Contacts of the strand formed by residues 660 - 668 (chain B) in PDB entry 1GGT
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 LEU 660 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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652B PHE* 3.7 34.1 - - + -
654B ASN* 3.9 24.5 - - + +
656B LEU* 4.0 17.7 - - + -
658B GLU* 4.7 2.2 - - + +
659B THR* 1.3 75.8 - - - +
661B ARG* 1.3 62.3 + - - +
663B VAL* 3.8 12.8 - - + +
682B GLU* 3.2 4.0 - - - +
683B ILE* 3.0 35.6 + - + +
709B MET* 4.8 5.4 - - - -
711B SER* 4.0 11.0 - - - +
713B SER* 3.8 24.7 - - - -
714B LEU* 4.0 20.4 - - + -
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Residues in contact with ARG 661 (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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659B THR* 3.8 21.2 + - - +
660B LEU* 1.3 79.6 - - - +
662B ASN* 1.3 87.5 + - - +
663B VAL* 3.4 1.8 - - - -
681B ARG* 3.2 8.6 + - - +
682B GLU* 3.4 34.4 + - + +
684B ARG* 4.6 8.9 - - - +
711B SER* 3.8 0.7 - - - -
712B ASP* 3.0 28.7 + - - +
713B SER* 3.9 7.7 + - - +
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Residues in contact with ASN 662 (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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661B ARG* 1.3 85.0 - - - +
663B VAL* 1.3 62.2 + - - +
664B TRP* 3.8 10.0 + - - +
679B MET* 3.4 35.5 - - - +
680B PHE 3.5 5.4 - - - -
681B ARG* 2.7 21.8 + - - +
710B SER 3.9 0.2 - - - +
711B SER* 3.4 12.8 - - - -
712B ASP* 3.2 25.6 + - + +
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Residues in contact with VAL 663 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
652B PHE* 4.9 0.2 - - + -
660B LEU* 3.8 33.7 - - + +
662B ASN* 1.3 75.5 - - - +
664B TRP* 1.3 58.8 + - - +
665B VAL* 4.3 8.1 - - + -
678B LYS 3.3 1.7 - - - +
679B MET* 3.1 7.0 - - - +
680B PHE* 2.9 46.9 + - + +
683B ILE* 3.7 33.4 - - + +
709B MET* 3.6 39.3 - - + -
710B SER 3.5 3.6 - - - -
711B SER* 4.0 3.8 - - - -
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Residues in contact with TRP 664 (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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288B PRO* 6.4 2.5 - - + -
662B ASN* 4.2 12.3 + - + +
663B VAL* 1.3 72.1 - - - +
665B VAL* 1.3 61.4 + - - +
666B HIS* 3.9 18.9 - - + +
677B LYS* 3.7 43.5 - - + -
678B LYS* 3.2 34.5 - - - -
679B MET* 3.9 30.8 - - + -
709B MET* 3.2 4.3 - - - +
710B SER* 2.6 49.1 + - - +
711B SER* 5.9 0.2 - - - -
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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
----------------------------------------------------------
632B ILE* 4.5 7.0 - - + -
650B VAL* 3.7 31.0 - - + -
652B PHE* 5.7 4.7 - - + -
663B VAL* 4.3 9.9 - - + -
664B TRP* 1.3 80.7 - - - +
666B HIS* 1.3 67.5 + - - +
677B LYS* 3.1 5.0 - - - +
678B LYS 2.9 30.3 + - - +
680B PHE* 3.3 35.2 - - + -
689B VAL* 5.7 3.6 - - + -
691B TRP* 3.8 18.3 - - + -
708B SER 3.2 10.3 - - - +
709B MET* 4.3 6.7 - - + -
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Residues in contact with HIS 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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287B VAL* 4.8 11.6 - - + +
291B ALA* 4.1 25.2 + - + +
292B TRP* 5.5 3.9 - + - -
293B THR* 3.9 17.7 + - + +
297B ASP* 4.5 12.1 + - - -
650B VAL* 5.9 0.2 - - - -
664B TRP* 3.9 26.1 - - + +
665B VAL* 1.3 82.3 - - - +
667B LEU* 1.3 60.4 + - - +
675B PRO* 6.3 0.6 - - - +
676B MET 3.0 7.5 + - - +
677B LYS* 3.6 32.2 - - + +
691B TRP* 4.3 1.8 - - - -
707B ALA* 3.0 28.9 - - - +
708B SER* 2.8 30.9 + - - +
710B SER 5.4 0.9 - - - -
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Residues in contact with LEU 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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634B ILE* 4.4 8.5 - - + -
648B VAL* 4.1 21.3 - - + -
650B VAL* 4.1 21.8 - - + -
666B HIS* 1.3 73.5 - - - +
668B ASP* 1.3 67.7 + - - +
673B THR* 4.3 7.9 - - + +
674B ARG 4.2 1.6 - - - +
675B PRO* 3.4 2.1 - - - +
676B MET* 2.7 43.0 + - + +
691B TRP* 3.9 20.7 - - + -
693B GLU* 4.3 23.6 - - + -
695B CYS* 4.3 16.6 - - - -
705B LEU* 4.4 11.7 - - + -
706B ILE 3.4 17.7 - - - +
707B ALA* 4.6 0.2 - - + -
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Residues in contact with ASP 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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226B SER* 3.9 16.8 + - - -
293B THR* 2.6 49.8 + - - +
294B GLY* 3.5 6.8 + - - -
296B VAL* 5.7 2.8 - - - +
297B ASP* 5.5 0.9 + - - +
667B LEU* 1.3 75.0 - - - +
669B GLY* 1.3 73.2 + - - +
673B THR* 3.9 10.0 - - - +
675B PRO* 3.8 28.8 - - - +
705B LEU* 3.4 8.0 - - - +
706B ILE* 2.6 39.3 + - + +
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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