Contacts of the helix formed by residues 178 - 192 (chain C) in PDB entry 2GD4
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 ASN 178 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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174C ASP* 3.4 8.1 + - + +
177C GLU* 1.3 89.0 - - - +
179C ALA* 1.3 68.9 + - - +
180C GLU 3.6 1.3 - - - -
181C GLN* 2.9 32.4 + - + +
182C SER* 3.0 3.6 + - - -
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Residues in contact with ALA 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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174C ASP 3.8 0.2 - - - -
175C PHE* 3.0 26.1 + - - +
176C LYS 5.5 0.2 - - - +
177C GLU 3.4 3.2 + - - +
178C ASN* 1.3 69.6 - - - +
180C GLU* 1.3 55.6 + - - +
182C SER* 2.4 48.4 + - - -
183C ARG* 3.0 3.3 + - - -
207C ILE* 4.3 11.7 - - + +
208C ASN* 4.2 23.3 - - - +
209C GLU* 4.5 3.6 - - + +
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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 ASN 3.6 0.4 - - - -
179C ALA* 1.3 78.4 - - - +
181C GLN* 1.3 64.7 + - - +
182C SER 2.9 0.9 + - - -
183C ARG* 3.0 52.7 + - - +
184C ALA* 3.1 19.5 + - + +
207C ILE 4.9 4.1 + - - +
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Residues in contact with GLN 181 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178C ASN* 2.9 35.3 + - + +
180C GLU* 1.3 79.5 - - - +
182C SER* 1.3 57.0 + - - +
184C ALA* 4.5 2.2 - - - +
185C ALA* 3.4 16.6 + - - +
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Residues in contact with SER 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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173C LEU* 3.9 31.5 - - - +
174C ASP* 4.1 11.4 - - - -
175C PHE* 3.5 20.5 - - - -
178C ASN 3.0 6.9 + - - -
179C ALA* 2.4 41.5 + - - -
181C GLN* 1.3 67.0 - - - +
183C ARG* 1.3 73.8 + - - +
185C ALA* 2.8 20.1 + - - +
186C ILE* 3.0 10.8 + - - +
207C ILE* 4.7 0.5 - - - +
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Residues in contact with ARG 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 ALA 3.0 1.9 + - - +
180C GLU* 3.0 43.6 + - - +
182C SER* 1.3 79.6 + - - +
184C ALA* 1.3 74.0 + - - +
185C ALA 2.5 13.0 + - - -
186C ILE* 2.5 27.2 + - - +
187C ASN* 3.4 15.3 + - - +
202C ILE* 4.1 22.4 - - + -
203C PRO 3.2 13.1 + - - -
204C SER* 2.7 47.2 + - - +
205C GLU 3.9 3.8 - - - +
206C ALA 5.8 0.6 - - - +
207C ILE* 4.1 29.6 + - + +
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Residues in contact with ALA 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 14.0 + - + +
181C GLN* 4.5 3.1 - - - +
183C ARG* 1.3 94.6 - - - +
185C ALA* 1.3 58.0 + - - +
186C ILE 3.4 0.2 - - - -
187C ASN* 4.1 14.1 - - + +
188C LYS* 3.7 18.9 + - - +
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Residues in contact with ALA 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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173C LEU* 4.8 11.7 - - + -
181C GLN 3.4 15.6 + - - +
182C SER* 2.8 18.5 + - - +
183C ARG 2.5 6.1 + - - -
184C ALA* 1.3 75.7 - - - +
186C ILE* 1.3 63.8 + - - +
188C LYS* 3.9 6.2 + - - +
189C TRP* 3.4 15.2 + - - +
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Residues in contact with ILE 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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147C PHE* 3.2 60.3 - - + -
173C LEU* 5.0 5.2 - - + -
175C PHE* 4.7 7.2 - - + -
182C SER 3.0 9.8 + - - +
183C ARG* 2.5 20.7 + - - +
185C ALA* 1.3 69.1 - - - +
187C ASN* 1.3 61.3 + - - +
189C TRP* 2.5 37.5 + - - +
190C VAL* 3.1 8.0 + - + -
201C VAL* 4.8 7.6 - - + -
202C ILE* 3.7 28.7 - - + -
207C ILE* 3.9 16.4 - - + -
214C VAL* 4.7 1.6 - - + -
216C VAL* 4.8 1.8 - - + -
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Residues in contact with ASN 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 ARG* 3.7 19.4 - - - +
184C ALA* 4.1 13.8 - - - +
186C ILE* 1.3 73.8 - - - +
188C LYS* 1.3 67.4 + - - +
190C VAL* 2.6 19.1 + - - +
191C SER* 3.0 10.9 + - - -
199C THR* 5.6 1.3 - - - +
200C ASP* 3.3 38.2 + - - +
201C VAL* 3.9 11.4 - - - +
202C ILE* 3.3 41.7 + - - +
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Residues in contact with LYS 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 ALA 3.7 15.2 + - - +
185C ALA* 4.0 6.5 - - - +
186C ILE 3.2 0.6 + - - -
187C ASN* 1.3 77.9 - - - +
189C TRP* 1.3 61.9 + - - +
191C SER* 3.1 11.7 + - - -
192C ASN* 2.9 23.8 + - - +
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Residues in contact with TRP 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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143C ALA* 4.3 8.5 - - + -
144C ASN 4.1 24.9 - - - -
145C ARG* 3.7 53.8 - - + +
147C PHE* 4.4 17.7 - + + -
168C ALA* 5.4 7.2 - - + -
185C ALA 3.4 10.0 + - - +
186C ILE* 2.5 24.3 + - - +
188C LYS* 1.3 70.6 - - - +
190C VAL* 1.3 86.6 + - + +
192C ASN* 3.1 16.0 + - + +
193C LYS* 3.2 31.8 + - + +
216C VAL* 5.9 1.1 - - + -
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Residues in contact with VAL 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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143C ALA* 4.0 9.2 - - + +
186C ILE* 4.1 6.7 - - + +
187C ASN* 2.6 14.0 + - - +
189C TRP* 1.3 87.0 - - + +
191C SER* 1.3 65.0 + - - +
193C LYS* 2.8 4.9 + - - +
194C THR* 2.8 34.3 + - + +
198C ILE* 3.3 37.9 - - + +
199C THR* 4.7 1.8 - - - +
201C VAL* 3.5 29.6 - - + -
216C VAL* 4.7 10.3 - - + -
218C THR* 4.0 7.2 - - - +
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Residues in contact with SER 191 (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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187C ASN 3.0 7.1 + - - -
188C LYS* 3.2 15.1 - - - -
190C VAL* 1.3 77.3 - - - +
192C ASN* 1.3 53.6 + - - +
193C LYS 2.6 12.1 + - - -
194C THR* 4.1 1.6 - - - -
195C GLU* 2.9 21.8 + - - -
196C GLY* 3.1 16.4 + - - +
198C ILE 3.6 13.4 + - - -
199C THR* 3.5 22.9 + - - -
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Residues in contact with ASN 192 (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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188C LYS 2.9 18.1 + - - +
189C TRP* 3.1 10.2 + - + +
191C SER* 1.3 69.7 - - - +
193C LYS* 1.3 58.0 + - - +
195C GLU* 4.4 4.9 - - - +
701C NAG 1.5 63.2 + - - +
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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