Contacts of the helix formed by residues 598 - 603 (chain G) in PDB entry 3RCW
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 ASP 598 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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596G VAL* 3.7 5.2 - - - +
597G PRO* 1.3 75.5 - - - +
599G TYR* 1.3 68.0 + - - +
600G LEU 3.3 2.5 - - - -
601G ASP* 2.9 37.5 + - - +
602G HIS* 3.5 21.7 + - + +
641G TYR* 2.7 36.3 + - - -
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Residues in contact with TYR 599 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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591G VAL* 2.9 46.2 - - + +
593G LEU* 4.4 7.4 - - + -
596G VAL* 3.3 23.1 + - + +
597G PRO 3.2 3.4 - - - -
598G ASP* 1.3 82.6 + - - +
600G LEU* 1.3 70.3 + - + +
602G HIS* 3.2 4.9 + - - +
603G ILE* 3.0 54.9 + - + +
606G PRO* 4.3 11.5 - - + +
607G MET 5.5 2.3 + - - -
637G ASN* 3.4 29.6 + - - +
638G CYS* 4.8 1.7 + - - -
641G TYR* 4.0 32.3 - + + -
642G ASN* 5.8 1.3 - - - -
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Residues in contact with LEU 600 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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593G LEU* 3.6 36.7 - - + +
597G PRO 4.7 2.6 + - - +
598G ASP 3.3 0.4 - - - -
599G TYR* 1.3 87.8 - - + +
601G ASP* 1.3 65.7 + - - +
602G HIS 3.4 0.2 - - - -
603G ILE 3.7 21.7 - - - +
604G LYS* 5.2 1.5 - - - +
606G PRO* 3.6 32.5 - - + -
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Residues in contact with ASP 601 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
597G PRO 4.8 1.2 - - - +
598G ASP* 2.9 30.2 + - - +
600G LEU* 1.3 82.3 - - - +
602G HIS* 1.3 69.8 + - + +
603G ILE 3.9 0.2 + - - -
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Residues in contact with HIS 602 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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598G ASP* 3.5 31.2 + - + -
599G TYR 3.2 5.6 + - - +
601G ASP* 1.3 83.9 - - + +
603G ILE* 1.3 72.4 + - + +
604G LYS 4.1 1.5 + - - -
640G LYS 6.0 0.9 - - - -
641G TYR* 4.0 29.1 - + + -
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Residues in contact with ILE 603 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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599G TYR* 3.0 51.5 + - + +
600G LEU* 3.7 26.2 - - - +
601G ASP 3.5 0.6 - - - -
602G HIS* 1.3 90.6 - - + +
604G LYS* 1.3 64.7 + - - +
605G HIS 4.0 0.7 - - - +
606G PRO* 3.8 10.5 - - - +
637G ASN* 3.4 57.4 - - - +
640G LYS* 4.4 12.1 - - + -
641G TYR* 4.3 11.0 - - + -
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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