Contacts of the strand formed by residues 193 - 201 (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 GLY 193 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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252C TRP 3.0 8.6 + - - -
40F HIS* 2.8 34.7 + - - -
41F PHE* 4.2 14.3 + - - -
42F CYS* 3.9 7.6 - - - -
43F GLY* 4.0 1.0 + - - -
141F TRP 4.6 0.9 + - - -
142F GLY* 3.6 11.0 + - - -
192G MET* 1.3 71.7 - - - +
194G ASP* 1.3 61.2 + - - +
195G SER 3.3 2.2 - - - -
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Residues in contact with ASP 194 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16F ILE* 2.6 41.2 + - - +
43F GLY* 4.2 2.7 + - - -
138F THR* 5.9 0.2 - - - -
139F THR 4.9 2.6 - - - +
140F GLY* 3.3 22.5 - - - -
142F GLY* 3.0 18.9 + - - -
190G SER* 3.5 3.5 - - - -
191G CYS 2.7 31.2 + - - +
193G GLY* 1.3 75.9 - - - +
195G SER* 1.3 65.6 + - - +
197G GLY* 3.1 16.8 + - - -
213G VAL* 3.2 23.2 - - + +
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Residues in contact with SER 195 (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* 2.0 55.1 + - - +
42F CYS* 3.3 19.5 - - - +
43F GLY 2.7 29.6 + - - -
57F HIS* 3.0 23.7 + - - -
58F CYS* 3.9 2.0 - - - -
193G GLY 3.3 0.6 - - - -
194G ASP* 1.3 76.7 - - - +
196G GLY* 1.3 53.9 + - - +
213G VAL* 3.5 9.3 - - - +
214G SER 3.4 0.5 + - - -
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Residues in contact with GLY 196 (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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43F GLY 3.2 12.3 - - - +
44F GLY* 3.5 10.9 - - - -
45F SER* 4.5 0.7 + - - -
53F VAL 3.7 2.1 - - - +
54F THR* 3.4 17.0 - - - -
55F ALA* 3.4 28.1 - - - +
58F CYS* 4.2 0.2 - - - -
195G SER* 1.3 70.2 - - - +
197G GLY* 1.3 63.6 + - - +
212G ILE* 3.6 11.4 - - - +
213G VAL 2.8 13.3 + - - -
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Residues in contact with GLY 197 (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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30F GLN* 4.5 1.6 - - - -
43F GLY* 3.6 14.5 - - - -
44F GLY 3.9 0.9 - - - -
45F SER* 4.4 1.6 - - - -
139F THR 4.7 1.8 - - - -
194G ASP 3.1 16.5 + - - -
195G SER 3.2 1.6 + - - -
196G GLY* 1.3 80.8 - - - +
198G PRO* 1.3 72.1 - - - +
209G LEU* 5.2 0.2 - - - -
212G ILE* 3.3 6.3 - - - +
213G VAL* 2.8 29.5 + - - +
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Residues in contact with PRO 198 (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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29F TRP* 4.1 15.7 - - + +
30F GLN* 3.4 22.0 - - - +
44F GLY 4.2 1.1 - - - +
45F SER* 3.1 23.8 - - - +
137F VAL 4.4 0.2 - - - -
138F THR* 2.8 34.6 + - - -
139F THR* 3.3 21.6 + - + +
197G GLY* 1.3 86.2 - - - +
199G LEU* 1.3 57.1 + - - +
200G VAL* 3.9 14.8 - - + -
209G LEU* 3.3 17.7 - - + -
213G VAL* 4.6 0.7 - - - -
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Residues in contact with LEU 199 (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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136F CYS* 3.9 15.9 - - + -
137F VAL 3.5 9.6 - - - +
138F THR* 4.2 4.0 - - - -
160G LEU* 3.6 34.1 - - + -
162G LEU* 3.9 13.9 - - + -
181G ILE* 4.8 4.5 - - + -
183G ALA* 3.8 22.2 - - + -
198G PRO* 1.3 72.5 - - - +
200G VAL* 1.3 57.6 - - - +
209G LEU* 3.7 2.3 - - - -
210G VAL* 2.9 30.7 + - + -
211G GLY* 3.0 28.7 + - - +
228G TYR* 3.8 30.5 - - + -
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Residues in contact with VAL 200 (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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27F TRP* 4.3 14.8 - - + -
29F TRP* 3.9 15.7 - - + +
121F VAL* 3.5 33.4 - - + -
136F CYS* 3.0 2.3 - - - +
137F VAL* 2.7 53.0 + - + +
139F THR* 5.9 2.0 - - + -
198G PRO* 4.1 6.3 - - + -
199G LEU* 1.3 77.6 - - - +
201G CYS* 1.3 63.8 + - - +
207G TRP* 3.5 28.3 - - + -
208G THR 3.1 10.8 - - - +
209G LEU* 4.0 8.1 - - + -
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Residues in contact with CYS 201 (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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130F PHE* 4.5 11.1 - - + -
134F THR* 4.9 7.0 - - + -
135F THR 5.0 0.4 - - - +
136F CYS* 2.0 49.4 - - - +
162G LEU* 4.1 4.5 - - - -
199G LEU* 5.2 0.4 - - - -
200G VAL* 1.3 73.4 - - - +
202G LYS* 1.3 63.4 + - - +
203G LYS* 3.9 1.8 + - + +
206G ALA 3.6 1.0 - - - +
207G TRP* 3.5 4.3 - - - -
208G THR* 2.9 32.6 + - - +
210G VAL* 3.4 38.8 - - + -
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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