Contacts of the helix formed by residues 877 - 881 (chain A) in PDB entry 3POZ
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 877 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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723A PHE* 6.4 1.6 - - + -
836A ARG 4.5 9.2 - - - +
837A ASP* 3.5 22.0 - - - +
841A ARG* 3.4 26.5 - - - +
875A LYS* 4.4 3.1 - - - +
876A VAL* 1.3 84.3 - - + +
878A ILE* 1.3 63.6 + - - +
879A LYS 3.2 2.9 - - - -
880A TRP* 3.0 24.6 + - + -
881A MET* 3.4 20.2 + - + +
891A TYR* 6.0 0.2 - - - +
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Residues in contact with ILE 878 (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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876A VAL* 2.9 38.7 + - + +
877A PRO* 1.3 70.3 - - - +
879A LYS* 1.3 59.0 + - + +
881A MET* 3.0 32.8 + - + +
886A ILE* 4.0 35.7 - - + +
920A ALA* 3.6 42.4 - - + +
923A ILE* 3.7 24.0 - - + +
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Residues in contact with LYS 879 (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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877A PRO 3.1 1.2 + - - -
878A ILE* 1.3 78.7 - - + +
880A TRP* 1.3 77.6 + - + +
881A MET 3.6 0.7 - - - -
898A TRP* 5.3 0.9 + - - -
902A VAL* 3.9 15.4 - - - +
914A PRO* 3.4 19.7 + - + +
915A TYR* 3.1 58.1 + - + -
916A ASP* 4.8 1.2 - - - +
917A GLY 4.6 3.4 - - - +
918A ILE 2.6 31.7 + - - +
920A ALA* 4.4 11.8 - - + +
923A ILE* 4.0 19.3 - - + -
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Residues in contact with TRP 880 (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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799A LEU* 6.0 1.3 - - + -
837A ASP* 5.7 1.1 - - - +
838A LEU 3.5 25.6 - - - +
839A ALA* 3.4 9.3 - - + +
841A ARG* 3.3 33.4 - - - +
877A PRO* 3.0 24.3 + - + +
879A LYS* 1.3 98.1 - - + +
881A MET* 1.3 60.3 + - - +
898A TRP* 3.6 5.9 - - - -
899A SER* 2.7 38.0 + - - +
902A VAL* 3.4 24.9 - - + +
903A THR* 4.5 0.2 - - - -
906A GLU* 2.9 39.7 + - - -
914A PRO* 3.6 27.1 - - + -
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Residues in contact with MET 881 (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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836A ARG 5.3 3.4 - - - +
876A VAL* 3.8 24.5 - - + -
877A PRO* 3.4 36.3 - - + +
878A ILE* 3.0 20.8 + - + +
879A LYS 5.3 0.2 - - - -
880A TRP* 1.3 81.5 - - + +
882A ALA* 1.3 63.8 + - - +
883A LEU 3.7 0.7 + - - -
885A SER* 3.7 31.9 - - - +
886A ILE* 3.7 24.6 - - + +
891A TYR* 3.3 30.3 - - + +
898A TRP* 3.3 14.9 + - - -
899A SER* 4.5 2.5 - - - +
927A LEU* 4.5 1.6 - - - +
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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