Contacts of the strand formed by residues 655 - 660 (chain A) in PDB entry 1T7P
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 GLU 655 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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452A ARG* 4.0 1.4 + - - -
474A ILE 3.1 11.1 - - - +
475A ASP* 3.0 21.2 - - - +
625A TRP* 4.1 2.6 - - - -
650A ALA 3.9 0.2 - - - +
651A TRP* 3.2 7.6 - - - -
652A VAL* 2.8 53.5 + - + +
653A HIS 3.5 0.6 - - - -
654A ASP* 1.3 77.3 - - - +
656A ILE* 1.3 62.7 + - - +
657A GLN* 2.8 31.2 + - + -
700A TRP* 3.6 22.6 + - - -
704A HIS* 2.9 34.3 + - - -
22P 2DA 4.5 1.9 + - - +
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Residues in contact with ILE 656 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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472A ALA 3.6 0.7 - - - +
473A GLY* 3.3 3.5 - - - -
474A ILE* 2.9 49.9 + - + +
625A TRP* 3.8 28.0 - - + -
626A ILE* 3.7 28.5 - - + -
629A THR* 4.4 21.5 - - + +
648A TYR* 4.2 18.6 - - + +
650A ALA 3.3 9.2 - - - +
651A TRP* 3.7 8.1 - - + -
655A GLU* 1.3 79.2 - - - +
657A GLN* 1.3 65.4 + - - +
658A VAL* 4.0 15.9 - - + -
673A ALA* 4.7 0.7 - - + -
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Residues in contact with GLN 657 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232A PHE* 4.3 17.0 - - + -
471A GLN* 2.9 30.9 + - - +
472A ALA 3.6 0.7 - - - -
473A GLY* 3.2 23.4 - - - -
648A TYR* 4.1 0.5 - - - -
649A MET* 2.9 28.5 + - + +
650A ALA* 3.0 15.3 + - + +
655A GLU* 2.8 26.8 + - + +
656A ILE* 1.3 73.3 + - - +
658A VAL* 1.3 62.0 + - - +
700A TRP* 3.3 38.6 - - + +
703A CYS* 3.4 21.1 + - - +
704A HIS* 4.0 0.2 - - - +
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Residues in contact with VAL 658 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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471A GLN* 3.5 2.1 - - - -
472A ALA* 2.9 41.9 + - + +
646A PHE* 3.9 19.7 - - + -
647A ALA 3.5 20.2 - - - +
648A TYR* 4.2 19.1 - - + +
649A MET* 3.7 3.5 - - - +
656A ILE* 4.3 23.1 - - + -
657A GLN* 1.3 77.5 - - - +
659A GLY* 1.3 74.5 + - - +
660A CYS* 3.7 3.4 + - - -
669A VAL* 4.1 26.5 - - + -
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Residues in contact with GLY 659 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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457A ALA* 3.9 6.1 - - - -
469A TRP* 3.5 12.6 - - - -
470A VAL 3.6 6.1 - - - -
642A TRP* 4.7 1.8 - - - -
646A PHE* 3.1 7.3 - - - +
647A ALA 2.8 38.1 + - - -
649A MET* 3.5 21.0 - - - +
658A VAL* 1.3 73.6 - - - +
660A CYS* 1.3 57.6 + - - -
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Residues in contact with CYS 660 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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469A TRP* 3.4 6.6 - - - +
470A VAL* 2.6 42.2 + - - +
472A ALA* 4.0 6.1 - - - -
645A ASP 3.5 4.7 - - - -
646A PHE* 4.7 0.4 - - - -
658A VAL* 3.8 13.5 - - - -
659A GLY* 1.3 78.6 - - - -
661A ARG* 1.3 64.8 + - - +
662A THR 3.2 18.0 + - - +
665A ILE* 4.0 6.3 - - + -
666A ALA* 3.5 31.9 - - + +
669A VAL* 3.9 20.6 - - - -
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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