Contacts of the strand formed by residues 623 - 627 (chain B) in PDB entry 2R92
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 GLU 623 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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380B TYR* 2.7 30.5 + - - -
384B ARG* 4.9 4.5 + - - -
578B THR* 3.5 5.6 - - - +
579B ARG* 2.9 44.7 + - + +
581B PHE* 4.0 11.4 - - + -
616B ILE 3.5 1.6 - - - +
617B ARG* 3.5 4.2 - - - +
618B ASP* 2.9 39.0 + - + +
621B GLU* 3.6 20.0 - - + +
622B LYS* 1.3 83.6 - - - +
624B LEU* 1.3 61.3 + - - +
625B LYS* 4.0 19.3 - - + +
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Residues in contact with LEU 624 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
558B LEU* 5.1 2.0 - - + -
578B THR* 5.2 4.3 - - + -
579B ARG 3.1 7.9 + - - -
580B VAL* 3.3 38.4 - - + -
581B PHE* 2.5 37.5 + - - +
593B PRO* 6.1 2.9 - - + -
596B LEU* 3.8 26.0 - - + -
597B MET* 3.6 29.8 - - + -
600B LEU* 4.4 4.9 - - + -
616B ILE 3.3 18.2 - - - +
617B ARG* 4.0 8.5 - - + -
623B GLU* 1.3 72.7 - - - +
625B LYS* 1.3 59.2 + - - +
626B ILE* 4.3 20.6 - - + -
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Residues in contact with LYS 625 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222B ILE* 5.0 12.1 - - - +
223B VAL* 4.9 11.7 - - - +
380B TYR* 4.6 9.7 + - - -
581B PHE* 3.4 26.8 - - + +
584B GLY* 6.4 0.2 - - - -
615B MET* 2.9 3.3 - - - -
616B ILE* 2.5 61.2 + - + +
618B ASP* 6.0 3.6 - - + -
623B GLU* 4.0 24.0 - - + +
624B LEU* 1.3 76.3 - - - +
626B ILE* 1.3 61.2 + - - +
627B PHE* 4.2 27.2 - - + -
696B GLU* 5.7 4.7 - - + -
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Residues in contact with ILE 626 (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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554B ILE* 4.6 21.3 - - + -
558B LEU* 4.7 9.2 - - + -
580B VAL* 5.3 1.1 - - + -
581B PHE 2.6 12.1 + - - +
582B VAL* 2.9 31.5 - - + +
583B ASN 2.6 33.1 + - - -
600B LEU* 3.7 29.8 - - + -
609B ILE* 6.3 0.2 - - + -
613B VAL* 4.0 16.2 - - + -
614B SER 3.2 7.2 - - - +
615B MET* 3.6 18.6 - - + -
624B LEU* 4.3 17.0 - - + -
625B LYS* 1.3 78.0 - - - +
627B PHE* 1.3 60.5 + - - +
628B THR* 6.2 0.2 - - - -
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Residues in contact with PHE 627 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222B ILE* 4.1 24.7 - - + -
402B GLY 5.6 0.7 - - - -
405B ARG* 4.2 18.6 - - - -
581B PHE* 6.0 0.7 - - + -
582B VAL 4.9 0.4 - - - -
583B ASN* 3.4 12.6 - - - -
584B GLY* 3.5 25.8 - - - -
613B VAL* 2.7 30.3 - - - +
614B SER* 2.6 38.6 + - - +
616B ILE* 5.3 1.8 - - + -
625B LYS* 4.4 32.1 - - + -
626B ILE* 1.3 82.5 - - - +
628B THR* 1.3 56.8 - - - +
629B ASP* 3.5 8.7 - - + +
632B ARG* 3.6 14.9 + - - +
696B GLU* 4.3 28.3 - - + -
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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