* 1.3 69.4 - - - +
678A THR* 1.4 52.8 + - - +
680A LYS 3.1 17.3 - - - +
681A GLY* 4.5 0.9 - - - -
685A ARG* 2.6 46.5 + - + -
9001A 6BN 5.3 0.2 - - - -
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Residues in contact with THR 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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112A SER 4.1 8.7 - - - +
113A TRP* 4.1 0.2 - - - +
658A TYR* 3.4 30.6 + - + +
663A CYS* 5.3 0.7 - - - -
665A PHE* 3.8 22.3 + - + +
676A ASP* 2.6 22.9 + - - -
677A ALA* 1.4 74.9 - - - +
679A ARG* 1.3 63.3 + - - +
685A ARG* 3.0 17.6 + - - +
9001A 6BN 3.7 47.7 - - + +
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Residues in contact with ARG 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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112A SER 4.2 5.3 - - - +
113A TRP* 3.1 9.7 - - - -
114A SER* 3.0 22.7 + - - -
644A GLU* 3.3 29.3 + - - +
650A GLU* 5.5 0.4 + - - -
654A ARG* 3.8 31.8 - - - +
657A VAL* 6.1 0.8 - - - +
658A TYR* 2.9 40.8 + - - -
676A ASP 4.7 0.6 + - - -
678A THR* 1.3 80.1 - - + +
680A LYS* 1.3 67.4 + - + +
9001A 6BN 3.8 17.8 + - - +
222E ARG* 5.8 10.1 - - - +
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Residues in contact with LYS 680 (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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113A TRP* 5.0 0.9 - - - -
114A SER* 3.3 20.2 - - - +
116A LEU* 3.6 17.0 - - + -
120A PHE* 3.7 31.5 - - + -
122A VAL* 5.3 0.2 - - - +
643A GLY* 3.4 3.8 - - - -
644A GLU* 3.1 36.1 + - + +
676A ASP 3.3 5.5 - - - +
677A ALA* 3.1 25.0 - - - -
679A ARG* 1.3 85.2 - - - +
681A GLY* 1.3 57.8 + - - +
218E VAL* 3.6 21.6 + - - +
591S TRP* 3.5 28.0 - - + -
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Residues in contact with GLY 681 (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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113A TRP* 3.1 20.2 - - - -
114A SER 3.0 5.9 + - - +
116A LEU* 3.0 30.8 + - - +
642A CYS 3.5 15.5 - - - -
677A ALA* 4.4 5.8 - - - -
680A LYS* 1.3 75.3 - - - +
682A ASN* 1.3 61.2 + - - -
685A ARG* 4.4 4.5 - - - -
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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