Contacts of the helix formed by residues 204 - 209 (chain B) in PDB entry 2GTP
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 GLN 204 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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42B GLY* 3.4 13.6 - - - +
43B GLU* 4.7 3.2 - - - +
178B ARG* 4.1 5.9 - - - +
180B LYS* 4.1 10.3 - - + +
181B THR 4.2 2.6 - - - +
202B GLY 3.7 0.8 - - - -
203B GLY* 1.3 79.6 + - - +
205B ARG* 1.3 68.1 + - - +
206B SER* 4.2 4.5 - - - +
207B GLU* 2.7 17.2 + - + +
208B ARG* 3.1 10.0 + - - +
235B ALA* 6.1 4.2 - - + +
236B GLU* 3.5 29.8 + - + +
355B ALF 2.9 31.4 - - - -
137C ASN* 2.8 48.8 + - - +
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Residues in contact with ARG 205 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204B GLN* 1.3 68.5 - - - +
206B SER* 1.3 63.2 + - - +
208B ARG* 3.1 34.0 + - - +
209B LYS* 4.3 4.2 + - - -
234B LEU* 3.5 16.2 - - - +
236B GLU* 3.1 28.3 + - + +
237B ASP* 3.0 30.7 + - - +
240B MET* 3.6 17.8 - - - +
245B GLU* 2.9 39.8 + - - +
135C GLN* 4.5 8.6 - - - +
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Residues in contact with SER 206 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204B GLN* 4.2 2.0 - - - +
205B ARG* 1.3 78.0 - - - +
207B GLU* 1.3 63.8 + - - +
208B ARG 3.6 0.2 + - - -
209B LYS* 3.7 21.8 - - - +
210B LYS* 4.7 5.9 - - - +
236B GLU* 5.4 1.5 - - - +
97C GLU* 5.0 1.2 + - - -
135C GLN* 3.4 47.8 + - - +
136C ILE 3.9 10.1 - - - -
137C ASN* 3.4 33.1 + - - +
138C ILE 5.3 0.2 - - - -
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Residues in contact with GLU 207 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181B THR 4.2 0.2 - - - -
182B THR* 2.8 31.0 + - - -
183B GLY* 2.9 22.1 + - - +
202B GLY* 3.2 33.0 - - - +
204B GLN* 2.7 16.6 + - - +
206B SER* 1.3 75.4 + - - +
208B ARG* 1.3 56.2 + - - +
209B LYS 3.4 0.4 - - - -
210B LYS* 2.9 50.6 + - - +
211B TRP* 3.4 7.0 - - - -
97C GLU* 4.5 0.7 - - - +
137C ASN* 3.1 38.1 + - - +
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Residues in contact with ARG 208 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41B ALA* 4.1 10.9 - - - +
203B GLY 2.6 32.3 + - - +
204B GLN* 3.1 16.5 - - - +
205B ARG* 3.1 30.7 + - - +
207B GLU* 1.3 73.6 - - - +
209B LYS* 1.3 62.6 + - - +
210B LYS 2.9 6.3 + - - -
211B TRP* 3.0 57.8 + - + +
212B ILE 4.6 0.3 + - - -
234B LEU* 5.6 0.4 - - - +
236B GLU* 4.4 3.0 + - - -
245B GLU* 2.5 36.8 + - - +
249B LEU* 3.7 32.0 - - + +
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Residues in contact with LYS 209 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205B ARG 4.3 4.5 + - - -
206B SER* 3.7 19.1 - - - +
208B ARG* 1.3 76.9 - - - +
210B LYS* 1.3 71.8 + - + +
211B TRP 3.3 0.6 + - - -
212B ILE* 3.9 16.7 - - - +
213B HIS* 4.9 2.1 + - - -
130C SER 5.0 1.0 + - - -
131C ASP* 4.8 3.2 + - - +
132C ALA 2.6 31.1 + - - -
133C ALA* 3.7 19.8 - - - +
135C GLN* 3.9 19.5 + - - +
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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