Contacts of the strand formed by residues 653 - 658 (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 653 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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607B ALA* 5.5 7.9 - - + -
608B CYS* 4.2 13.5 - - - -
652B ALA* 1.3 75.9 - - - +
654B ASN* 1.3 72.3 + - - +
655B CYS* 4.3 9.4 + - - -
668B GLN* 3.2 19.1 - - - +
669B TYR* 3.2 31.1 + - + +
1J NAG 4.7 1.3 - - - -
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Residues in contact with ASN 654 (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* 4.7 0.5 - - - -
646B LYS* 4.2 8.1 - - - +
653B VAL* 1.3 82.2 - - - +
655B CYS* 1.3 63.4 + - - +
656B THR* 5.1 0.7 + - - -
666B ARG* 4.9 6.1 + - - -
667B PHE 3.4 12.8 - - - +
668B GLN* 4.1 4.0 - - + -
1J NAG 1.5 84.2 + - - +
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Residues in contact with CYS 655 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
607B ALA 5.2 0.2 - - - -
608B CYS* 2.0 58.8 - - + -
611B LYS* 5.9 0.7 - - - -
646B LYS* 4.3 1.0 + - - -
653B VAL* 4.5 9.6 - - - -
654B ASN* 1.3 78.3 - - - +
656B THR* 1.3 70.3 + - - +
666B ARG* 3.5 4.3 + - - +
667B PHE* 3.0 58.7 + - + +
669B TYR* 5.1 6.7 - - - -
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Residues in contact with THR 656 (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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752A HIS* 5.2 3.9 - - - +
754A PHE* 3.2 38.1 - - + +
608B CYS* 5.2 1.5 - - - +
654B ASN* 5.1 1.2 + - - -
655B CYS* 1.3 85.0 + - - +
657B TYR* 1.3 69.2 + - - +
664B VAL* 3.4 16.8 - - + -
665B VAL 3.4 6.7 - - - +
666B ARG* 3.3 27.7 + - + +
667B PHE* 4.6 0.8 - - - -
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Residues in contact with TYR 657 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
754A PHE* 3.6 9.9 - - - -
608B CYS 5.8 2.0 - - - +
612B LYS* 3.2 39.7 - - + +
615B VAL* 2.8 25.6 - - + +
616B GLU* 2.9 40.3 + - + +
620B PHE* 4.3 0.9 - - - -
656B THR* 1.3 77.6 - - - +
658B LYS* 1.3 69.3 + - - +
659B ASN* 4.2 7.2 - - - -
664B VAL* 2.9 10.2 - - - -
665B VAL* 2.6 77.2 + - + +
667B PHE* 3.5 30.1 - + + -
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Residues in contact with LYS 658 (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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754A PHE* 3.6 32.4 - - + -
954A GLY 4.2 18.4 + - - +
955A ILE* 6.1 0.7 - - + -
956A GLN* 6.2 0.2 - - - +
612B LYS* 4.1 6.9 + - - -
657B TYR* 1.3 86.2 - - - +
659B ASN* 1.3 63.7 + - - +
662B ASP* 3.8 37.5 + - - +
663B CYS 3.1 15.7 - - - +
664B VAL* 4.1 6.5 - - + -
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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