Contacts of the strand formed by residues 608 - 614 (chain B) in PDB entry 2A2N
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 608 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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508B PHE* 4.3 8.5 - - + -
512B CYS* 3.3 21.3 - - - -
565B GLU 5.0 0.2 - - - +
566B PHE* 5.5 0.6 - - - +
570B LEU* 3.6 45.1 - - + +
571B ARG 4.1 2.7 - - - -
572B HIS* 3.4 35.2 - - + +
577B THR* 3.6 24.9 - - + -
578B LEU 3.5 6.3 - - - +
579B SER* 3.6 2.9 - - - +
606B HIS 3.2 2.9 + - - +
607B THR* 1.3 70.2 - - - +
609B PHE* 1.3 61.6 + - - +
610B GLY 4.0 9.9 - - - +
611B ARG* 4.6 7.2 - - - +
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Residues in contact with PHE 609 (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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507B LEU* 3.5 10.1 - - + +
508B PHE* 2.9 32.2 + - - -
512B CYS* 4.4 5.4 - - + -
515B THR* 3.6 33.2 - - + -
516B VAL* 4.1 15.1 - - + +
519B PHE* 3.7 38.8 - + + -
578B LEU* 2.8 43.9 + - + -
579B SER 3.5 16.8 - - - -
580B MET* 3.5 27.6 - - + -
592B PHE* 4.1 4.7 - - + -
607B THR* 3.8 13.0 - - + -
608B VAL* 1.3 74.4 - - - +
610B GLY* 1.3 57.9 + - - +
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Residues in contact with GLY 610 (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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506B LYS 3.0 13.7 - - - -
508B PHE* 3.4 16.3 - - - -
577B THR* 3.9 4.5 - - - +
578B LEU* 2.9 40.0 + - - +
608B VAL* 4.0 0.2 - - - +
609B PHE* 1.3 80.1 - - - +
611B ARG* 1.3 67.7 + - - +
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Residues in contact with ARG 611 (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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505B THR* 3.3 4.8 - - - -
506B LYS* 2.8 43.0 + - + +
508B PHE* 4.0 28.4 - - + -
569B THR 4.8 3.4 + - - -
570B LEU* 4.6 9.1 - - - +
571B ARG 2.9 33.1 + - - +
573B ASP* 4.5 2.0 + - - -
574B ARG* 3.4 56.0 - - - +
575B PRO 4.7 2.0 - - - -
576B TYR 3.4 18.6 - - - +
577B THR* 2.8 35.4 + - - +
578B LEU* 4.3 1.7 - - - +
608B VAL* 4.6 1.6 - - - +
610B GLY* 1.3 77.4 - - - +
612B VAL* 1.3 66.7 + - - +
613B THR* 3.5 1.0 + - + +
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Residues in contact with VAL 612 (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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503B ILE* 3.6 28.0 - - + -
504B HIS 3.2 7.4 - - - +
505B THR* 4.3 3.8 - - + +
576B TYR* 2.9 34.9 + - + +
577B THR 5.9 0.2 - - - -
578B LEU* 6.0 0.9 - - + +
594B ILE* 4.0 19.3 - - + -
611B ARG* 1.3 78.4 - - - +
613B THR* 1.3 60.2 + - - +
614B LYS 3.2 31.2 - - - +
615B GLY 4.0 1.1 - - - +
616B MET* 3.9 23.8 - - + +
619B VAL* 4.0 3.1 - - + -
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Residues in contact with THR 613 (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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504B HIS* 2.6 29.4 + - - +
505B THR 4.2 0.7 + - - -
506B LYS* 3.7 38.2 + - + +
611B ARG* 3.9 1.8 - - + +
612B VAL* 1.3 75.5 - - - +
614B LYS* 1.3 61.8 + - - +
616B MET* 3.6 13.5 - - - +
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Residues in contact with LYS 614 (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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504B HIS* 2.7 69.8 + - + +
612B VAL* 3.2 6.6 - - - +
613B THR* 1.3 82.3 + - - +
615B GLY* 1.3 63.8 + - - +
616B MET* 3.5 7.4 - - + -
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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