Contacts of the helix formed by residues 178 - 188 (chain A) in PDB entry 2M8N
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 SER 178 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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176A GLN* 5.1 1.0 - - - +
177A ALA* 1.3 79.1 - - - +
179A GLN* 1.3 66.0 + - - +
180A GLU* 3.3 13.0 + - - +
181A VAL* 3.3 19.6 + - - +
182A LYS* 3.1 19.5 + - - +
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Residues in contact with GLN 179 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178A SER* 1.3 73.8 + - - +
180A GLU* 1.3 61.5 + - + +
182A LYS* 3.6 23.5 + - - +
183A ASN* 2.8 44.0 + - - +
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Residues in contact with GLU 180 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28A GLU* 2.9 30.8 - - - +
178A SER* 3.3 9.9 + - - +
179A GLN* 1.3 80.6 - - + +
181A VAL* 1.3 62.6 + - + +
183A ASN* 3.5 11.7 + - - +
184A TRP* 3.3 41.6 + - + +
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Residues in contact with VAL 181 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62A HIS* 5.8 5.6 - - - +
175A GLU* 5.4 0.4 - - - +
177A ALA* 4.5 7.6 - - + -
178A SER* 3.3 24.8 + - - +
179A GLN 3.2 0.4 - - - -
180A GLU* 1.3 79.1 - - + +
182A LYS* 1.3 64.3 + - - +
184A TRP* 3.3 18.4 + - + +
185A MET* 3.1 45.0 + - + +
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Residues in contact with LYS 182 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172A LEU* 3.8 39.0 - - + +
173A ARG* 6.0 1.1 - - - -
175A GLU* 5.4 3.1 - - - +
177A ALA* 3.7 32.1 - - + +
178A SER 3.1 11.6 + - - +
179A GLN* 3.1 29.2 + - - +
181A VAL* 1.3 75.7 - - - +
183A ASN* 1.3 67.5 + - - +
185A MET* 3.1 11.8 + - - +
186A THR* 3.0 28.3 + - + +
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Residues in contact with ASN 183 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179A GLN* 2.8 33.8 + - - +
180A GLU* 3.7 14.3 - - - +
182A LYS* 1.3 80.4 + - - +
184A TRP* 1.3 66.4 + - + +
186A THR* 3.2 8.1 + - - -
187A GLU* 3.0 41.1 + - - +
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Residues in contact with TRP 184 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28A GLU* 4.2 31.0 - - + -
29A GLU* 5.2 8.7 - - + -
31A ALA* 6.5 0.9 - - + -
180A GLU* 3.3 27.3 + - + +
181A VAL* 3.6 19.1 - - + +
183A ASN* 1.3 81.1 - - + +
185A MET* 1.3 58.6 + - - +
187A GLU* 5.0 5.6 - - - -
188A THR* 2.8 40.5 + - - +
189A LEU* 3.2 13.4 + - + +
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Residues in contact with MET 185 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150A ILE* 3.9 29.4 - - + -
151A LEU* 5.4 3.8 - - + -
168A PHE* 3.1 16.7 - - + -
172A LEU* 3.2 32.8 - - + -
175A GLU* 3.3 30.7 - - - +
177A ALA* 4.6 2.0 - - + -
181A VAL* 3.1 40.9 + - + +
182A LYS* 3.1 11.4 + - - +
184A TRP* 1.3 76.8 - - - +
186A THR* 1.3 59.0 + - - +
189A LEU* 3.4 15.9 + - + -
190A LEU 3.1 27.4 + - - -
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Residues in contact with THR 186 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168A PHE* 4.4 8.5 - - + -
169A TYR* 5.2 6.7 - - + -
172A LEU* 3.5 31.4 - - + -
182A LYS 3.0 9.8 + - - +
183A ASN* 3.2 13.7 + - - -
185A MET* 1.3 77.9 - - - +
187A GLU* 1.3 70.7 + - - +
188A THR 3.8 0.2 + - - -
190A LEU* 3.8 20.8 - - - +
191A VAL* 5.7 1.2 - - - +
211A LEU* 4.9 14.5 - - + +
214A MET* 5.8 2.4 - - - +
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Residues in contact with GLU 187 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183A ASN* 3.0 30.8 + - - +
184A TRP* 4.7 5.0 - - - +
186A THR* 1.3 86.0 - - - +
188A THR* 1.3 69.8 + - + +
191A VAL* 4.7 10.8 - - - +
214A MET* 5.7 2.8 - - - +
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Residues in contact with THR 188 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184A TRP* 2.8 25.6 + - - +
187A GLU* 1.3 90.5 - - + +
189A LEU* 1.3 65.8 + - - +
190A LEU 3.3 2.2 - - - -
191A VAL* 3.4 7.4 + - - +
192A GLN* 2.9 34.3 + - - +
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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