Contacts of the strand formed by residues 608 - 614 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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508A PHE* 4.3 9.4 - - + -
512A CYS* 3.3 20.8 - - - -
565A GLU 4.9 1.4 + - - +
566A PHE* 5.4 1.0 - - - +
570A LEU* 3.5 45.1 - - + +
571A ARG 4.1 6.7 - - - +
572A HIS* 3.3 41.7 - - + +
577A THR* 3.6 20.4 - - + -
578A LEU 4.3 0.2 - - - +
579A SER* 3.6 5.8 - - - +
606A HIS 3.2 1.9 + - - +
607A THR* 1.3 69.2 - - - +
609A PHE* 1.3 62.4 + - - +
610A GLY 4.3 5.6 - - - +
611A ARG* 4.7 2.5 - - - +
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Residues in contact with PHE 609 (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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507A LEU* 3.4 12.9 - - + +
508A PHE* 2.9 30.9 + - - -
512A CYS* 4.3 6.1 - - + -
515A THR* 3.4 33.7 - - + -
516A VAL* 4.0 14.3 - - + +
519A PHE* 3.6 39.3 - + + -
578A LEU* 2.9 43.8 + - + -
579A SER* 3.5 24.7 - - - -
580A MET* 3.5 18.2 - - - -
592A PHE* 4.1 6.7 - - + -
607A THR 3.7 9.2 - - - -
608A VAL* 1.3 73.8 - - - +
610A GLY* 1.3 58.2 + - - +
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Residues in contact with GLY 610 (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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506A LYS 3.0 14.4 - - - -
507A LEU* 4.1 0.4 - - - -
508A PHE* 3.4 16.2 - - - -
577A THR* 3.8 7.6 - - - +
578A LEU* 2.9 38.6 + - - +
608A VAL* 4.3 0.2 - - - +
609A PHE* 1.3 80.0 - - - +
611A ARG* 1.3 63.9 + - - +
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Residues in contact with ARG 611 (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 THR* 3.5 3.5 - - - -
506A LYS* 2.9 38.5 + - + +
508A PHE* 4.2 30.2 - - + -
569A THR 5.0 2.8 + - - -
570A LEU* 4.6 7.3 - - - +
571A ARG 3.2 28.5 + - - +
573A ASP* 4.6 2.4 + - - -
574A ARG* 3.2 51.0 - - + +
575A PRO 4.5 1.6 - - - +
576A TYR 3.4 20.0 - - - +
577A THR* 2.8 33.2 + - - +
578A LEU* 4.2 2.1 - - - +
608A VAL* 4.7 2.0 - - - +
610A GLY* 1.3 73.6 - - - +
612A VAL* 1.3 69.4 + - - +
613A THR* 3.5 2.1 + - + +
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Residues in contact with VAL 612 (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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503A ILE* 3.6 26.2 - - + -
504A HIS 3.4 7.0 - - - +
505A THR* 4.3 5.8 - - + +
576A TYR* 2.9 33.8 + - + +
578A LEU* 5.7 1.3 - - + -
594A ILE* 3.7 25.4 - - + -
611A ARG* 1.3 80.0 - - - +
613A THR* 1.3 63.1 + - - +
614A LYS 3.5 21.5 - - - +
615A GLY 4.1 0.4 - - - -
616A MET* 3.8 30.3 - - + +
619A VAL* 4.2 2.5 - - + -
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Residues in contact with THR 613 (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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504A HIS* 2.8 22.9 + - - +
506A LYS* 3.7 36.8 + - + +
611A ARG* 3.8 3.6 - - + +
612A VAL* 1.3 76.1 - - - +
614A LYS* 1.3 63.3 + - - +
616A MET* 3.6 14.6 - - - +
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Residues in contact with LYS 614 (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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504A HIS* 2.8 69.3 + - + +
612A VAL* 3.5 5.1 - - - +
613A THR* 1.3 82.9 + - - +
615A GLY* 1.3 61.9 + - - +
616A MET* 3.5 7.4 - - - -
617A GLU* 5.1 2.0 - - - +
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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