Contacts of the strand formed by residues 673 - 681 (chain J) in PDB entry 5LS6
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 J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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121J MET* 3.9 30.7 - - + -
298J PRO* 5.0 9.0 - - + -
299J PHE* 6.3 1.1 - + - -
519J ASN* 3.6 42.6 - - + -
645J ILE* 3.7 26.7 - - + -
646J ILE* 3.5 13.2 - - - -
647J SER* 4.3 7.9 - - - -
669J LEU* 3.2 17.2 + - + -
670J ASN* 3.1 34.9 + - - +
672J ASP* 1.3 92.1 - - + +
674J VAL* 1.3 67.3 + - - +
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Residues in contact with VAL 674 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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644J GLU 3.5 0.2 - - - +
645J ILE* 3.4 4.1 - - - -
646J ILE* 2.8 41.6 + - + +
648J GLN* 3.2 36.1 - - + +
651J ALA* 3.9 23.1 - - + -
666J LEU* 4.1 14.6 - - + -
667J PHE 3.2 28.9 - - - +
668J ASN* 4.0 4.9 - - + +
669J LEU* 4.2 1.3 - - - +
673J PHE* 1.3 73.1 - - - +
675J VAL* 1.3 72.4 + - - +
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Residues in contact with VAL 675 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119J ASN* 4.2 14.8 - - - +
641J TYR* 3.9 20.0 - - + +
642J CYS 3.9 3.6 - - - +
643J GLY* 3.8 24.9 - - - +
644J GLU 3.0 9.9 - - - +
645J ILE* 4.4 1.8 - - + -
665J PHE 4.0 0.4 - - - +
666J LEU* 3.3 4.5 - - - -
667J PHE* 2.8 39.4 + - + +
669J LEU* 3.9 25.9 - - + +
674J VAL* 1.3 74.9 - - - +
676J ASP* 1.3 63.3 + - - +
677J ALA 4.4 1.3 - - - +
708J ILE* 4.0 24.7 - - + -
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Residues in contact with ASP 676 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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643J GLY* 4.3 0.2 - - - -
644J GLU* 2.7 40.6 + - + +
646J ILE* 4.4 8.5 - - + -
654J ARG* 3.0 32.4 + - - +
658J TYR* 2.8 21.1 + - - -
665J PHE 3.3 7.8 - - - +
666J LEU* 3.3 21.1 - - + +
675J VAL* 1.3 73.1 - - - +
677J ALA* 1.3 61.2 + - - +
678J THR* 2.9 29.1 + - - -
679J ARG 4.0 0.7 + - - -
680J LYS 3.5 2.3 - - - +
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Residues in contact with ALA 677 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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641J TYR* 3.8 23.8 - - + +
642J CYS 3.6 20.0 - - - +
665J PHE* 3.2 9.9 + - + +
675J VAL* 4.1 2.4 - - - +
676J ASP* 1.3 71.5 - - - +
678J THR* 1.3 58.4 + - - +
679J ARG 3.4 0.2 - - - -
680J LYS 3.3 20.2 - - - +
681J GLY* 3.7 3.3 + - - -
685J ARG* 2.6 46.1 + - + +
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Residues in contact with THR 678 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112J SER 4.7 2.8 - - - +
113J TRP* 3.9 3.8 - - - +
658J TYR* 3.5 32.8 - - + +
665J PHE* 3.7 23.9 + - - +
676J ASP* 2.9 19.7 + - - -
677J ALA* 1.3 78.7 - - - +
679J ARG* 1.3 69.4 + - + +
685J ARG* 3.1 18.2 + - - +
809J 74D 4.0 46.4 - - + +
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Residues in contact with ARG 679 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112J SER 4.4 3.0 - - - +
113J TRP* 3.1 26.4 - - - -
114J SER* 3.1 4.5 + - - -
122J VAL* 5.3 4.9 - - - +
125J GLU* 4.4 13.1 + - - +
644J GLU* 3.2 30.4 + - - +
650J GLU* 4.8 0.6 + - - -
654J ARG* 3.5 40.0 - - - +
658J TYR* 5.0 2.3 + - - +
676J ASP 4.0 2.8 + - - -
677J ALA 3.4 0.2 - - - -
678J THR* 1.3 83.8 - - + +
680J LYS* 1.3 66.9 + - + +
809J 74D 6.1 0.8 - - - -
236K ARG* 3.4 47.8 - - - +
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Residues in contact with LYS 680 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113J TRP* 4.6 1.3 - - - -
114J SER* 3.0 26.7 - - - +
116J LEU* 3.8 16.6 - - + -
120J PHE* 4.1 26.9 - - + -
122J VAL* 4.9 2.0 - - - +
643J GLY* 3.2 18.4 - - - -
644J GLU* 3.3 36.1 + - + -
676J ASP 3.5 2.5 + - - +
677J ALA* 3.3 12.9 - - - +
679J ARG* 1.3 83.1 - - - +
681J GLY* 1.3 56.2 + - - +
232K VAL* 3.9 31.9 - - - +
591L TRP* 4.1 20.7 - - + -
595L LYS* 6.2 0.2 - - - +
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Residues in contact with GLY 681 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113J TRP* 3.8 9.7 - - - -
114J SER 3.2 4.6 + - - -
115J PRO* 3.4 6.4 - - - +
116J LEU* 2.6 35.6 + - - +
642J CYS 3.5 16.4 - - - -
643J GLY* 4.0 3.4 - - - -
677J ALA* 3.7 11.3 + - - -
680J LYS* 1.3 73.2 - - - +
682J ASN* 1.3 58.8 + - - -
685J ARG* 4.5 2.0 - - - -
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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