Contacts of the strand formed by residues 212 - 218 (chain G) in PDB entry 8GCH
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 G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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53F VAL* 3.1 35.9 - - + -
54F THR 3.8 11.4 - - - +
55F ALA* 3.8 6.3 - - + +
102F ASP 4.3 2.0 - - - +
103F ILE* 3.4 31.0 - - + -
196G GLY* 3.6 31.9 - - - +
197G GLY 3.3 4.0 - - - +
209G LEU* 4.0 8.5 - - + -
211G GLY* 1.3 77.8 - - - +
213G VAL* 1.3 74.0 + - - +
214G SER* 2.9 2.3 + - - -
228G TYR* 3.2 4.5 - - - +
229G ALA* 2.9 39.1 + - + +
231G VAL* 4.1 10.1 - - + -
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Residues in contact with VAL 213 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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252C TRP* 4.1 12.1 - - + -
55F ALA* 3.8 6.9 - - - +
138F THR* 3.6 24.0 - - - +
139F THR 4.9 2.0 - - - +
190G SER* 3.9 16.8 - - - +
194G ASP* 3.2 47.1 - - + +
195G SER* 3.5 8.4 - - - +
196G GLY* 2.8 24.9 + - - +
197G GLY* 2.8 25.5 + - - +
198G PRO 4.2 0.7 - - - +
211G GLY 4.2 0.2 - - - -
212G ILE* 1.3 69.9 - - - +
214G SER* 1.3 59.7 + - - +
228G TYR* 3.6 16.0 - - + -
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Residues in contact with SER 214 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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252C TRP* 3.0 13.2 + - - -
57F HIS* 2.8 24.3 - - - -
99F ILE* 3.6 2.9 + - - +
102F ASP* 2.6 34.1 + - - +
180G MET* 5.9 1.5 - - - +
195G SER* 3.4 0.9 + - - -
212G ILE 2.9 9.0 + - - -
213G VAL* 1.3 75.8 - - - +
215G TRP* 1.3 77.2 + - - +
227G VAL 3.1 17.1 + - - -
228G TYR* 3.9 6.7 - - - -
229G ALA* 3.9 6.1 - - - -
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Residues in contact with TRP 215 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250C GLY 3.3 25.8 - - - +
251C ALA* 3.9 3.6 - - - -
252C TRP* 3.3 15.1 - - - +
98F THR 5.3 1.1 - - - -
99F ILE* 3.9 24.6 - - + +
172G TRP* 3.5 43.3 - + + -
175G LYS* 3.7 35.7 - - + -
176G ILE* 4.0 5.4 - - + -
180G MET* 3.8 21.4 - - + +
214G SER* 1.3 93.5 - - - +
216G GLY* 1.3 72.9 + - - +
227G VAL* 2.7 69.7 + - + +
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Residues in contact with GLY 216 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250C GLY 2.9 28.5 + - - -
252C TRP* 3.3 14.8 - - - -
172G TRP* 3.6 18.4 - - - -
215G TRP* 1.3 89.9 - - - +
217G SER* 1.3 63.4 + - - -
218G SER 3.5 0.2 + - - -
225G PRO 4.4 4.9 - - - -
227G VAL 4.5 0.4 - - - -
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Residues in contact with SER 217 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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252C TRP* 3.1 23.1 + - - -
172G TRP* 3.5 15.0 - - - -
216G GLY* 1.3 71.0 - - - -
218G SER* 1.3 58.9 + - - +
219G THR* 2.9 16.6 + - - +
220G CYS* 3.0 15.6 + - - -
221G SER* 3.2 29.6 + - - -
224G THR* 3.1 27.2 + - - +
225G PRO 4.8 0.2 + - - -
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Residues in contact with SER 218 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250C GLY* 4.1 20.4 - - - +
252C TRP* 5.2 0.7 - - - +
146F TYR* 3.0 29.9 + - - -
172G TRP* 5.2 0.8 - - - -
192G MET* 4.4 7.1 - - - +
216G GLY 3.5 2.6 + - - -
217G SER* 1.3 72.5 + - - +
219G THR* 1.3 61.1 + - - +
220G CYS* 3.6 1.6 - - - -
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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