Contacts of the strand formed by residues 584 - 588 (chain B) in PDB entry 2H5G
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 CYS 584 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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582B GLY 3.3 8.7 + - - -
583B ILE* 1.3 77.4 - - - +
585B HIS* 1.3 61.8 + - - +
612B CYS 3.5 24.5 - - - -
613B ASN* 3.8 14.8 - - - +
614B ALA 3.5 16.6 - - - +
615B LEU* 3.8 3.3 - - - +
616B GLU* 2.9 27.2 + - - +
617B THR 3.2 8.3 + - - -
695B HIS* 4.0 6.1 - - - -
696B THR* 3.1 38.1 - - - +
697B ASP* 3.9 0.4 - - - -
725B THR* 4.6 4.9 - - + -
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Residues in contact with HIS 585 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
583B ILE* 3.9 16.1 + - + +
584B CYS* 1.3 76.2 - - - +
586B MSE 1.3 62.7 + - - +
615B LEU* 3.9 2.2 - - - -
617B THR* 3.2 35.6 + - + +
619B LEU* 4.0 8.3 - - + -
664B LEU 4.9 0.6 + - - -
687B HIS* 3.3 32.6 + + - -
688B ILE* 3.7 25.5 - - + +
691B TYR* 4.4 3.4 - - - +
692B GLY* 3.5 34.0 - - - -
696B THR 4.1 0.5 - - - +
697B ASP* 2.8 29.5 + - - +
698B VAL* 2.9 25.1 + - - +
725B THR* 4.1 4.2 - - - +
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Residues in contact with MSE 586 (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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585B HIS* 1.3 76.0 - - - +
587B TYR* 1.3 62.9 + - - +
588B VAL* 4.6 1.1 - - + -
600B LEU* 3.9 23.1 - - + +
601B VAL* 3.8 28.5 - - - -
604B SER* 3.3 24.5 - - - +
615B LEU* 3.4 15.2 - - + +
617B THR 3.2 6.1 + - - -
618B LEU* 3.5 14.7 - - + +
619B LEU* 2.9 25.7 + - - -
698B VAL* 3.2 32.1 - - + +
700B VAL* 3.8 24.2 - - + -
723B ALA 4.0 9.9 - - - +
724B SER* 4.3 1.1 - - - -
725B THR* 4.5 2.9 - - + +
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Residues in contact with TYR 587 (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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585B HIS* 4.2 0.4 - - - +
586B MSE 1.3 72.5 - - - +
588B VAL* 1.3 72.4 + - - +
589B ASP* 2.7 38.5 + - + -
619B LEU* 3.4 16.8 - - + -
621B HIS* 3.4 17.4 + - + -
678B VAL* 3.6 24.9 - - + -
680B ASN 3.6 0.2 - - - -
681B VAL* 3.3 33.0 + - + -
684B ALA* 3.5 21.3 - - + -
688B ILE* 5.0 0.9 - - + -
698B VAL 2.6 15.2 + - - +
699B ILE* 3.5 27.2 - - + -
700B VAL 2.8 28.6 + - - -
710B PHE* 4.0 15.9 - + + -
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Residues in contact with VAL 588 (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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586B MSE 4.6 6.7 - - + -
587B TYR* 1.3 74.7 - - - +
589B ASP* 1.3 60.7 + - - +
592B ALA* 3.7 22.7 - - + -
597B VAL* 4.0 28.9 - - + -
601B VAL* 4.7 1.3 - - + -
618B LEU* 3.7 29.2 - - + -
619B LEU 2.7 14.1 + - - +
620B ILE* 4.4 9.9 - - + -
621B HIS* 3.2 25.1 + - - +
624B LEU* 3.7 15.3 - - + +
629B LEU* 4.1 6.3 - - + -
633B ILE* 4.8 3.6 - - + -
700B VAL* 3.9 6.5 - - + -
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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