Contacts of the strand formed by residues 501 - 507 (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 GLY 501 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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496B ILE 3.8 0.5 - - - +
498B THR* 2.8 38.3 + - - +
499B SER 3.4 1.2 + - - -
500B MET* 1.3 81.3 - - - +
502B ASP* 1.3 66.5 + - - -
503B ILE 3.8 0.3 + - - -
618B VAL* 3.9 9.8 - - - +
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Residues in contact with ASP 502 (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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495B ILE* 4.2 4.3 - - + +
496B ILE 3.8 1.1 - - - -
497B HIS* 2.7 47.5 + - - +
498B THR 5.1 0.3 - - - +
501B GLY* 1.3 71.8 - - - -
503B ILE* 1.3 61.8 + - - +
504B HIS* 3.6 26.6 + - + -
614B LYS* 5.9 0.2 - - - -
615B GLY* 3.3 22.0 - - - -
618B VAL* 4.0 4.7 - - - +
641B ILE* 5.4 0.5 - - - +
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Residues in contact with ILE 503 (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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495B ILE* 3.4 1.7 - - - -
496B ILE* 2.7 51.4 + - + +
498B THR* 3.6 24.9 - - + -
502B ASP* 1.3 71.9 - - - +
504B HIS* 1.3 59.5 + - - +
505B THR* 3.6 11.7 + - + -
533B PHE* 4.4 10.1 - - + -
542B ILE* 4.9 0.7 - - + -
594B ILE* 4.2 10.5 - - + -
612B VAL* 3.6 36.8 - - + -
614B LYS 3.7 2.5 - - - -
615B GLY* 4.4 0.9 - - - +
618B VAL* 3.8 16.8 - - + -
619B VAL* 3.9 20.4 - - + -
622B ILE* 4.1 12.8 - - + -
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Residues in contact with HIS 504 (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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494B ALA 3.6 6.1 - - - +
495B ILE* 3.4 33.1 - - + +
502B ASP* 3.6 30.9 + - + -
503B ILE* 1.3 70.9 - - - +
505B THR* 1.3 55.8 + - - +
612B VAL* 3.2 6.1 - - - +
613B THR* 2.6 47.3 + - - +
614B LYS* 2.7 60.5 + - + +
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Residues in contact with THR 505 (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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493B SER* 3.2 6.5 - - - -
494B ALA* 2.8 51.7 + - - +
496B ILE* 3.9 28.4 - - + +
503B ILE* 3.9 16.2 - - + +
504B HIS* 1.3 76.0 - - - +
506B LYS* 1.3 65.8 + - - +
507B LEU* 3.8 10.0 - - - +
519B PHE* 4.9 1.4 - - - -
578B LEU* 4.5 14.5 - - + +
594B ILE* 4.8 2.5 - - + -
611B ARG 3.3 8.7 - - - -
612B VAL* 4.4 9.2 - - + -
613B THR* 4.7 1.3 - - - -
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Residues in contact with LYS 506 (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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492B ASP* 3.6 10.8 - - + +
493B SER* 4.5 2.5 - - - +
505B THR* 1.3 73.3 - - - +
507B LEU* 1.3 71.1 + - - +
508B PHE* 3.7 26.5 - - + -
610B GLY* 3.0 5.0 - - - -
611B ARG* 2.8 40.1 + - + +
613B THR* 3.7 22.8 - - + +
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Residues in contact with LEU 507 (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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491B SER 3.5 19.5 - - - +
492B ASP* 2.9 17.0 + - - +
493B SER 4.2 18.2 - - - +
494B ALA* 4.4 0.7 - - + -
505B THR* 3.8 17.7 - - - +
506B LYS* 1.3 87.5 - - - +
508B PHE* 1.3 68.8 + - - +
509B PRO* 3.1 11.1 - - - +
516B VAL* 3.9 10.5 - - + -
519B PHE* 4.1 16.8 - - + -
520B CYS* 3.5 32.5 - - - -
578B LEU* 3.8 21.5 - - + -
609B PHE* 3.5 15.5 - - + +
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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