Contacts of the helix formed by residues 1031 - 1037 (chain M) in PDB entry 6G0L
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 ILE1031 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1025M PHE* 4.5 23.8 - - + +
1027M ASN 4.7 12.8 - - - +
1028M LEU* 4.6 1.0 - - - -
1030M GLU* 1.3 84.0 - - + +
1032M LEU* 1.3 62.9 + - - +
1033M ASP* 3.2 3.4 - - - +
1034M GLU* 3.1 26.9 + - + +
1035M LEU* 3.1 27.1 + - + +
1144M LYS* 6.0 7.2 - - - +
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Residues in contact with LEU1032 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1028M LEU* 3.3 39.3 + - + +
1029M LYS* 5.1 4.7 - - - -
1030M GLU 3.5 2.8 + - - +
1031M ILE* 1.3 78.3 - - - +
1033M ASP* 1.3 58.9 + - - +
1035M LEU* 3.0 6.4 + - + +
1036M ILE* 2.9 54.9 + - + +
1041M LEU* 3.9 17.3 - - + -
1046M PHE* 3.6 35.9 - - + +
1049M TYR* 4.0 21.5 - - + -
1050M GLY 5.6 0.2 - - - +
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Residues in contact with ASP1033 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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350M TYR* 5.3 1.2 + - - -
1031M ILE* 3.2 2.1 - - - +
1032M LEU* 1.3 77.0 - - - +
1034M GLU* 1.3 65.8 + - + +
1036M ILE* 3.8 4.4 + - - +
1037M ALA* 3.5 24.4 + - - +
1046M PHE* 3.2 31.3 - - - -
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Residues in contact with GLU1034 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1031M ILE* 3.1 24.7 + - + +
1033M ASP* 1.3 82.4 - - + +
1035M LEU* 1.3 64.7 + - + +
1036M ILE 3.4 1.0 + - - -
1037M ALA* 4.3 5.2 + - - +
1038M ASP* 4.0 17.7 + - - +
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Residues in contact with LEU1035 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1021M ALA* 5.1 6.1 - - + +
1025M PHE* 3.6 61.9 - - + -
1028M LEU* 3.7 33.7 - - + -
1031M ILE* 3.3 26.0 - - + +
1032M LEU* 3.0 15.3 + - + +
1034M GLU* 1.3 82.6 - - + +
1036M ILE* 1.3 57.7 + - - +
1038M ASP* 2.8 24.7 - - + +
1040M THR* 4.9 0.5 - - - -
1041M LEU* 3.5 19.8 + - + +
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Residues in contact with ILE1036 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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350M TYR* 4.4 14.5 - - + +
1032M LEU* 2.9 27.9 + - + +
1033M ASP* 4.3 3.8 - - - +
1034M GLU 3.4 0.2 - - - -
1035M LEU* 1.3 77.4 - - - +
1037M ALA* 1.3 62.0 + - - +
1038M ASP* 3.1 10.0 + - - +
1039M GLY* 3.5 5.9 + - - -
1041M LEU* 3.4 46.6 - - + +
1042M PRO 4.1 8.7 - - - +
1043M VAL* 5.1 5.8 - - + -
1044M LYS 5.2 3.6 - - - +
1046M PHE* 3.6 32.8 - - + -
1049M TYR* 4.0 20.0 - - + -
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Residues in contact with ALA1037 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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345M LYS* 4.1 20.2 - - - +
350M TYR* 3.5 47.6 - - + +
1033M ASP 3.5 16.4 + - - +
1034M GLU* 4.3 5.4 + - - +
1036M ILE* 1.3 76.2 - - - +
1038M ASP* 1.3 61.6 + - - +
1039M GLY 3.2 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