Contacts of the helix formed by residues 178 - 190 (chain C) in PDB entry 2XV6
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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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177C ALA* 1.3 77.8 - - - +
179C GLN* 1.3 58.3 + - - +
180C GLU* 3.6 9.7 + - - +
181C VAL* 3.1 29.1 + - - +
182C LYS* 3.0 25.9 + - - +
59D TYR 4.7 0.7 + - - -
60D ASP* 4.0 21.7 + - - -
61D ASP* 4.8 17.8 + - - -
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Residues in contact with GLN 179 (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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177C ALA 4.0 1.2 + - - +
178C SER* 1.3 71.7 - - - +
180C GLU* 1.3 52.2 + - - +
182C LYS* 3.2 26.3 + - - +
183C ASN* 2.8 47.0 + - - +
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Residues in contact with GLU 180 (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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178C SER* 3.3 8.9 + - - +
179C GLN* 1.3 77.7 - - - +
181C VAL* 1.3 61.5 + - + +
183C ASN* 3.5 7.7 + - - +
184C TRP* 3.1 22.7 + - - +
58D VAL* 4.0 19.0 - - + +
59D TYR 4.5 2.9 + - - +
61D ASP* 4.0 5.0 - - - +
64D LYS* 2.6 39.7 + - - -
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Residues in contact with VAL 181 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177C ALA* 3.9 19.7 - - + -
178C SER* 3.1 23.1 + - - +
180C GLU* 1.3 74.8 - - - +
182C LYS* 1.3 58.1 + - - +
184C TRP* 3.2 4.5 + - - +
185C MET* 3.0 33.7 + - + +
47D LEU* 4.1 35.4 - - + +
48D ILE 5.3 1.3 - - - +
58D VAL* 4.0 19.5 - - + -
59D TYR* 3.7 30.5 - - - +
60D ASP* 3.9 5.2 - - - +
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Residues in contact with LYS 182 (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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172C LEU* 3.1 42.9 + - + +
173C ARG* 2.9 24.5 + - - +
175C GLU* 2.8 30.1 + - - -
177C ALA* 3.4 28.8 + - + +
178C SER 3.0 13.1 + - - +
179C GLN* 3.2 26.1 + - - +
181C VAL* 1.3 74.9 - - - +
183C ASN* 1.3 61.6 + - - +
185C MET 3.2 1.9 + - - -
186C THR* 3.1 26.8 + - - +
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Residues in contact with ASN 183 (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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179C GLN* 2.8 32.6 + - - +
180C GLU* 3.7 7.7 - - - +
182C LYS* 1.3 69.6 - - - +
184C TRP* 1.3 65.0 + - - +
186C THR* 2.7 30.1 + - - +
187C GLU* 3.1 20.2 + - + +
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Residues in contact with TRP 184 (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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180C GLU 3.1 13.6 + - - +
181C VAL 3.5 7.9 - - - +
183C ASN* 1.3 75.6 - - - +
185C MET* 1.4 74.3 + - + +
187C GLU* 3.2 8.3 + - + +
188C THR* 2.9 59.0 + - + +
33D VAL* 3.8 8.3 - - + -
50D ALA* 3.5 17.7 - - + -
51D ILE* 3.6 30.3 - - - -
52D ARG* 3.6 18.8 - - + +
56D SER* 2.8 45.7 + - - -
57D THR 3.9 6.8 + - - -
58D VAL* 3.5 33.4 - - + -
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Residues in contact with MET 185 (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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150C ILE* 4.0 16.8 - - + -
151C LEU* 4.4 9.4 - - + -
168C PHE* 3.8 2.1 - - - -
172C LEU* 4.0 18.8 - - + -
181C VAL* 3.0 21.9 + - + +
182C LYS 3.2 8.7 + - - +
184C TRP* 1.4 90.6 - - + +
186C THR* 1.4 55.3 + - - +
188C THR* 3.6 2.5 - - - -
189C LEU* 2.8 60.6 + - + +
33D VAL* 4.4 1.8 - - + -
35D ALA* 4.8 0.2 - - + -
47D LEU* 3.6 29.2 - - + -
50D ALA* 3.5 32.1 - - + -
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Residues in contact with THR 186 (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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168C PHE* 4.0 11.2 - - + -
169C TYR* 3.8 34.1 - - + +
172C LEU* 3.5 16.8 - - + +
182C LYS* 3.1 17.7 + - + +
183C ASN* 2.7 25.6 + - - +
185C MET* 1.4 77.3 - - - +
187C GLU* 1.3 70.0 + - - +
190C LEU* 3.4 25.7 + - - +
191C VAL 5.0 0.3 + - - -
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Residues in contact with GLU 187 (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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183C ASN* 3.1 23.2 + - + +
184C TRP* 3.2 7.4 + - + +
186C THR* 1.3 88.5 + - - +
188C THR* 1.3 60.3 + - - +
190C LEU 5.0 0.4 + - - -
191C VAL* 5.6 4.7 + - - +
209C ALA 5.6 1.9 - - - +
214C MET* 6.2 0.2 - - - +
52D ARG* 4.4 13.2 + - - +
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Residues in contact with THR 188 (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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184C TRP* 2.9 55.6 + - + +
185C MET* 3.3 5.7 + - - -
187C GLU* 1.3 79.6 - - + +
189C LEU* 1.3 66.0 + - - +
191C VAL 5.3 0.4 - - - -
192C GLN* 3.4 20.6 + - - +
32D ASN* 4.7 3.5 + - - -
33D VAL* 3.9 13.2 - - - +
52D ARG* 2.9 43.8 - - - +
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Residues in contact with LEU 189 (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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150C ILE* 3.8 31.4 - - + +
151C LEU* 3.9 12.6 - - + -
168C PHE* 3.7 10.8 - - + -
185C MET* 2.8 42.6 + - - +
188C THR* 1.3 80.7 + - - +
190C LEU* 1.3 58.2 + - - +
191C VAL 3.4 2.5 - - - -
192C GLN* 3.8 6.3 - - + -
193C ASN* 2.7 57.6 + - - +
33D VAL* 3.7 29.4 - - + -
95D SER* 4.2 9.0 - - - +
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Residues in contact with LEU 190 (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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161C PHE* 4.6 8.8 - - + -
164C TYR* 2.6 50.3 + - + -
165C VAL* 4.3 12.3 - - + -
168C PHE* 3.7 38.8 - - + -
169C TYR* 4.3 12.3 - - + +
186C THR* 3.4 21.0 + - - +
188C THR 3.9 0.2 - - - -
189C LEU* 1.3 76.1 - - - +
191C VAL* 1.3 60.3 - - + +
194C ALA* 3.5 3.3 + - - +
202C LEU* 5.4 0.4 - - - -
211C LEU* 3.6 30.1 - - + -
214C MET* 4.2 17.9 - - + -
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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