Contacts of the helix formed by residues 191 - 205 (chain D) in PDB entry 2GL7
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 191 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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153D ILE* 3.7 16.3 - - - +
157D THR* 4.6 0.7 + - - -
187D ALA 3.5 12.9 + - - -
188D ILE 3.1 12.8 + - - +
189D MET 4.5 2.2 - - - -
190D ARG* 1.3 78.3 - - - +
192D PRO* 1.3 64.2 - - - +
193D GLN* 3.6 12.0 + - - +
194D MET* 3.3 25.9 + - - +
195D VAL* 3.2 14.4 + - - +
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Residues in contact with PRO 192 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189D MET 4.8 2.0 - - - +
190D ARG* 3.3 13.9 - - - +
191D SER* 1.3 80.2 - - - +
193D GLN* 1.3 84.7 + - - +
194D MET 3.3 0.2 - - - -
195D VAL* 4.0 8.2 - - + +
196D SER* 3.0 29.1 + - - -
230D ALA* 6.4 1.1 - - + -
234D SER* 5.1 2.4 - - - -
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Residues in contact with GLN 193 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157D THR* 3.5 25.0 - - + +
191D SER* 3.2 10.1 + - - +
192D PRO* 1.3 101.8 - - - +
194D MET* 1.3 61.7 + - - +
196D SER* 3.9 4.5 - - - -
197D ALA* 3.2 15.4 + - - +
200D ARG* 5.1 2.4 + - - -
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Residues in contact with MET 194 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153D ILE* 4.1 20.0 - - + +
156D LEU* 4.4 5.6 - - - +
157D THR* 3.5 25.3 + - - +
160D LEU* 3.2 35.4 - - + -
175D VAL* 3.7 23.3 - - + -
188D ILE* 3.9 26.5 - - + +
191D SER* 3.2 24.9 + - - +
193D GLN* 1.3 77.6 - - - +
195D VAL* 1.3 60.1 + - - +
197D ALA* 3.1 5.6 + - + +
198D ILE* 3.0 39.6 + - + +
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Residues in contact with VAL 195 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188D ILE* 3.3 35.4 - - + +
189D MET* 4.2 9.0 - - - -
191D SER 3.2 7.9 + - - +
192D PRO* 4.3 6.3 - - + +
194D MET* 1.3 76.4 - - - +
196D SER* 1.3 62.0 + - - +
198D ILE* 3.4 8.5 + - - +
199D VAL* 3.1 26.2 + - + +
218D LEU* 4.8 8.7 - - + -
221D LEU* 4.4 9.6 - - + -
230D ALA* 3.8 23.1 - - + +
231D ILE* 4.5 4.0 - - - +
234D SER* 3.3 23.1 - - - +
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Residues in contact with SER 196 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192D PRO 3.0 21.0 + - - -
193D GLN* 3.9 5.6 - - - -
195D VAL* 1.3 76.3 - - - +
197D ALA* 1.3 57.3 + - - +
199D VAL* 3.3 4.2 + - - +
200D ARG* 2.9 47.2 + - - +
234D SER* 3.6 24.2 + - - -
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Residues in contact with ALA 197 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157D THR* 4.2 6.7 - - + -
160D LEU* 3.9 19.5 - - + -
161D ASN* 3.4 31.4 + - - +
193D GLN 3.2 12.7 + - - +
194D MET* 3.1 11.5 + - + +
196D SER* 1.3 79.2 - - - +
198D ILE* 1.3 55.5 + - - +
200D ARG* 3.9 5.9 - - - +
201D THR* 2.9 35.3 + - - -
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Residues in contact with ILE 198 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160D LEU* 3.9 8.7 - - + -
175D VAL* 3.9 9.6 - - + -
188D ILE* 3.9 17.5 - - + -
194D MET* 3.0 42.3 + - + +
195D VAL* 3.6 11.2 - - + +
196D SER 3.3 0.2 - - - -
