Contacts of the strand formed by residues 664 - 671 (chain B) in PDB entry 1L5G
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 VAL 664 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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754A PHE* 4.1 14.4 - - + -
756A PRO* 5.8 4.0 - - + -
954A GLY* 5.4 5.6 - - - -
955A ILE* 4.2 13.2 - - + +
656B THR* 3.4 30.5 - - + -
657B TYR 2.9 14.8 - - - +
658B LYS* 4.1 10.3 - - + +
662B ASP 4.4 0.2 + - - -
663B CYS* 1.3 69.4 - - - +
665B VAL* 1.3 61.1 + - - +
666B ARG* 3.9 2.0 + - + +
685B PRO* 3.8 3.8 - - - +
686B GLU* 2.9 74.9 + - + +
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Residues in contact with VAL 665 (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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615B VAL* 5.0 0.9 - - + -
620B PHE* 4.1 15.0 - - + -
656B THR* 3.4 2.3 - - - -
657B TYR* 2.6 73.5 + - + +
659B ASN* 3.7 34.3 - - + +
663B CYS 4.0 1.6 - - - +
664B VAL* 1.3 73.2 - - - +
666B ARG* 1.3 61.9 + - - +
667B PHE* 5.0 0.4 - - + -
681B VAL* 3.9 26.0 - - + -
685B PRO* 4.2 18.4 - - + -
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Residues in contact with ARG 666 (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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758A PRO* 3.1 36.8 - - - +
646B LYS* 3.3 22.9 + - - +
654B ASN* 4.9 7.0 + - - -
655B CYS 3.5 4.9 - - - +
656B THR* 3.3 33.0 + - + +
664B VAL* 3.9 1.7 + - + +
665B VAL* 1.3 80.2 - - - +
667B PHE* 1.3 59.7 + - - +
681B VAL* 3.8 0.6 - - - -
682B VAL* 2.8 55.6 + - + +
685B PRO* 5.5 1.0 - - - +
686B GLU* 3.4 36.5 + - - +
1J NAG 3.4 23.8 + - - +
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Residues in contact with PHE 667 (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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608B CYS 4.2 6.5 - - - -
611B LYS* 3.5 28.3 - - + -
612B LYS* 3.5 26.9 - - + -
615B VAL* 3.9 14.8 - - + -
646B LYS* 2.8 19.7 + - - -
654B ASN* 3.4 0.5 - - - -
655B CYS* 3.0 52.0 + - + -
656B THR 4.6 0.4 - - - -
657B TYR* 3.5 40.2 - + + -
665B VAL* 5.0 0.7 - - + -
666B ARG* 1.3 74.2 - - - +
668B GLN* 1.3 71.1 + - - +
669B TYR* 5.1 0.7 - - + -
679B LEU* 4.0 11.0 - - + -
680B TYR 3.3 14.6 - - - +
681B VAL* 4.2 16.6 - - + -
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Residues in contact with GLN 668 (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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646B LYS* 3.1 24.8 - - - +
647B ASP* 3.2 38.0 + - - +
649B GLY 5.0 2.9 - - - +
652B ALA* 4.8 6.2 - - + +
653B VAL 3.2 21.1 - - - +
654B ASN* 4.1 1.3 - - + +
655B CYS 4.5 0.9 - - - +
667B PHE* 1.3 84.8 - - - +
669B TYR* 1.3 63.5 + - - +
670B TYR* 4.3 13.7 - - - -
678B ILE 3.3 3.5 - - - +
679B LEU* 3.3 9.8 - - - -
680B TYR* 3.2 33.1 + - + +
1J NAG 2.7 29.5 + - - +
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Residues in contact with TYR 669 (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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607B ALA* 5.1 11.7 - - + -
611B LYS* 3.9 43.4 + - + -
637B ASP* 5.0 0.3 + - - -
652B ALA* 3.0 21.1 - - - +
653B VAL* 3.2 28.3 + - + +
655B CYS* 5.1 6.4 - - - -
667B PHE* 5.1 1.0 - - + -
668B GLN* 1.3 70.7 - - - +
670B TYR* 1.3 71.9 + - - +
671B GLU* 4.1 30.2 + - + -
677B SER* 3.3 36.5 + - - -
678B ILE 3.9 1.3 - - - -
679B LEU* 4.0 20.2 - - + -
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Residues in contact with TYR 670 (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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647B ASP* 5.8 3.1 - - + -
649B GLY* 4.0 29.7 - - - -
651B ASP* 4.1 10.6 + - - -
652B ALA* 3.8 20.6 - - + -
668B GLN* 4.3 11.4 - - - +
669B TYR* 1.3 80.4 - - - +
671B GLU* 1.3 82.0 + - - +
672B ASP* 3.7 34.5 + - + +
676B LYS* 3.0 18.7 - - - +
677B SER* 3.6 3.3 - - - -
678B ILE* 3.2 43.9 + - + +
680B TYR* 4.1 16.2 - + + -
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Residues in contact with GLU 671 (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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651B ASP* 5.4 8.9 + - - +
652B ALA* 5.2 0.6 - - - +
669B TYR* 4.1 29.2 + - + -
670B TYR* 1.3 86.7 - - - +
672B ASP* 1.3 66.1 + - - +
675B GLY* 3.8 19.6 - - - +
676B LYS 3.0 9.9 - - - +
677B SER* 5.2 0.4 - - - -
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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