Contacts of the strand formed by residues 212 - 218 (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 ILE 212 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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53B VAL* 4.7 11.0 - - + -
54B THR 4.1 4.9 - - - +
55B ALA* 4.0 15.7 - - + +
102B ASP 4.3 2.0 - - - +
103B ILE* 3.6 43.3 - - + -
196C GLY* 3.6 31.4 - - - +
197C GLY 3.5 3.8 - - - +
209C LEU* 4.6 10.1 - - + -
211C GLY* 1.3 76.5 - - - +
213C VAL* 1.4 68.4 + - - +
214C SER* 3.1 2.1 + - - -
228C TYR* 3.2 3.1 - - - -
229C ALA* 2.8 39.9 + - + +
231C VAL* 3.9 16.4 - - + -
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Residues in contact with VAL 213 (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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55B ALA* 3.9 4.2 - - - +
138B THR* 3.7 15.7 - - - +
139B THR 5.2 1.6 - - - +
190C SER* 3.8 16.4 - - - +
194C ASP* 3.6 22.2 - - + +
195C SER* 3.3 21.3 - - - +
196C GLY* 2.7 25.5 + - - -
197C GLY* 2.8 26.4 + - - +
198C PRO 4.4 0.7 - - - +
212C ILE* 1.4 71.0 - - - +
214C SER* 1.3 60.8 + - - +
227C VAL 5.2 0.2 - - - +
228C TYR* 3.5 27.1 - - + -
504D TYR* 3.8 24.7 - - + -
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Residues in contact with SER 214 (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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57B HIS* 3.3 12.0 - - - -
99B ILE* 3.7 5.0 + - - +
102B ASP* 2.6 33.0 + - - +
180C MET* 6.1 1.2 - - - +
212C ILE 3.1 8.6 + - - -
213C VAL* 1.3 74.8 - - - +
215C TRP* 1.3 78.2 + - - +
227C VAL* 3.2 18.9 + - - -
228C TYR 4.1 0.9 - - - -
229C ALA* 4.0 9.0 - - - -
504D TYR* 3.0 23.4 + - - +
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Residues in contact with TRP 215 (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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98B THR 4.5 3.1 + - - -
99B ILE* 4.0 24.7 - - + +
172C TRP* 3.4 43.7 - + - -
175C LYS* 3.8 36.8 - - + -
176C ILE* 3.9 7.9 - - + -
180C MET* 3.8 15.1 - - + +
214C SER* 1.3 99.8 - - - +
216C GLY* 1.3 76.8 + - - +
227C VAL* 2.9 60.9 + - + +
501D PRO* 3.5 22.7 - - + -
502D GLY 3.3 17.5 - - - +
503D ALA* 3.9 7.9 - - + -
504D TYR* 3.7 14.4 - - - -
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Residues in contact with GLY 216 (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 TRP* 3.8 13.7 - - - -
215C TRP* 1.3 87.3 - - - +
217C SER* 1.3 59.3 + - - +
226C GLY* 4.6 4.9 - - - -
227C VAL* 4.6 4.5 - - - -
501D PRO* 3.4 3.6 - - - +
502D GLY 2.6 32.6 + - - +
504D TYR* 3.4 11.2 - - - -
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Residues in contact with SER 217 (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 TRP* 3.6 14.2 - - - -
189C SER* 6.0 0.2 - - - -
216C GLY* 1.3 74.5 - - - +
218C SER* 1.3 62.3 + - - +
219C THR* 3.1 13.5 + - - -
220C CYS 3.4 3.3 + - - -
221C SER* 2.9 35.0 + - - -
224C THR* 4.2 23.1 - - - -
225C PRO 5.0 1.4 + - - -
501D PRO* 4.5 0.4 - - - -
504D TYR* 3.3 25.2 + - - -
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Residues in contact with SER 218 (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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146B TYR* 3.7 13.6 - - - -
192C MET* 3.6 25.4 - - - +
216C GLY 3.7 1.2 + - - -
217C SER* 1.3 72.1 + - - +
219C THR* 1.3 69.7 + - - +
220C CYS 3.5 0.4 - - - -
501D PRO* 4.2 16.5 - - - +
502D GLY* 4.1 12.5 - - - +
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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