Contacts of the strand formed by residues 657 - 664 (chain A) in PDB entry 5OF4
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 ALA 657 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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503A ALA* 4.7 1.3 - - + -
504A LYS 3.3 2.2 + - - -
505A VAL* 3.8 26.9 - - + -
506A GLN 3.7 9.2 + - - -
621A ASN* 3.4 17.3 - - - +
644A LEU* 4.0 15.3 - - + -
645A ARG 4.6 7.4 - - - +
647A LYS* 4.6 2.2 - - + -
655A TYR* 3.4 13.7 - - - -
656A ASN* 1.3 94.2 + - - +
658A PHE* 1.3 66.3 + - - +
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Residues in contact with PHE 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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505A VAL* 4.4 0.4 - - - -
506A GLN* 4.2 13.2 - - + -
508A ALA* 6.0 0.7 - - + -
550A PHE* 4.9 3.8 - + - -
551A HIS* 3.6 23.6 - + - -
554A ARG* 4.8 15.3 - - - -
621A ASN 3.3 4.4 + - - -
622A VAL* 3.1 16.7 - - + +
623A LEU 2.9 24.6 + - - -
644A LEU* 3.4 8.4 - - - +
647A LYS* 4.9 5.2 - - - -
655A TYR* 3.5 32.8 - + - -
656A ASN 3.3 26.7 - - - -
657A ALA* 1.3 77.2 - - - +
659A PHE* 1.3 59.8 + - - +
660A TYR* 3.4 42.2 - + + -
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Residues in contact with PHE 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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505A VAL* 4.2 1.4 - - - +
506A GLN 4.2 6.0 + - - +
507A CYS* 4.0 28.3 - - + -
508A ALA* 3.0 39.6 + - - +
509A GLU* 5.2 1.3 - - + -
623A LEU* 3.3 39.0 - - + -
625A GLN* 3.7 20.9 - - + -
640A LEU* 4.3 21.1 - - + -
644A LEU* 4.2 8.3 - - + -
658A PHE* 1.3 74.0 - - - +
660A TYR* 1.3 73.7 + - - +
661A SER* 3.9 17.7 - - - -
676A ARG* 3.3 33.0 - - - -
680A LEU* 4.9 11.0 - - + -
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Residues in contact with TYR 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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508A ALA* 3.3 19.7 - - + -
510A VAL* 4.4 13.9 - - + -
547A LEU* 3.7 48.3 - - + +
550A PHE* 4.2 14.9 - - - -
551A HIS* 4.0 7.9 - - - -
622A VAL* 3.9 15.7 - - + -
623A LEU 2.9 10.3 + - - +
624A ILE* 3.1 8.8 - - + +
625A GLN 2.9 26.0 + - - +
658A PHE* 3.4 41.5 - + + -
659A PHE* 1.3 82.9 - - - +
661A SER* 1.3 61.5 - - - +
662A LEU* 3.9 3.6 - - + -
690A ILE* 4.7 11.8 - - + +
693A LEU* 5.6 4.7 - - + -
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Residues in contact with SER 661 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
508A ALA 3.3 7.9 + - - -
509A GLU* 4.5 7.6 - - - -
510A VAL* 2.9 29.8 + - - +
625A GLN 3.0 10.9 + - - -
626A ILE 4.7 0.5 + - - -
628A SER* 3.4 18.2 + - - -
659A PHE* 3.9 23.6 - - - -
660A TYR* 1.3 73.1 - - - +
662A LEU* 1.3 60.6 + - - +
663A VAL* 3.3 19.8 + - - +
676A ARG* 3.9 13.6 + - - -
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Residues in contact with LEU 662 (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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510A VAL* 3.4 13.2 - - + +
512A CYS* 5.7 3.6 - - + -
540A LYS* 3.7 39.6 - - + +
543A ALA* 3.7 22.0 - - + -
544A CYS* 3.8 14.4 - - + +
547A LEU* 3.8 23.8 - - + -
624A ILE* 3.8 20.2 - - + -
625A GLN 3.0 12.3 + - - +
626A ILE* 3.6 38.2 - - + +
660A TYR* 3.8 9.0 - - + +
661A SER* 1.3 75.7 + - - +
663A VAL* 1.3 61.2 + - - +
664A SER 4.2 0.3 + - - -
669A GLU* 4.3 0.3 - - - +
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Residues in contact with VAL 663 (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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509A GLU* 5.2 6.7 - - + -
510A VAL 2.8 20.2 + - - +
511A TRP* 3.3 12.1 - - + -
512A CYS* 2.9 32.2 + - - +
540A LYS* 4.8 2.7 - - - -
628A SER* 3.4 19.1 - - - +
661A SER* 3.3 29.6 - - - +
662A LEU* 1.3 72.7 - - - +
664A SER* 1.3 77.0 + - - +
669A GLU* 3.6 11.0 - - + +
670A MET* 4.1 1.3 - - - +
673A SER* 3.2 26.0 - - - +
676A ARG* 5.7 0.2 - - - -
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Residues in contact with SER 664 (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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512A CYS 5.2 1.1 - - - -
514A MET* 5.5 2.9 - - - -
534A TYR* 3.3 21.7 + - - +
537A ASN* 5.8 0.7 - - - +
540A LYS* 3.2 25.3 - - - +
662A LEU 4.2 0.4 + - - -
663A VAL* 1.3 72.9 - - - +
665A GLN* 1.3 63.2 + - - +
667A THR* 3.5 21.9 + - - -
669A GLU* 2.7 21.8 + - - +
670A MET 3.3 22.2 + - - -
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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