Contacts of the strand formed by residues 674 - 681 (chain G) 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 VAL 674 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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644G GLU 3.4 0.7 - - - +
645G ILE* 3.5 2.6 - - - -
646G ILE* 2.7 41.1 + - + +
647G SER 4.4 0.2 - - - +
648G GLN* 3.3 36.8 - - - +
651G ALA* 3.8 26.0 - - + -
666G LEU* 4.2 14.4 - - + -
667G PHE 3.5 24.0 - - - +
668G ASN* 4.1 10.5 - - + +
669G LEU 4.3 1.3 - - - +
673G PHE* 1.3 73.2 - - - +
675G VAL* 1.3 74.5 + - - +
729G SER* 5.6 2.2 - - - +
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Residues in contact with VAL 675 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119G ASN* 4.2 14.1 - - - +
641G TYR* 4.3 15.0 - - + +
642G CYS 3.9 7.0 - - - +
643G GLY* 3.6 31.6 - - - +
644G GLU 3.2 5.2 - - - +
645G ILE* 4.6 5.6 - - + -
665G PHE 4.0 0.7 - - - +
666G LEU* 3.5 3.5 - - - -
667G PHE* 2.9 40.2 + - + +
669G LEU* 3.8 38.6 - - + -
674G VAL* 1.3 76.6 - - - +
676G ASP* 1.3 63.2 + - - +
708G ILE* 4.4 8.5 - - + -
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Residues in contact with ASP 676 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
643G GLY* 4.1 0.4 - - - -
644G GLU* 2.7 41.2 + - + +
646G ILE* 4.2 6.5 - - + -
654G ARG* 2.6 36.8 + - - +
658G TYR* 2.9 14.4 + - - -
665G PHE 3.4 8.8 - - - +
666G LEU* 3.3 22.8 - - + +
675G VAL* 1.3 74.5 - - - +
677G ALA* 1.3 57.0 + - - +
678G THR* 2.8 30.9 + - - -
679G ARG 4.0 0.7 + - - -
680G LYS 3.3 2.9 - - - +
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Residues in contact with ALA 677 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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641G TYR* 3.7 30.6 - - + +
642G CYS 3.7 10.7 + - - +
643G GLY* 4.2 1.9 - - - -
665G PHE* 3.3 12.6 + - + +
675G VAL 4.2 0.6 - - - -
676G ASP* 1.3 69.5 - - - +
678G THR* 1.3 56.5 + - - +
679G ARG 3.2 2.5 + - - -
680G LYS 3.1 18.2 - - - +
681G GLY* 4.1 2.7 - - - -
685G ARG* 2.5 52.0 + - + +
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Residues in contact with THR 678 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111G TYR 5.8 0.2 - - - +
112G SER 4.9 2.9 - - - +
113G TRP* 4.6 3.3 - - - +
658G TYR* 3.1 36.9 - - + +
665G PHE* 3.8 21.7 + - - +
676G ASP* 2.8 23.5 + - - -
677G ALA* 1.3 79.4 - - - +
679G ARG* 1.3 65.5 + - + +
685G ARG* 3.6 11.1 + - - +
809G 74D 3.7 46.4 - - + +
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Residues in contact with ARG 679 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112G SER 4.4 2.2 - - - +
113G TRP* 3.4 11.6 - - - -
114G SER* 3.4 19.8 + - - -
122G VAL* 5.4 3.6 - - - +
125G GLU* 4.0 12.9 + - - -
129G HIS* 5.7 0.4 - - - -
644G GLU* 3.3 34.0 + - - +
654G ARG* 3.4 34.1 - - - +
658G TYR* 4.8 3.3 + - - +
676G ASP 4.0 2.2 + - - -
677G ALA 3.2 0.8 - - - -
678G THR* 1.3 85.2 - - + +
680G LYS* 1.3 67.3 + - + +
809G 74D 5.3 11.5 - - - +
236H ARG* 3.2 55.3 - - - +
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Residues in contact with LYS 680 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113G TRP* 4.8 2.0 - - - -
114G SER* 3.1 33.4 - - - +
116G LEU* 3.6 19.7 - - + -
120G PHE* 3.6 32.2 - - + -
122G VAL* 5.2 0.2 - - - +
643G GLY* 3.3 7.3 - - - -
644G GLU* 3.3 36.5 + - + -
676G ASP 3.3 6.3 + - - +
677G ALA* 3.1 22.5 - - - -
679G ARG* 1.3 80.9 - - - +
681G GLY* 1.3 56.4 + - - +
232H VAL* 3.9 26.6 - - - +
591I TRP* 4.0 17.3 - - + -
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Residues in contact with GLY 681 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113G TRP* 3.6 9.3 - - - -
114G SER 3.3 2.7 + - - +
115G PRO* 3.4 7.4 - - - +
116G LEU* 2.7 32.4 + - - +
642G CYS 3.7 15.7 - - - -
643G GLY* 4.0 4.0 - - - -
677G ALA* 4.1 9.1 + - - -
680G LYS* 1.3 75.9 - - - +
682G ASN* 1.3 57.8 + - - -
685G ARG* 4.2 2.7 - - - -
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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