Contacts of the strand formed by residues 564 - 570 (chain A) in PDB entry 2FO1
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 564 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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545A GLU 4.8 11.0 - - - +
546A TYR* 3.9 23.8 - - + -
562A CYS* 3.7 11.9 - - - +
563A PRO* 1.3 79.8 - - - +
565A VAL* 1.3 64.4 + - - +
566A GLY* 3.5 0.8 + - - -
583A GLY* 2.9 25.7 - - - -
584A ARG* 3.0 42.4 + - + +
585A ASP* 5.8 1.3 - - - +
586A PHE* 4.4 1.3 - - - -
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Residues in contact with VAL 565 (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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563A PRO 4.0 1.5 + - - +
564A VAL* 1.3 75.3 - - - +
566A GLY* 1.3 65.4 + - - +
567A SER 4.5 4.0 - - - +
581A LEU* 4.5 17.0 - - + -
582A HIS 3.4 8.7 - - - +
583A GLY* 4.3 0.7 - - - -
586A PHE* 4.2 4.9 - - + -
642A LEU* 3.9 31.9 - - + -
650A TYR 5.5 1.3 - - - +
652A SER* 3.7 44.0 - - - +
654A LEU* 4.1 21.6 - - + +
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Residues in contact with GLY 566 (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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564A VAL* 3.5 3.7 + - - -
565A VAL* 1.3 71.3 - - - +
567A SER* 1.3 59.8 + - - +
582A HIS* 2.4 26.0 + - - -
583A GLY* 4.5 2.7 - - - -
654A LEU* 4.2 10.6 - - - +
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Residues in contact with SER 567 (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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565A VAL* 4.7 1.7 - - - +
566A GLY* 1.3 77.0 - - - +
568A LEU* 1.3 58.7 + - - +
569A GLU* 3.6 4.5 + - - -
581A LEU* 3.5 1.7 - - - +
582A HIS* 2.9 38.3 + - - +
654A LEU* 3.9 6.7 - - - -
1161E ARG* 3.9 27.4 - - - +
1162E ASN* 2.6 32.8 + - - -
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Residues in contact with LEU 568 (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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567A SER* 1.3 71.7 - - - +
569A GLU* 1.3 86.2 + - - +
570A VAL* 4.5 10.9 - - + +
579A VAL* 4.0 11.4 - - + -
580A GLU 3.3 3.4 - - - -
581A LEU* 3.5 22.4 - - + -
640A ILE* 3.7 34.3 - - + -
654A LEU* 3.5 27.4 - - + +
655A THR 4.7 10.3 - - - +
656A PHE* 4.8 10.3 - - + -
1161E ARG* 3.5 13.1 + - - +
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Residues in contact with GLU 569 (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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567A SER* 3.6 8.2 + - - -
568A LEU* 1.3 112.6 + - - +
570A VAL* 1.3 63.4 + - - +
579A VAL* 3.2 5.4 - - - -
580A GLU* 2.6 61.6 + - + +
582A HIS* 4.3 4.9 + - + -
1126E SER* 2.8 27.9 + - - +
1128E ARG* 2.8 26.2 + - - +
1160E ASP* 5.0 0.3 - - - +
1161E ARG* 2.8 24.4 + - - +
1162E ASN* 3.5 16.2 - - - +
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Residues in contact with VAL 570 (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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568A LEU* 4.5 10.3 - - + +
569A GLU* 1.3 83.8 - - - +
571A ASP* 1.3 73.2 + - - +
572A GLY 5.2 4.5 - - - +
577A SER* 5.8 2.5 - - - -
578A ARG 3.1 16.2 - - - +
579A VAL* 4.6 7.2 - - + -
613A ILE* 5.2 5.6 - - + -
656A PHE* 4.7 13.0 - - + -
1103E LEU* 4.5 11.9 - - + +
1128E ARG* 5.0 0.2 + - - -
1133E GLN* 3.5 12.0 - - - +
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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