Contacts of the helix formed by residues 687 - 695 (chain C) in PDB entry 4PE5
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 SER 687 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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484C PHE* 4.3 4.5 - - - -
486C THR* 3.6 2.2 - - - +
523C ARG* 3.9 7.6 - - - +
683C THR* 3.8 2.6 + - - -
684C VAL* 2.5 32.2 + - - -
686C GLN* 1.3 76.3 - - - +
688C SER* 1.3 64.7 + - - +
689C VAL 3.7 0.9 + - - -
690C ASP* 3.2 12.7 + - - +
691C ILE* 3.1 25.3 + - - +
731C TRP* 3.5 33.6 - - - -
940C GLY* 4.3 3.6 - - - -
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Residues in contact with SER 688 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
518C THR* 3.2 26.8 - - - -
520C ASN* 5.1 5.7 + - - +
523C ARG* 2.8 23.6 + - - +
538C LEU* 5.2 4.4 - - - +
687C SER* 1.3 73.0 - - - +
689C VAL* 1.3 62.3 + - - +
691C ILE* 3.3 8.9 + - - +
692C TYR* 2.9 27.9 + - - +
732C ASP* 5.8 0.7 - - - -
754C PHE* 5.5 6.0 - - - -
940C GLY* 2.6 30.5 + - - -
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Residues in contact with VAL 689 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
538C LEU* 3.7 33.2 - - + -
683C THR* 3.5 33.4 - - + +
687C SER* 3.3 1.1 - - - +
688C SER* 1.3 74.5 - - - +
690C ASP* 1.3 60.9 + - - +
692C TYR* 3.2 5.1 + - - +
693C PHE* 2.9 61.4 + - + -
730C ILE* 3.8 20.2 - - + +
731C TRP* 3.8 18.4 - - + -
732C ASP* 5.4 0.2 - - - +
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Residues in contact with ASP 690 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
486C THR* 5.3 2.5 - - + +
683C THR* 4.4 6.7 - - + +
684C VAL 4.2 2.9 - - - +
685C LYS* 5.2 0.2 - - - -
686C GLN* 3.6 22.3 + - - +
687C SER* 3.2 26.1 + - - +
689C VAL* 1.3 80.9 - - - +
691C ILE* 1.3 57.7 + - + +
693C PHE* 3.5 2.2 + - - -
694C ARG* 2.9 30.4 + - - +
703C TYR* 3.1 32.8 + - - -
706C MET* 5.1 2.3 - - - +
707C GLU* 5.8 0.3 - - - +
710C ASN* 4.1 17.9 + - - -
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Residues in contact with ILE 691 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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485C GLY 4.1 2.0 - - - +
486C THR* 3.7 29.8 - - + -
487C GLN* 5.4 0.9 - - + +
498C TRP* 4.9 2.5 - - + -
520C ASN* 3.9 18.8 - - - +
522C GLU* 3.8 39.0 - - + +
523C ARG* 3.9 20.2 - - + +
687C SER 3.1 13.3 + - - +
688C SER* 3.6 7.4 - - - +
690C ASP* 1.3 74.4 - - - +
692C TYR* 1.3 65.2 + - - +
694C ARG* 3.1 31.8 + - - +
695C ARG* 3.2 16.3 + - + +
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Residues in contact with TYR 692 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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784B PHE 4.3 3.4 - - - -
785B GLY* 3.5 25.1 - - - +
787B GLY* 4.8 11.1 - - - -
790B GLU* 5.9 1.9 - - - +
538C LEU* 4.8 5.4 - - + -
688C SER 2.9 16.5 + - - +
689C VAL* 3.2 7.2 + - - +
691C ILE* 1.3 78.4 - - - +
693C PHE* 1.3 89.3 + + - +
695C ARG 4.1 3.3 + - - +
696C GLN* 3.8 33.6 + - - +
699C LEU* 4.7 11.6 - - + +
753C PHE* 4.1 30.0 - + - +
754C PHE* 3.4 41.7 + + + -
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Residues in contact with PHE 693 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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667C ILE* 6.0 2.7 - - + -
672C LEU* 6.4 0.4 - - + -
681C TYR* 5.3 1.6 - + - -
689C VAL* 2.9 48.8 + - + +
692C TYR* 1.3 95.7 - + - +
694C ARG* 1.3 64.1 + - - +
696C GLN 4.3 1.1 - - - +
699C LEU* 3.4 30.6 - - + +
700C SER* 5.2 0.3 - - - -
702C MET* 3.6 46.7 - - + -
703C TYR* 3.2 34.5 - - + +
706C MET* 3.4 28.7 - - + -
730C ILE* 4.4 17.9 - - + -
753C PHE* 4.6 8.7 - + - -
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Residues in contact with ARG 694 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
486C THR* 5.7 1.2 - - - -
487C GLN* 3.3 54.2 + - - +
522C GLU* 4.2 10.7 - - - +
690C ASP* 2.9 19.9 + - - +
691C ILE* 3.1 32.9 + - - +
693C PHE* 1.3 79.6 - - - +
695C ARG* 1.3 62.5 + - - +
696C GLN 2.8 20.3 + - - +
703C TYR* 3.5 33.4 - - + +
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Residues in contact with ARG 695 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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785B GLY 5.0 6.4 - - - +
786B ASP* 5.8 1.4 - - - -
522C GLU* 4.1 21.3 - - + +
691C ILE 3.2 9.6 + - - +
692C TYR 4.4 3.5 - - - +
694C ARG* 1.3 85.2 - - - +
696C GLN* 1.3 63.6 + - - +
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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