Contacts of the helix formed by residues 7039 - 7044 (chain C) in PDB entry 6W75
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 SER7039 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6832C ALA* 4.2 2.0 - - - -
6833C THR* 2.4 36.0 + - - -
6834C LEU* 4.4 2.2 - - - -
6847C GLN* 4.1 2.2 - - - +
6995C VAL* 3.7 13.2 - - - -
7038C SER* 1.3 71.2 - - - +
7040C TYR* 1.3 57.1 + - - +
7041C SER 3.2 2.9 - - - -
7042C LEU* 2.8 48.7 + - - +
7043C PHE* 3.6 14.8 - - - -
7111C FMT 3.1 11.8 + - - -
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Residues in contact with TYR7040 (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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6802C ALA* 3.5 21.1 - - + +
6803C TRP* 3.6 37.9 - + + -
6833C THR* 5.5 1.6 - - - -
7036C GLN* 4.1 14.4 + - - -
7038C SER* 3.2 19.8 + - - +
7039C SER* 1.3 82.4 - - - +
7041C SER* 1.3 61.1 + - - +
7042C LEU 3.1 1.3 + - - -
7043C PHE* 3.4 26.1 + + - +
7044C ASP* 4.6 1.7 + - - +
7111C FMT 3.5 35.0 + - - -
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Residues in contact with SER7041 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6803C TRP 3.8 13.2 + - - -
6804C GLN 3.8 8.1 + - - -
6805C PRO* 3.4 20.6 - - - +
6847C GLN* 3.2 22.4 + - - +
6850C GLN* 2.8 43.0 + - - -
7038C SER* 4.8 0.2 + - - -
7039C SER 3.1 0.6 + - - -
7040C TYR* 1.3 75.9 - - - +
7042C LEU* 1.3 59.1 + - - +
7043C PHE 3.4 0.7 + - - -
7044C ASP* 3.7 10.8 + - - +
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Residues in contact with LEU7042 (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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6834C LEU* 4.5 0.2 - - + -
6835C PRO* 3.9 28.2 - - + +
6843C ALA* 3.5 37.0 - - + +
6846C THR* 3.9 10.5 - - + -
6847C GLN* 3.7 28.0 - - + +
6850C GLN* 4.4 2.0 - - - +
6995C VAL* 3.9 11.7 - - + -
7039C SER* 2.8 21.4 + - - +
7041C SER* 1.3 80.0 - - - +
7043C PHE* 1.3 62.4 + - - +
7044C ASP 3.3 0.4 + - - -
7045C MET* 3.6 20.2 - - - +
4298D LEU* 3.7 32.4 - - + +
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Residues in contact with PHE7043 (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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6833C THR* 4.2 12.8 - - + -
6834C LEU 5.1 0.2 - - - -
6835C PRO* 3.7 35.0 - - + -
7039C SER* 3.6 33.9 - - - -
7040C TYR* 3.4 18.3 + + - +
7041C SER 3.4 0.8 - - - -
7042C LEU* 1.3 78.4 - - + +
7044C ASP* 1.3 57.9 + - - +
7045C MET* 3.9 2.9 + - - +
4299D CYS 5.5 2.1 - - - +
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Residues in contact with ASP7044 (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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6850C GLN* 4.0 6.8 + - - -
7040C TYR 4.6 1.7 + - - +
7041C SER* 3.7 16.2 + - - +
7043C PHE* 1.3 78.0 - - - +
7045C MET* 1.3 60.1 + - - +
7046C SER* 2.7 33.6 + - - -
7047C LYS 5.0 1.4 + - - -
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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