Contacts of the helix formed by residues 897 - 904 (chain A) in PDB entry 3PE3
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 PRO 897 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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800A THR* 5.3 1.1 - - - +
801A THR* 4.7 13.7 - - + -
808A ALA* 3.4 31.2 - - + +
809A THR* 5.2 0.7 - - - -
895A VAL 4.8 0.2 - - - +
896A ALA* 1.3 92.5 - - + +
898A LYS* 1.3 66.0 + - - +
899A GLU 3.3 0.4 - - - +
900A GLU* 3.1 22.7 + - + +
901A HIS* 2.9 19.2 + - - +
315B THR* 4.5 20.9 - - + -
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Residues in contact with LYS 898 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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557A ASN* 5.6 0.4 - - - +
559A PRO* 5.6 0.9 - - - -
562A HIS* 3.0 50.6 + - + +
698A HIS* 4.8 4.4 + - - -
701A MET* 5.0 0.9 - - + -
702A PHE* 4.0 22.8 - - + -
808A ALA 3.4 1.8 + - - -
809A THR* 3.3 27.8 - - - +
810A GLY 4.5 0.4 - - - +
896A ALA 3.7 1.0 + - - -
897A PRO* 1.3 70.8 - - - +
899A GLU* 1.3 64.7 + - - +
901A HIS* 3.1 13.4 + - + +
902A VAL* 3.0 31.4 + - + +
921A THR* 4.0 11.4 - - - +
925A ASP* 3.6 27.0 + - - -
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Residues in contact with GLU 899 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
702A PHE* 4.1 19.9 - - + -
704A HIS* 2.7 39.7 + - + +
705A LEU* 5.0 1.1 - - + +
800A THR* 4.0 13.9 + - - +
807A ALA 3.2 26.8 - - - +
808A ALA* 3.0 9.8 + - - +
809A THR 4.8 0.2 - - - -
810A GLY 4.7 0.7 - - - +
814A PRO* 4.2 5.4 - - + -
818A ILE* 3.6 8.4 - - - +
898A LYS* 1.3 78.9 - - - +
900A GLU* 1.3 58.5 + - - +
902A VAL* 3.5 2.0 + - - +
903A ARG* 2.7 67.2 + - - +
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Residues in contact with GLU 900 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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797A GLY 4.0 12.0 - - - +
798A LEU* 3.6 16.9 - - - +
800A THR* 4.8 5.9 + - - +
808A ALA* 4.5 0.4 + - - +
825A TYR* 2.7 39.8 + - - +
896A ALA* 3.5 16.9 - - + +
897A PRO* 3.1 29.7 + - + +
899A GLU* 1.3 80.5 + - - +
901A HIS* 1.3 58.4 + - - +
903A ARG* 3.4 24.8 - - - +
904A ARG* 2.9 36.0 + - - +
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Residues in contact with HIS 901 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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837A PHE* 3.4 49.1 + + + +
866A LEU* 4.7 6.7 - - + +
896A ALA* 4.2 13.0 - - + +
897A PRO 2.9 13.0 + - - +
898A LYS* 3.3 17.9 - - + +
900A GLU* 1.3 79.3 - - - +
902A VAL* 1.3 67.3 + - + +
904A ARG* 3.5 26.7 + - - +
905A GLY* 3.7 5.2 + - - -
922A THR* 4.6 5.9 + - + +
925A ASP* 3.0 36.8 + - + +
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Residues in contact with VAL 902 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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698A HIS* 4.7 0.7 - - + -
702A PHE* 3.7 37.0 - - + -
705A LEU* 3.7 19.9 - - + +
898A LYS* 3.0 18.7 + - + +
899A GLU 4.0 3.1 - - - +
901A HIS* 1.3 81.1 - - + +
903A ARG* 1.3 63.6 + - - +
905A GLY* 3.3 8.8 + - - -
925A ASP* 4.0 42.6 - - - +
928A TRP* 4.2 10.8 - - + -
929A ALA* 3.8 15.7 - - - +
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Residues in contact with ARG 903 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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704A HIS* 4.8 0.7 - - - -
705A LEU* 3.8 18.6 - - + +
727A ASN* 4.0 10.3 - - - +
797A GLY* 3.1 38.0 + - - -
800A THR* 3.7 7.5 - - - +
818A ILE* 3.6 22.8 - - - +
820A THR* 2.6 46.9 + - - +
824A GLN* 5.2 0.2 + - - -
825A TYR* 4.8 3.0 + - - -
899A GLU* 2.7 54.4 + - - +
900A GLU* 3.4 21.8 + - - +
902A VAL* 1.3 78.4 - - - +
904A ARG* 1.3 57.1 + - - +
905A GLY 3.1 0.2 - - - -
906A GLN* 3.0 47.7 + - - +
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Residues in contact with ARG 904 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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820A THR* 4.1 12.3 - - + -
825A TYR* 3.4 56.7 - - + +
837A PHE* 4.7 5.7 - - + -
864A TRP* 3.4 23.7 - - + -
866A LEU* 3.3 34.9 - - - +
893A SER* 4.0 6.5 - - - -
894A PRO* 3.0 31.5 + - - +
896A ALA* 3.8 24.0 - - - +
900A GLU* 2.9 21.1 + - + +
901A HIS* 3.5 20.6 + - - +
903A ARG* 1.3 72.0 - - - +
905A GLY* 1.3 64.4 + - - +
906A GLN 3.0 2.5 - - - -
907A LEU* 3.0 20.9 + - + +
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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