Contacts of the helix formed by residues 191 - 199 (chain C) in PDB entry 3GBA
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 SER 191 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108C LEU* 3.5 7.1 - - - -
109C GLY 2.8 33.5 + - - -
111C SER* 5.1 0.4 - - - -
189C MET 3.6 0.6 + - - -
190C GLU* 1.3 72.6 - - - +
192C THR* 1.3 58.8 + - - +
194C ILE* 3.6 13.7 - - - +
195C GLU* 2.9 29.7 + - - +
206C GLN* 4.2 6.8 - - - +
210C LEU* 3.7 28.2 - - - +
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Residues in contact with THR 192 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16C TYR* 3.3 14.3 + - - +
106C MET* 3.6 23.8 - - + -
107C THR 3.4 26.0 - - - +
108C LEU* 3.8 6.8 - - + +
190C GLU* 3.9 5.9 - - - +
191C SER* 1.3 75.2 + - - +
193C SER* 1.3 64.7 + - - +
195C GLU* 3.5 6.6 + - - +
196C TYR* 3.3 8.3 + - - +
216C TYR* 2.8 24.2 + - + -
247C LYS* 4.4 9.9 - - - +
251C TRP* 3.0 29.7 + - - +
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Residues in contact with SER 193 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13C GLU* 4.1 5.7 + - - -
14C GLU 5.0 5.6 + - - -
15C PRO* 6.1 0.2 - - - -
16C TYR* 4.5 6.7 - - - -
189C MET* 3.9 22.0 - - - -
190C GLU 3.0 8.6 + - - -
192C THR* 1.3 77.1 + - - +
194C ILE* 1.3 66.1 + - - +
196C TYR* 3.2 7.0 + - - +
197C VAL* 3.0 29.0 + - - +
251C TRP* 5.7 0.2 - - - -
258C DYH 2.7 38.9 + - - -
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Residues in contact with ILE 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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111C SER* 3.7 31.4 - - - -
112C ILE 3.7 11.9 - - - +
113C LEU* 4.3 9.0 - - + -
189C MET* 3.3 41.5 - - + +
190C GLU 3.0 15.8 + - - +
191C SER* 3.3 8.0 + - - +
193C SER* 1.3 75.9 - - - +
195C GLU* 1.3 56.5 + - - +
197C VAL* 4.6 2.0 - - - -
198C THR* 2.8 51.3 + - + +
206C GLN* 3.8 30.7 - - + +
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Residues in contact with GLU 195 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191C SER 2.9 18.0 + - - +
192C THR* 3.6 6.0 - - - +
193C SER 3.3 0.2 - - - -
194C ILE* 1.3 76.6 - - - +
196C TYR* 1.3 62.9 + - - +
198C THR* 3.8 5.2 - - - -
199C GLN* 3.1 39.5 + - + +
200C ARG* 4.5 0.2 + - - -
247C LYS* 3.6 24.4 + - - -
251C TRP* 3.8 22.3 + - + +
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Residues in contact with TYR 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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14C GLU* 3.9 33.3 + - + +
15C PRO* 3.5 39.9 - - + +
18C MET* 4.7 8.0 - - - +
192C THR 3.3 4.6 + - - +
193C SER* 3.2 10.4 + - - +
195C GLU* 1.3 80.3 - - - +
197C VAL* 1.3 71.0 + - + +
200C ARG* 2.9 73.7 + - - +
250C TRP 3.4 21.7 + - - -
251C TRP* 3.7 20.8 - + - +
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Residues in contact with VAL 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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113C LEU* 4.0 24.2 - - + -
177C ILE* 3.6 35.4 - - + -
189C MET* 4.3 7.9 - - + -
193C SER* 3.0 20.5 + - - +
194C ILE* 3.9 4.7 - - - +
196C TYR* 1.3 83.4 - - + +
198C THR* 1.3 65.8 + - - +
200C ARG* 3.0 3.4 + - - -
201C ASN* 2.9 43.6 + - - +
204C LEU* 4.1 12.1 - - + -
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Residues in contact with THR 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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113C LEU* 3.6 25.1 - - + -
194C ILE* 2.8 35.1 + - + +
195C GLU* 3.4 9.0 + - - -
197C VAL* 1.3 73.0 - - - +
199C GLN* 1.3 73.6 + - - +
200C ARG 3.1 0.6 + - - -
201C ASN* 3.2 22.5 + - - +
202C CYS* 4.1 0.2 - - - -
204C LEU* 3.9 9.1 - - - +
205C THR* 3.7 24.7 - - - +
206C GLN* 4.0 1.1 - - + +
256C CYS* 3.4 12.6 - - - -
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Residues in contact with GLN 199 (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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195C GLU* 3.1 29.7 + - + +
197C VAL 3.2 0.8 - - - -
198C THR* 1.3 88.3 + - - +
200C ARG* 1.3 75.0 + - - +
202C CYS* 4.7 0.7 - - - -
251C TRP 5.6 1.8 - - - +
253C GLY* 6.1 0.8 - - - -
254C ASN 5.4 0.2 + - - -
255C GLY* 3.4 47.9 + - - +
256C CYS* 3.9 16.4 - - - +
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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