Contacts of the helix formed by residues 171 - 175 (chain G) in PDB entry 6CM9
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 LEU 171 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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135G CYS 4.2 9.4 - - - +
136G ARG* 5.0 10.3 - - + +
139G ALA* 3.7 27.4 - - + -
164G VAL* 3.6 23.8 - - + +
165G ILE* 4.8 0.9 - - - -
168G VAL* 3.3 32.3 - - + +
169G PRO 3.2 1.0 - - - -
170G GLU* 1.3 78.4 - - - +
172G MET* 1.3 57.5 + - - +
173G GLU* 3.1 15.2 + - - +
174G MET* 3.3 45.0 - - + +
175G PHE* 3.8 7.2 - - + -
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Residues in contact with MET 172 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165G ILE* 3.7 27.7 - - + +
168G VAL 4.5 0.6 + - - -
169G PRO 3.8 18.8 + - - +
171G LEU* 1.3 77.1 - - - +
173G GLU* 1.3 64.7 + - - +
174G MET 3.2 0.4 - - - -
175G PHE* 3.4 11.5 + - - +
176G LEU 3.6 0.5 + - - -
201G MET* 3.4 72.5 - - - +
204G ARG* 3.7 27.1 - - + -
205G SER* 3.9 16.8 - - - -
208G MET* 3.8 22.4 - - + -
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Residues in contact with GLU 173 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170G GLU 2.9 30.6 - - - +
171G LEU* 3.2 11.9 - - - +
172G MET* 1.3 77.1 + - + +
174G MET* 1.3 61.7 + - + +
175G PHE 3.3 1.3 - - - -
176G LEU* 3.7 6.9 + - + +
177G PRO* 3.4 18.0 - - - +
208G MET* 4.1 18.4 - - + -
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Residues in contact with MET 174 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139G ALA* 4.2 13.7 - - - +
140G GLY* 4.3 11.2 - - - +
143G GLU* 4.2 39.9 - - + +
171G LEU* 3.3 37.0 - - + +
173G GLU* 1.3 82.8 - - + +
175G PHE* 1.3 70.7 + - + +
177G PRO* 3.9 14.7 - - - +
178G ALA* 4.4 1.7 - - - +
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Residues in contact with PHE 175 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139G ALA* 4.2 18.2 - - + -
142G VAL* 4.7 2.7 - - + -
143G GLU* 3.6 30.3 - - + -
146G LEU* 3.6 23.7 - - + +
161G ALA* 3.6 17.7 - - + -
164G VAL* 3.6 31.2 - - + -
165G ILE* 3.9 25.1 - - + -
171G LEU* 3.8 24.2 - - + -
172G MET* 3.4 6.4 + - - +
173G GLU 3.3 0.6 - - - -
174G MET* 1.3 84.3 - - + +
176G LEU* 1.3 60.1 + - - +
177G PRO 3.4 2.0 - - - -
178G ALA* 3.0 18.1 + - + +
179G THR* 3.0 20.8 + - - +
197G LEU* 5.1 6.1 - - + -
201G MET* 4.7 4.9 - - - -
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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