Contacts of the strand formed by residues 730 - 735 (chain I) in PDB entry 5G04
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 VAL 730 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28I TRP* 3.6 30.5 - - + -
33I ASP* 5.0 2.2 - - - -
49I LEU* 3.4 43.5 - - + -
725I ASN* 2.8 51.6 + - + +
728I ARG* 3.2 7.6 + - + +
729I LYS* 1.3 77.4 - - - +
731I SER* 1.3 82.0 + - - +
743I VAL* 3.9 0.4 - - + -
744I PHE 3.3 17.5 - - - +
745I GLU* 4.4 5.3 - - + +
746I MET* 4.2 2.9 - - - +
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Residues in contact with SER 731 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28I TRP* 3.2 14.2 - - - +
644I TYR* 3.3 10.9 - - - -
650I THR* 4.8 4.4 + - - -
666I LEU* 6.3 0.4 - - - -
723I ALA 3.3 11.7 - - - -
724I GLY* 3.5 12.1 - - - -
730I VAL* 1.3 82.3 + - - +
732I CYS* 1.3 63.4 + - - +
733I VAL* 6.1 1.6 - - - -
743I VAL* 3.5 3.3 - - - +
744I PHE* 2.9 31.9 + - - +
746I MET* 3.2 30.6 - - - -
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Residues in contact with CYS 732 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26I LEU* 4.7 13.9 - - - -
28I TRP* 3.2 27.8 - - + +
35I ILE* 5.2 2.7 - - + -
52I PHE* 4.6 6.1 - - - -
721I TYR 4.1 0.2 - - - +
722I VAL* 3.7 2.3 - - - +
723I ALA* 2.8 39.5 + - + -
731I SER* 1.3 78.1 - - - +
733I VAL* 1.3 70.8 + - - +
734I LEU* 4.2 1.1 + - - -
741I VAL* 4.1 24.2 - - - -
742I ARG 3.6 4.7 - - - -
743I VAL* 3.9 20.2 - - + -
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Residues in contact with VAL 733 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
652I VAL* 4.8 4.9 - - + -
666I LEU* 4.1 17.0 - - + -
714I LEU* 4.7 6.5 - - + -
717I MET* 3.5 11.0 - - + +
719I ALA* 3.3 33.4 - - + -
721I TYR 3.5 11.7 - - - +
722I VAL* 4.6 10.1 - - + -
731I SER* 6.1 1.3 - - - -
732I CYS* 1.3 81.6 - - - +
734I LEU* 1.3 63.2 + - - +
741I VAL* 3.3 5.7 - - - +
742I ARG 2.9 39.9 + - - +
744I PHE* 3.5 26.9 - - + -
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Residues in contact with LEU 734 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23I ILE* 4.1 25.4 - - + +
26I LEU* 4.6 18.8 - - + -
569I LEU* 3.9 29.2 - - + -
717I MET* 4.4 2.0 - - - -
720I GLN 3.1 3.4 + - - -
721I TYR* 2.8 48.4 + - + +
732I CYS* 4.2 1.3 + - - -
733I VAL* 1.3 74.8 - - - +
735I SER* 1.3 67.6 + - - +
738I LEU* 3.5 32.1 - - + +
740I HIS 3.6 6.7 - - - +
741I VAL* 3.3 26.2 - - + -
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Residues in contact with SER 735 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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717I MET* 3.3 21.9 + - - +
718I LYS* 4.4 6.1 - - - -
719I ALA* 3.9 2.5 - - - +
720I GLN* 3.8 6.8 - - - +
734I LEU* 1.3 77.8 - - - +
736I SER* 1.3 61.1 + - - +
737I ASN* 3.0 22.7 - - - -
738I LEU* 2.8 26.7 + - - +
740I HIS* 3.1 38.5 + - - +
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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