Contacts of the helix formed by residues 2125 - 2138 (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 GLU2125 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2122C ASP 4.8 1.9 + - - +
2123C GLN 2.8 1.4 + - - -
2124C LEU* 1.3 78.9 - - - +
2126C TYR* 1.3 57.1 + - - +
2127C GLN 2.9 10.6 + - - -
2128C GLU* 3.5 7.1 + - - +
2129C GLU* 3.0 22.5 + - - +
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Residues in contact with TYR2126 (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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178A CYS* 5.9 1.1 - - - -
2123C GLN* 2.9 26.3 + - + +
2125C GLU* 1.3 76.5 - - - +
2127C GLN* 1.3 56.8 + - + +
2129C GLU* 3.6 9.5 - - - +
2130C LEU* 3.2 33.1 + - + +
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Residues in contact with GLN2127 (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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2112C LEU* 3.8 8.0 - - - +
2115C ASN* 3.0 56.3 + - - +
2116C GLU* 3.2 20.2 + - + +
2119C ILE* 3.4 30.7 - - + +
2123C GLN* 3.7 3.6 - - + +
2124C LEU* 4.6 7.4 - - - +
2125C GLU 2.9 1.6 - - - -
2126C TYR* 1.3 75.8 - - + +
2128C GLU* 1.3 54.5 + - - +
2129C GLU 3.0 0.9 - - - -
2130C LEU* 3.2 16.7 + - + +
2131C ARG* 2.7 37.6 + - - +
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Residues in contact with GLU2128 (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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2124C LEU 4.7 3.9 + - - +
2125C GLU* 3.5 11.0 + - - +
2127C GLN* 1.3 77.4 - - - +
2129C GLU* 1.3 62.0 + - - +
2131C ARG* 3.7 10.0 - - - +
2132C SER* 3.1 23.6 + - - -
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Residues in contact with GLU2129 (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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178A CYS* 4.0 23.6 - - - -
2125C GLU 3.0 18.9 + - - +
2126C TYR* 3.6 12.1 - - - +
2127C GLN 3.0 0.4 - - - -
2128C GLU* 1.3 78.2 - - - +
2130C LEU* 1.3 61.5 + - - +
2132C SER* 3.3 7.9 + - - -
2133C HIS* 3.2 29.2 + - + +
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Residues in contact with LEU2130 (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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178A CYS* 5.6 0.6 - - - -
2058C GLN* 5.9 5.2 - - + +
2061C LEU* 4.6 24.5 - - + -
2062C GLN* 4.9 21.5 - - - +
2112C LEU* 4.9 9.9 - - + -
2115C ASN* 4.4 16.2 - - - +
2126C TYR* 3.2 22.2 + - + +
2127C GLN* 3.3 28.9 - - + +
2129C GLU* 1.3 74.0 - - - +
2131C ARG* 1.3 62.1 + - + +
2132C SER 3.0 5.2 - - - -
2133C HIS* 3.5 10.5 - - + +
2134C TYR* 2.6 38.6 + - + +
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Residues in contact with ARG2131 (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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2112C LEU* 6.1 3.6 - - + -
2127C GLN* 2.7 22.3 + - - +
2128C GLU* 3.7 11.7 - - - +
2130C LEU* 1.3 77.5 - - + +
2132C SER* 1.3 56.2 + - - +
2134C TYR* 3.9 16.6 - - + +
2135C LYS* 3.3 23.6 + - - +
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Residues in contact with SER2132 (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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2128C GLU 3.1 11.4 + - - -
2129C GLU* 3.4 11.0 - - - -
2130C LEU 3.0 0.8 - - - -
2131C ARG* 1.3 75.6 - - - +
2133C HIS* 1.3 61.8 + - - +
2134C TYR 3.1 1.1 - - - -
2135C LYS* 4.2 3.9 - - - +
2136C ASP* 2.8 32.6 + - - +
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Residues in contact with HIS2133 (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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177A LEU 4.7 3.6 + - - -
178A CYS* 3.7 28.3 - - + -
179A PRO* 2.7 44.9 + - + +
2062C GLN* 5.9 1.8 + - - +
2065C VAL 4.5 19.3 - - - +
2129C GLU* 3.2 23.1 + - + -
2130C LEU* 3.2 10.4 + - + +
2132C SER* 1.3 77.9 - - - +
2134C TYR* 1.3 57.2 + - - +
2136C ASP* 4.1 6.1 - - + +
2137C MET* 3.1 28.6 + - - +
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Residues in contact with TYR2134 (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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2064C SER 5.7 4.5 - - - -
2106C ASP 4.8 6.0 + - - -
2109C GLY* 4.1 27.2 - - - -
2112C LEU* 5.3 13.0 - - + -
2130C LEU* 2.6 24.0 + - + +
2131C ARG* 4.0 15.3 - - + +
2133C HIS* 1.3 71.0 - - - +
2135C LYS* 1.3 61.4 + - + +
2137C MET* 3.0 7.3 + - + +
2138C LEU* 2.7 69.2 + - + +
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Residues in contact with LYS2135 (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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2131C ARG 3.3 16.9 + - - +
2132C SER* 3.5 4.2 + - - +
2134C TYR* 1.3 83.1 - - + +
2136C ASP* 1.3 58.6 + - - +
2138C LEU* 3.0 32.3 + - + +
2139C SER* 3.7 6.6 + - - -
2140C GLU* 4.2 3.8 + - - +
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Residues in contact with ASP2136 (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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2132C SER 2.8 25.0 + - - +
2133C HIS* 4.1 7.4 - - + +
2135C LYS* 1.3 73.3 - - - +
2137C MET* 1.3 57.8 + - - +
2140C GLU* 3.1 28.1 - - - +
2141C LEU* 4.0 2.3 + - - +
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Residues in contact with MET2137 (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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2064C SER 5.1 1.3 - - - +
2065C VAL* 3.7 28.9 - - + -
2133C HIS 3.1 19.0 + - - +
2134C TYR* 3.0 7.6 + - + +
2136C ASP* 1.3 74.2 - - - +
2138C LEU* 1.3 64.2 + - - +
2141C LEU* 3.5 24.4 - - + +
2142C SER 4.4 0.2 + - - -
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Residues in contact with LEU2138 (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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2106C ASP* 5.9 6.3 - - + -
2134C TYR* 2.7 60.5 + - + +
2135C LYS* 3.0 17.4 + - + +
2137C MET* 1.3 76.5 - - - +
2139C SER* 1.3 69.4 + - - +
2140C GLU 3.0 1.6 + - - -
2141C LEU 3.1 0.3 + - - -
2142C SER* 2.6 39.4 + - - -
2149C ILE* 4.5 31.0 - - + +
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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