Contacts of the helix formed by residues 201 - 216 (chain A) in PDB entry 2GC5
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 VAL 201 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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165A GLU* 5.7 3.4 - - - +
166A VAL 4.0 18.0 + - - +
178A ILE* 3.7 35.2 - - + -
199A ASN 3.7 2.7 + - - +
200A LEU* 1.3 73.0 - - - +
202A PRO* 1.3 77.2 - - + +
203A ASP* 4.6 1.8 - - + +
204A ALA* 2.9 9.3 + - + +
205A ALA 2.8 18.4 + - - -
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Residues in contact with PRO 202 (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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200A LEU 3.8 1.5 - - - +
201A VAL* 1.3 88.1 - - + -
203A ASP* 1.3 60.3 - - - +
205A ALA* 3.4 7.7 + - + +
206A ALA* 2.9 30.7 + - - +
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Residues in contact with ASP 203 (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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177A THR* 6.0 1.0 - - - -
178A ILE* 3.6 29.5 + - + +
179A THR* 3.7 21.8 + - - +
182A ALA* 5.0 0.2 - - - -
201A VAL* 3.1 2.3 + - + +
202A PRO* 1.3 83.5 - - - +
204A ALA* 1.3 61.4 + - - +
206A ALA* 3.6 6.0 + - - +
207A VAL* 3.3 27.4 + - - +
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Residues in contact with ALA 204 (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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166A VAL* 3.8 32.3 - - + +
178A ILE* 3.6 9.4 - - + +
182A ALA* 3.8 15.6 - - + +
200A LEU* 3.9 16.6 - - + -
201A VAL* 2.9 11.4 + - + +
203A ASP* 1.3 77.2 - - - +
205A ALA* 1.3 65.7 + - - +
207A VAL* 3.3 3.6 + - - +
208A VAL* 3.0 26.7 + - - +
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Residues in contact with ALA 205 (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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200A LEU* 3.6 14.9 - - + +
201A VAL 2.8 11.9 + - - +
202A PRO* 3.6 11.9 - - + +
204A ALA* 1.3 76.1 - - - +
206A ALA* 1.3 52.2 + - - +
208A VAL* 3.3 1.0 + - - -
209A ALA* 2.8 36.7 + - - +
219A TRP* 3.8 7.6 - - + -
221A ARG* 3.8 34.5 - - - +
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Residues in contact with ALA 206 (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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202A PRO 2.9 17.1 + - - +
203A ASP* 3.7 8.5 - - - +
204A ALA 3.2 0.2 - - - -
205A ALA* 1.3 75.3 - - - +
207A VAL* 1.3 64.2 + - + +
209A ALA* 3.5 7.1 + - - +
210A ALA* 3.1 23.7 + - - +
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Residues in contact with VAL 207 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179A THR* 3.8 29.2 - - + +
182A ALA* 3.7 38.8 - - + +
183A LYS* 3.7 19.5 - - + +
186A ALA* 4.0 11.2 - - + -
203A ASP 3.3 13.7 + - - +
204A ALA 3.3 7.4 + - - +
206A ALA* 1.3 76.9 - - + +
208A VAL* 1.3 58.8 + - + +
210A ALA* 3.4 6.4 + - - +
211A LYS* 2.9 27.6 + - + +
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Residues in contact with VAL 208 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163A LEU* 3.8 23.8 - - + -
182A ALA* 5.7 1.3 - - + +
186A ALA* 4.9 4.0 - - + -
189A ILE* 4.5 12.1 - - + -
195A VAL* 4.9 0.4 - - + -
197A THR* 4.5 5.6 - - + -
200A LEU* 3.5 26.5 - - + -
204A ALA* 3.0 13.4 + - + +
205A ALA 3.8 2.9 - - - +
207A VAL* 1.3 74.3 - - + +
209A ALA* 1.3 60.4 + - - +
211A LYS* 3.2 5.9 + - - +
212A VAL* 2.8 39.8 + - + +
219A TRP* 3.6 35.9 - - + +
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Residues in contact with ALA 209 (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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205A ALA 2.8 17.4 + - - +
206A ALA* 3.8 7.2 - - - +
208A VAL* 1.3 77.0 - - - +
210A ALA* 1.3 57.2 + - - +
212A VAL* 3.4 7.1 - - - +
213A ALA* 3.0 28.6 + - - +
219A TRP* 3.9 21.3 - - + -
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Residues in contact with ALA 210 (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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206A ALA 3.1 17.4 + - - +
207A VAL* 3.7 5.6 - - - +
209A ALA* 1.3 72.8 - - - +
211A LYS* 1.3 66.9 + - - +
213A ALA* 3.3 8.5 + - - +
214A THR* 3.2 27.6 + - + +
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Residues in contact with LYS 211 (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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186A ALA* 3.5 30.7 - - + +
187A GLY* 4.9 5.8 + - - -
189A ILE* 3.5 41.6 + - + -
207A VAL* 2.9 17.9 + - + +
208A VAL* 3.2 8.3 + - - +
210A ALA* 1.3 76.7 - - - +
212A VAL* 1.3 57.0 + - - +
214A THR* 2.8 28.7 + - - +
215A THR* 3.0 26.5 + - + +
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Residues in contact with VAL 212 (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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189A ILE* 4.3 6.7 - - + -
195A VAL* 3.6 30.7 - - + -
208A VAL* 2.8 29.4 + - + +
209A ALA* 3.4 19.1 - - - +
211A LYS* 1.3 70.5 - - - +
213A ALA* 1.3 59.5 + - - +
215A THR* 3.4 6.1 - - - -
216A GLY* 2.8 30.7 + - - -
217A SER* 3.5 21.5 + - - +
219A TRP* 4.1 23.3 - - + -
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Residues in contact with ALA 213 (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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209A ALA 3.0 14.5 + - - +
210A ALA* 3.4 13.7 - - - +
211A LYS 3.2 0.2 - - - -
212A VAL* 1.3 79.4 - - - +
214A THR* 1.3 61.4 + - + +
216A GLY* 4.0 4.7 + - - -
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Residues in contact with THR 214 (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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191A ARG* 4.6 14.9 + - - -
210A ALA 3.4 13.7 - - - +
211A LYS* 2.8 28.0 + - - +
213A ALA* 1.3 79.7 - - + +
215A THR* 1.3 66.7 + - - +
216A GLY 3.4 0.2 - - - -
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Residues in contact with THR 215 (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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189A ILE* 3.7 15.4 - - + +
190A LYS* 3.8 10.1 - - - -
191A ARG* 3.4 19.6 + - + +
192A GLY* 2.9 24.9 + - - -
211A LYS* 3.0 40.2 + - - +
212A VAL* 3.4 9.0 - - - -
214A THR* 1.3 79.6 - - - +
216A GLY* 1.3 58.3 + - - +
217A SER* 2.7 32.4 + - - -
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Residues in contact with GLY 216 (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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192A GLY* 4.4 7.4 - - - -
212A VAL 2.8 11.1 + - - -
213A ALA 4.0 4.1 + - - -
214A THR 3.4 3.0 + - - -
215A THR* 1.3 77.4 - - - +
217A SER* 1.3 63.5 + - - +
218A GLN 3.6 1.9 + - - -
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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