Contacts of the helix formed by residues 204 - 209 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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42A GLY* 3.4 11.9 - - - +
43A GLU* 4.4 7.7 + - - +
178A ARG* 4.1 4.9 - - - +
180A LYS* 4.2 8.7 - - + +
181A THR 4.4 1.0 - - - +
202A GLY 4.0 1.0 - - - -
203A GLY* 1.3 83.2 - - - +
205A ARG* 1.3 67.0 + - - +
206A SER* 3.1 5.6 - - - +
207A GLU* 2.7 15.7 + - - +
208A ARG* 3.2 11.2 + - - +
235A ALA* 5.9 4.8 - - + +
236A GLU* 3.4 30.3 + - + +
355A ALF 2.7 32.4 - - - -
137D ASN* 3.0 42.9 + - - +
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Residues in contact with ARG 205 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204A GLN* 1.3 70.0 - - - +
206A SER* 1.3 61.9 + - - +
208A ARG* 3.1 40.7 + - - +
209A LYS* 4.2 7.5 + - - +
234A LEU* 3.3 16.4 - - - +
236A GLU* 3.0 32.4 + - + +
237A ASP* 3.0 31.6 + - - +
240A MET* 3.8 10.1 - - - +
245A GLU* 3.0 31.7 + - - -
130D SER* 5.9 1.0 + - - -
135D GLN* 4.6 8.9 - - - +
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Residues in contact with SER 206 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204A GLN* 3.0 2.5 + - - +
205A ARG* 1.3 77.9 - - - +
207A GLU* 1.3 63.4 + - - +
209A LYS* 3.6 18.6 - - - +
210A LYS* 4.5 7.6 - - - +
236A GLU* 6.2 0.2 - - - +
135D GLN* 3.5 54.7 + - - +
136D ILE 3.8 5.2 - - - -
137D ASN* 3.2 34.9 + - - +
138D ILE 5.5 0.2 - - - -
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Residues in contact with GLU 207 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182A THR* 2.6 29.6 + - - -
183A GLY* 3.0 12.7 + - - +
202A GLY* 3.2 31.0 - - - +
204A GLN 2.7 15.9 + - - +
206A SER* 1.3 75.4 + - - +
208A ARG* 1.3 63.9 + - - +
209A LYS 3.4 0.9 - - - -
210A LYS* 2.8 53.4 + - + +
211A TRP* 3.3 7.9 - - - -
97D GLU* 4.5 1.8 - - - +
137D ASN* 3.1 39.0 + - - +
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Residues in contact with ARG 208 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41A ALA* 4.1 9.1 - - - +
42A GLY 4.5 0.2 - - - +
203A GLY 2.7 30.3 + - - +
204A GLN* 3.2 17.3 - - - +
205A ARG* 3.1 32.9 + - - +
207A GLU* 1.3 74.6 - - - +
209A LYS* 1.3 62.5 + - - +
210A LYS 2.9 6.6 + - - -
211A TRP* 3.0 59.5 + - + +
212A ILE* 4.5 1.9 + - - +
234A LEU* 6.0 0.4 - - - +
236A GLU* 4.3 3.0 + - - -
245A GLU* 2.5 40.2 + - - +
249A LEU* 3.7 32.1 - - - +
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Residues in contact with LYS 209 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205A ARG 4.2 4.6 + - - +
206A SER* 3.6 19.7 - - - +
208A ARG* 1.3 71.9 - - - +
210A LYS* 1.3 60.7 + - + +
211A TRP 3.3 0.4 - - - -
212A ILE* 3.6 25.2 - - - +
213A HIS* 5.1 1.6 - - - -
130D SER 3.5 9.5 + - - -
131D ASP* 4.4 5.5 + - - +
132D ALA 3.3 25.6 + - - +
133D ALA* 4.3 13.9 - - - +
135D GLN* 3.2 36.9 + - - +
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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