Contacts of the strand formed by residues 193 - 201 (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 GLY 193 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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40B HIS 5.8 1.8 - - - -
41B PHE 4.2 14.5 - - - +
42B CYS* 4.2 15.2 + - - -
43B GLY* 4.3 2.6 + - - -
141B TRP* 4.5 5.4 + - - +
142B GLY* 3.6 14.7 + - - -
192C MET* 1.3 73.6 - - - +
194C ASP* 1.3 59.8 + - - -
195C SER 3.4 1.3 + - - -
504D TYR 2.5 17.6 + - - -
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Residues in contact with ASP 194 (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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16B ILE* 2.7 38.1 + - - +
43B GLY* 4.3 2.7 + - - -
138B THR* 5.9 0.2 - - - +
139B THR 5.0 2.4 - - - +
140B GLY* 3.3 22.6 - - - -
141B TRP 5.2 0.7 - - - +
142B GLY* 2.8 25.2 + - - -
190C SER* 3.6 3.5 - - - +
191C CYS* 2.8 32.9 + - - +
193C GLY* 1.3 77.4 - - - +
195C SER* 1.4 64.3 + - - +
197C GLY* 3.0 18.0 + - - -
213C VAL* 3.6 19.4 - - + +
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Residues in contact with SER 195 (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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42B CYS* 3.5 19.9 - - - -
43B GLY 3.0 17.8 + - - -
57B HIS* 3.4 24.1 + - - -
58B CYS* 4.0 0.7 - - - -
193C GLY 3.4 1.0 - - - -
194C ASP* 1.4 76.7 - - - +
196C GLY* 1.3 59.1 + - - +
213C VAL* 3.3 11.1 - - - +
214C SER 3.8 0.2 + - - -
504D TYR* 1.6 52.9 + - - +
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Residues in contact with GLY 196 (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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43B GLY 3.3 12.0 - - - +
44B GLY* 3.5 9.7 - - - -
45B SER* 4.6 0.5 + - - -
53B VAL* 3.9 1.7 - - - +
54B THR* 3.4 25.2 - - - -
55B ALA* 3.5 17.6 - - - +
58B CYS* 4.3 0.4 - - - -
195C SER* 1.3 71.5 - - - +
197C GLY* 1.3 63.1 + - - +
212C ILE* 3.6 11.5 - - - +
213C VAL 2.7 15.7 + - - -
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Residues in contact with GLY 197 (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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30B GLN* 4.5 2.0 - - - -
43B GLY* 3.7 13.8 - - - -
44B GLY* 4.0 1.1 - - - -
45B SER* 4.6 0.9 - - - -
139B THR 4.7 2.0 - - - -
194C ASP 3.0 17.7 + - - -
195C SER 3.2 0.8 + - - -
196C GLY* 1.3 79.9 - - - +
198C PRO* 1.3 72.5 - - - +
212C ILE* 3.5 5.2 - - - -
213C VAL* 2.8 29.9 + - - +
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Residues in contact with PRO 198 (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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29B TRP* 4.1 17.7 - - + +
30B GLN* 3.4 22.4 - - - +
44B GLY 4.2 1.1 - - - +
45B SER* 3.2 23.5 - - - +
138B THR* 2.9 28.3 + - - -
139B THR* 3.5 19.9 + - - +
197C GLY* 1.3 86.0 - - - +
199C LEU* 1.4 60.6 + - - +
200C VAL* 3.9 12.8 - - + -
209C LEU* 3.5 18.6 - - + -
211C GLY 3.9 0.7 - - - +
212C ILE* 5.8 0.2 - - + -
213C VAL* 4.7 0.7 - - - -
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Residues in contact with LEU 199 (chain C).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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136B CYS* 4.1 15.7 - - + -
137B VAL 3.3 14.4 - - - +
138B THR* 4.2 4.9 - - - -
160C LEU* 3.9 25.4 - - + -
162C LEU* 3.8 22.9 - - + -
181C ILE* 4.7 4.0 - - + -
183C ALA* 4.4 10.3 - - + -
198C PRO* 1.4 73.3 - - - +
200C VAL* 1.3 59.4 + - - +
209C LEU* 4.0 0.5 - - - +
210C VAL* 3.0 31.6 + - + +
211C GLY* 3.0 32.6 + - - +
228C TYR* 3.9 33.9 - - + -
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Residues in contact with VAL 200 (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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27B TRP* 4.2 11.4 - - + -
29B TRP* 4.2 14.4 - - + +
121B VAL* 3.7 27.4 - - + -
136B CYS* 2.9 2.9 - - - +
137B VAL* 2.5 57.5 + - + +
139B THR* 6.1 1.6 - - + -
198C PRO* 4.2 11.7 - - + -
199C LEU* 1.3 75.6 - - - +
201C CYS* 1.4 62.6 + - - +
207C TRP* 3.5 30.6 - - + -
208C THR 3.3 13.7 - - - +
209C LEU* 4.2 3.1 - - - +
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Residues in contact with CYS 201 (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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130B PHE* 4.1 14.4 - - + -
134B THR* 4.7 5.6 - - + -
135B THR 5.1 0.7 - - - +
136B CYS* 2.0 48.2 - - - +
162C LEU* 4.2 7.6 - - - -
199C LEU* 5.0 0.7 - - - -
200C VAL* 1.4 72.5 - - - +
202C LYS* 1.4 63.2 - - - +
203C LYS 3.6 0.2 + - - -
207C TRP* 3.8 5.4 - - - -
208C THR* 2.6 41.9 + - - +
210C VAL* 3.7 33.7 - - + -
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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