Contacts of the helix formed by residues 2073 - 2079 (chain C) in PDB entry 6TM1
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 PRO2073 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2036C MET* 6.4 1.6 - - + -
2063C GLY 3.8 16.4 - - - +
2064C SER* 4.1 17.3 - - - +
2065C VAL* 4.0 11.0 - - + +
2072C GLY* 1.3 80.1 - - - +
2074C MET* 1.3 55.2 + - - +
2075C ALA* 2.9 16.9 + - + +
2076C TYR* 4.2 5.5 + - - +
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Residues in contact with MET2074 (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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2065C VAL* 6.0 4.2 - - + +
2069C VAL* 5.4 11.2 - - + +
2072C GLY* 2.7 13.2 + - - +
2073C PRO* 1.3 70.3 - - - +
2075C ALA* 1.3 58.4 + - - +
2076C TYR* 3.0 4.9 - - - +
2077C ALA* 2.8 30.6 + - + +
2078C ARG 4.2 0.2 + - - -
2141C LEU* 3.5 32.3 - - + -
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Residues in contact with ALA2075 (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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2032C ALA* 5.9 7.4 - - + -
2072C GLY 3.7 5.0 + - - +
2073C PRO* 2.9 10.2 - - + +
2074C MET* 1.3 76.4 - - - +
2076C TYR* 1.3 52.6 + - - +
2077C ALA 3.1 0.4 - - - -
2078C ARG* 2.8 33.4 + - + +
2079C ALA* 3.3 8.5 + - - +
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Residues in contact with TYR2076 (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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2073C PRO 4.2 4.6 + - - +
2074C MET* 3.0 3.7 - - - +
2075C ALA* 1.3 73.8 - - - +
2077C ALA* 1.3 58.9 + - - +
2078C ARG 3.1 0.2 - - - -
2079C ALA* 2.9 42.2 + - + +
2080C PHE* 3.3 10.2 - - + +
2102C ARG* 5.5 11.0 - - + -
2144C VAL* 4.0 5.8 - - + +
2145C MET* 6.3 2.7 - - + -
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Residues in contact with ALA2077 (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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2074C MET* 2.8 22.8 + - + +
2076C TYR* 1.3 78.8 - - - +
2078C ARG* 1.3 55.7 + - - +
2079C ALA 3.3 0.6 + - - -
2081C LEU* 4.6 11.1 + - - +
2141C LEU* 5.3 11.9 - - + -
2144C VAL* 4.1 26.3 - - + +
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Residues in contact with ARG2078 (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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2075C ALA* 2.8 14.4 + - + +
2077C ALA* 1.3 77.6 - - - +
2079C ALA* 1.3 58.3 + - - +
2080C PHE 3.9 1.6 - - - -
2081C LEU* 5.3 0.9 - - - -
2091C ASP* 5.4 6.4 - - - +
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Residues in contact with ALA2079 (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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2029C ILE* 6.5 0.7 - - + -
2032C ALA* 5.7 9.6 - - + -
2075C ALA 3.9 3.1 - - - +
2076C TYR* 2.9 31.2 + - + +
2077C ALA 3.3 0.2 - - - -
2078C ARG* 1.3 79.6 - - - +
2080C PHE* 1.3 61.2 + - - +
2091C ASP* 5.9 4.7 - - - -
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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