Contacts of the helix formed by residues 231 - 245 (chain C) in PDB entry 2GCT
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 231 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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103B ILE* 5.3 7.4 - - + -
123B LEU* 4.2 15.7 - - + -
124B PRO* 3.7 14.4 - - + -
209C LEU* 3.5 30.7 - - + +
210C VAL 3.1 21.3 + - - +
211C GLY 4.0 1.8 - - - +
212C ILE* 3.9 32.5 - - + -
229C ALA* 4.0 6.1 - - + +
230C ARG* 1.3 70.5 - - - +
232C THR* 1.3 59.5 + - - +
234C LEU* 3.0 6.0 + - + +
235C VAL* 2.9 33.7 + - + +
238C VAL* 5.7 1.6 - - + -
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Residues in contact with THR 232 (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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124B PRO* 3.7 19.7 - - + -
125B SER 3.6 16.6 - - - +
126B ALA* 3.5 28.2 - - - +
128B ASP* 4.1 21.5 + - + +
130B PHE* 4.2 10.8 - - + -
210C VAL* 4.7 3.5 + - + +
230C ARG* 3.4 22.2 + - - +
231C VAL* 1.3 74.6 - - - +
233C ALA* 1.3 60.9 + - - +
234C LEU 3.4 0.5 + - - -
235C VAL* 3.5 21.3 + - - +
236C ASN* 5.0 1.7 + - - +
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Residues in contact with ALA 233 (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 ASP* 4.6 2.2 - - + +
179C ALA* 4.0 26.7 - - + +
230C ARG* 3.3 23.5 + - + +
231C VAL 3.1 0.6 - - - -
232C THR* 1.3 81.0 + - - +
234C LEU* 1.3 63.5 + - - +
236C ASN 5.3 1.2 + - - -
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Residues in contact with LEU 234 (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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91B ASN* 3.9 19.3 - - - +
101B ASN* 3.5 36.3 - - - +
103B ILE* 4.0 31.4 - - + -
179C ALA* 4.2 6.1 - - + +
229C ALA* 4.1 23.3 - - + -
230C ARG 3.2 22.0 - - - +
231C VAL* 3.0 6.8 + - + +
233C ALA* 1.3 87.1 - - + +
235C VAL* 1.4 62.1 + - - +
236C ASN 3.3 3.4 - - - -
237C TRP* 3.2 12.9 + - - +
238C VAL* 3.2 21.6 + - - +
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Residues in contact with VAL 235 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123B LEU* 4.1 20.2 - - + -
124B PRO* 3.6 20.9 - - + +
125B SER 4.1 0.4 - - - -
126B ALA* 3.7 27.6 - - + +
231C VAL* 2.9 15.5 + - + +
232C THR* 3.5 20.0 - - - +
233C ALA 3.7 0.2 - - - -
234C LEU* 1.4 73.8 - - - +
236C ASN* 1.4 70.5 + - - +
238C VAL* 3.2 9.0 + - + +
239C GLN* 3.0 43.2 + - + +
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Residues in contact with ASN 236 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126B ALA* 3.7 28.6 - - - +
232C THR 5.0 1.3 + - - +
233C ALA 5.3 1.4 + - - +
234C LEU 3.3 1.0 - - - -
235C VAL* 1.4 78.4 - - - +
237C TRP* 1.3 63.8 + - - +
239C GLN* 3.3 9.6 + - - +
240C GLN* 3.0 31.9 + - + +
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Residues in contact with TRP 237 (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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89B PHE* 3.4 28.9 - - + -
90B LYS 4.1 1.8 - - - -
91B ASN* 3.3 49.6 - - - +
103B ILE* 3.6 28.0 - - + -
105B LEU* 3.8 28.0 - - + -
600B SO4 3.1 40.9 + - - -
234C LEU* 3.2 10.4 + - - +
235C VAL 3.2 0.6 - - - -
236C ASN* 1.3 76.6 - - - +
238C VAL* 1.3 78.2 + - + +
240C GLN* 3.2 9.5 + - + +
241C THR* 2.8 40.6 + - - -
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Residues in contact with VAL 238 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B ILE* 4.0 17.7 - - + -
53B VAL* 4.9 3.4 - - + -
103B ILE* 3.8 25.6 - - + -
105B LEU* 3.9 25.6 - - + -
123B LEU* 4.1 14.8 - - + -
231C VAL* 5.7 2.7 - - + -
234C LEU 3.2 14.6 + - - +
235C VAL* 3.2 18.0 + - + +
237C TRP* 1.3 86.3 - - + +
239C GLN* 1.4 56.1 + - - +
241C THR* 3.3 1.9 + - - -
242C LEU* 2.9 36.4 + - + +
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Residues in contact with GLN 239 (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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123B LEU* 4.1 15.9 - - - +
124B PRO 5.2 0.3 - - - +
235C VAL* 3.0 33.4 + - + +
236C ASN* 3.7 11.9 - - - +
238C VAL* 1.4 70.0 - - - +
240C GLN* 1.3 63.1 + - + +
242C LEU* 3.9 21.2 - - - +
243C ALA* 2.8 34.1 + - - +
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Residues in contact with GLN 240 (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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236C ASN* 3.0 23.5 + - + +
237C TRP* 3.2 9.2 + - + +
239C GLN* 1.3 79.2 - - - +
241C THR* 1.3 56.9 + - - +
243C ALA* 3.6 7.4 - - - +
244C ALA* 2.9 33.0 + - - +
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Residues in contact with THR 241 (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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51B TRP* 4.2 6.1 - - + -
89B PHE* 3.7 35.7 - - + -
105B LEU* 3.5 27.8 - - + -
600B SO4 4.4 4.3 + - - +
237C TRP* 2.8 35.0 + - + -
238C VAL 3.6 0.9 - - - -
240C GLN* 1.3 72.7 - - - +
242C LEU* 1.3 66.7 + - - +
244C ALA* 4.8 0.7 - - - -
245C ASN* 2.8 38.4 + - - +
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Residues in contact with LEU 242 (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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47B ILE* 4.1 14.4 - - + -
48B ASN* 4.3 9.6 - - - +
51B TRP* 3.3 57.4 + - + +
105B LEU* 4.7 3.6 - - + -
123B LEU* 5.1 2.7 - - + -
238C VAL* 2.9 31.3 + - + +
239C GLN* 3.9 25.6 - - - +
241C THR* 1.3 77.1 - - - +
243C ALA* 1.4 60.8 - - - +
245C ASN* 3.2 20.8 + - - +
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Residues in contact with ALA 243 (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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239C GLN 2.8 19.8 + - - +
240C GLN* 3.6 11.0 - - - +
242C LEU* 1.4 77.8 - - - +
244C ALA* 1.3 58.7 + - - +
245C ASN* 3.6 2.6 + - - +
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Residues in contact with ALA 244 (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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240C GLN* 2.9 18.3 + - - +
243C ALA* 1.3 76.1 - - - +
245C ASN* 1.4 75.4 + - - +
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Residues in contact with ASN 245 (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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51B TRP* 3.7 23.1 + - + -
87B LYS* 5.6 0.7 + - - -
89B PHE* 3.3 34.1 - - + -
107B LYS* 3.1 30.6 + - - +
241C THR* 2.8 34.4 + - - +
242C LEU 3.2 12.4 + - - +
243C ALA 4.5 2.6 - - - +
244C ALA* 1.4 93.6 - - - +
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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