Contacts of the helix formed by residues 598 - 603 (chain H) 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 H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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584B ALA* 4.1 3.6 - - - -
586B ILE* 3.9 11.7 - - + -
647B VAL* 3.2 26.5 - - + +
650B ARG* 4.3 8.1 + - - -
654B ARG* 3.6 12.8 + - - +
596H VAL* 3.4 3.5 - - - +
597H PRO* 1.3 73.6 - - - +
599H TYR* 1.3 67.3 + - - +
600H LEU 3.3 2.7 - - - -
601H ASP* 2.8 30.8 + - - +
602H HIS* 3.4 22.0 + - - -
641H TYR* 2.7 30.7 + - - -
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Residues in contact with TYR 599 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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591H VAL* 3.1 42.9 - - + +
593H LEU* 4.3 15.7 - - + -
596H VAL* 3.1 26.5 + - + +
597H PRO 3.3 1.6 - - - -
598H ASP* 1.3 76.7 + - - +
600H LEU* 1.3 58.7 + - + +
602H HIS* 3.0 8.5 + - - +
603H ILE* 2.9 54.5 + - + +
606H PRO* 4.1 18.7 - - + +
607H MET 5.6 0.9 + - - -
637H ASN* 3.5 27.6 + - - +
638H CYS* 4.4 2.9 + - - +
641H TYR* 3.6 36.6 - + + -
642H ASN* 5.5 2.7 - - - -
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Residues in contact with LEU 600 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
583B PRO* 3.8 23.4 - - + +
584B ALA* 4.0 19.8 - - - +
2H ACT 5.8 0.9 - - + -
593H LEU* 3.9 33.0 - - + +
597H PRO 5.0 0.4 + - - -
598H ASP 3.3 0.8 - - - -
599H TYR* 1.3 77.1 - - + +
601H ASP* 1.3 62.2 + - - +
602H HIS 3.2 0.4 - - - -
603H ILE 3.5 23.7 + - - +
604H LYS* 5.2 2.9 - - - +
606H PRO* 3.9 29.2 - - + -
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Residues in contact with ASP 601 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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581B LYS 5.0 2.2 - - - -
582B ASP* 3.9 7.6 - - - +
583B PRO* 3.3 21.5 - - + +
584B ALA* 3.0 35.8 + - - +
586B ILE* 4.1 7.6 - - - +
651B ALA* 4.3 4.0 - - - +
654B ARG* 3.2 30.2 + - - +
598H ASP* 2.8 26.9 + - - +
600H LEU* 1.3 73.4 - - - +
602H HIS* 1.3 66.5 + - + +
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Residues in contact with HIS 602 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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650B ARG* 5.7 2.2 - - - -
654B ARG* 3.5 36.2 + - - -
598H ASP* 3.4 33.5 + - - -
599H TYR 3.0 5.6 + - - +
601H ASP* 1.3 85.2 - - + +
603H ILE* 1.3 70.2 + - + +
604H LYS* 4.4 0.3 + - - +
640H LYS* 5.0 6.2 - - + +
641H TYR* 3.8 27.6 - + + +
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Residues in contact with ILE 603 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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599H TYR* 2.9 50.5 + - + +
600H LEU* 3.5 31.2 - - - +
602H HIS* 1.3 92.5 - - + +
604H LYS* 1.3 61.8 + - - +
605H HIS 3.6 8.7 - - - +
606H PRO* 3.9 8.7 - - + -
637H ASN* 3.5 57.9 - - - +
640H LYS* 4.0 13.7 - - + -
641H TYR* 4.6 3.4 - - + +
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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