197D ALA* 1.3 73.5 - - - +
199D VAL* 1.3 63.7 + - - +
202D MET* 3.0 24.6 + - - +
214D THR* 3.6 37.8 - - + +
217D THR* 3.9 22.7 - - + -
218D LEU* 3.9 16.6 - - + -
221D LEU* 5.3 2.5 - - + -
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Residues in contact with VAL 199 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195D VAL* 3.1 17.5 + - + +
196D SER* 3.7 4.9 - - - +
198D ILE* 1.3 77.9 - - - +
200D ARG* 1.3 62.7 + - - +
202D MET* 3.5 6.3 + - - +
203D GLN* 3.2 27.2 + - - +
218D LEU* 4.3 21.8 - - + -
231D ILE* 5.7 0.4 - - - -
234D SER* 3.6 28.0 - - - +
235D GLY 3.8 12.1 - - - +
236D GLY* 3.9 11.9 - - - -
239D ALA* 3.5 26.3 - - + +
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Residues in contact with ARG 200 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161D ASN* 3.4 36.8 + - - +
193D GLN 5.1 1.6 + - - -
196D SER* 2.9 29.9 + - - +
197D ALA* 3.9 14.7 - - - +
199D VAL* 1.3 79.0 - - - +
201D THR* 1.3 61.0 + - - +
203D GLN* 3.2 12.7 + - + +
204D ASN* 3.2 41.0 + - - +
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Residues in contact with THR 201 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160D LEU* 3.3 33.7 + - + +
161D ASN* 4.5 2.8 + - - -
168D VAL* 3.6 28.0 - - + -
197D ALA 2.9 21.4 + - - -
198D ILE 4.1 2.5 - - - -
200D ARG* 1.3 72.5 - - - +
202D MET* 1.3 67.0 + - - +
204D ASN* 3.8 8.1 - - - +
205D THR* 3.0 32.7 + - - -
210D THR* 3.7 17.9 - - + -
214D THR* 4.1 5.6 - - + -
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Residues in contact with MET 202 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198D ILE 3.0 17.5 + - - +
199D VAL* 3.6 3.1 - - - +
200D ARG 3.4 0.2 - - - -
201D THR* 1.3 78.5 - - - +
203D GLN* 1.3 61.3 + - - +
204D ASN 3.4 0.2 + - - -
205D THR* 3.6 16.2 + - - +
211D ALA* 4.5 6.4 - - - +
214D THR* 3.3 23.9 + - - +
215D ALA* 3.7 31.4 - - + +
218D LEU* 3.8 24.9 - - + -
239D ALA* 3.9 26.5 - - + -
240D LEU* 3.8 15.0 - - + -
243D MET* 3.7 43.3 - - + +
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Residues in contact with GLN 203 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199D VAL* 3.2 14.6 + - - +
200D ARG* 3.2 13.2 + - - +
202D MET* 1.3 81.6 - - - +
204D ASN* 1.3 58.9 + - + +
205D THR 4.9 1.4 - - - +
235D GLY 5.3 0.2 - - - +
238D PRO* 4.5 5.5 + - - +
239D ALA* 3.4 43.2 - - + +
242D LYS* 3.3 46.6 + - + +
243D MET* 3.7 9.8 - - - +
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Residues in contact with ASN 204 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165D GLN* 5.5 4.9 + - - +
200D ARG* 3.3 32.7 + - - +
201D THR* 3.6 11.3 + - - +
203D GLN* 1.3 76.7 - - + +
205D THR* 1.3 74.3 + - - +
206D ASN* 3.7 12.3 + - - -
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Residues in contact with THR 205 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165D GLN* 4.9 12.8 + - - +
168D VAL* 5.5 0.7 - - - +
201D THR* 3.0 23.5 + - - +
202D MET 3.6 11.9 - - - +
203D GLN 4.9 1.4 - - - +
204D ASN* 1.3 84.0 - - - +
206D ASN* 1.3 65.1 + - - +
207D ASP* 3.2 26.5 + - - +
210D THR* 3.5 22.6 - - + +
211D ALA* 3.8 22.7 - - + +
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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