Contacts of the helix formed by residues 194 - 205 (chain A) in PDB entry 4G1T
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 ALA 194 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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192A GLN* 3.0 6.7 + - - +
193A ASN* 1.3 71.5 - - - +
195A ILE* 1.3 55.1 + - - +
196A ASP 2.7 10.1 + - - -
197A PRO* 2.5 26.3 - - - +
198A LEU* 3.1 20.0 + - + +
218A LYS* 4.3 14.1 - - + +
179B ALA 5.0 0.4 - - - +
182B SER* 3.5 42.1 - - - +
183B TYR* 3.7 9.9 - - - +
186B ASP* 4.8 1.3 - - + -
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Residues in contact with ILE 195 (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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193A ASN* 4.7 5.4 - - - +
194A ALA* 1.3 77.6 - - - +
196A ASP* 1.3 74.9 + - - +
198A LEU* 4.0 11.1 - - - +
199A ARG* 3.0 38.1 + - - +
215A LEU* 4.0 13.8 - - + +
218A LYS* 4.1 30.2 - - + +
219A LEU* 3.6 29.8 - - + -
222A MET* 5.2 7.9 - - + -
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Residues in contact with ASP 196 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193A ASN* 3.4 27.6 + - - +
194A ALA 2.7 5.3 + - - -
195A ILE* 1.3 80.9 - - - +
197A PRO* 1.4 63.4 - - + +
198A LEU 3.1 1.3 - - - -
199A ARG* 2.6 30.4 + - - +
200A GLN* 2.9 23.2 + - + +
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Residues in contact with PRO 197 (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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193A ASN 3.0 17.3 - - - +
194A ALA* 2.5 28.7 - - - +
196A ASP* 1.4 79.9 - - + +
198A LEU* 1.3 54.6 + - - +
200A GLN* 3.1 24.3 - - + +
201A ALA* 2.8 32.2 + - - +
175B THR* 4.0 3.4 - - + +
178B LEU* 4.1 22.4 - - + -
179B ALA* 3.6 15.0 - - - +
182B SER* 4.5 10.1 - - - +
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Residues in contact with LEU 198 (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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194A ALA* 3.1 24.6 + - + +
195A ILE* 4.0 9.0 - - - +
196A ASP 3.0 0.4 + - - -
197A PRO* 1.3 77.7 - - - +
199A ARG* 1.3 51.9 + - - +
201A ALA* 3.4 1.4 + - - +
202A ILE* 2.8 43.8 + - - +
211A LEU* 3.5 30.7 - - + +
214A LEU* 3.5 42.2 - - + +
215A LEU* 3.9 12.3 - - + +
218A LYS* 4.6 4.9 - - + -
179B ALA* 3.8 25.3 - - + +
183B TYR* 4.1 17.0 - - + -
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Residues in contact with ARG 199 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195A ILE* 3.0 26.1 + - - +
196A ASP* 2.6 19.3 + - - +
198A LEU* 1.3 71.6 - - - +
200A GLN* 1.3 56.6 + - - +
202A ILE* 3.4 9.3 + - - +
203A ARG* 3.0 57.5 + - - +
215A LEU* 3.5 23.5 - - + +
219A LEU* 4.0 16.0 - - - +
231A GLU* 2.8 44.8 + - - -
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Residues in contact with GLN 200 (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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196A ASP* 2.9 21.4 + - + +
197A PRO* 3.1 35.5 - - + +
199A ARG* 1.3 76.9 - - + +
201A ALA* 1.3 61.9 + - - +
203A ARG* 3.3 21.7 - - - +
204A LEU* 3.1 29.0 + - + +
26B GLU* 5.9 1.4 + - - -
175B THR* 4.1 12.5 - - + +
178B LEU* 5.1 4.6 - - - +
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Residues in contact with ALA 201 (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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197A PRO 2.8 23.7 + - - +
198A LEU 3.5 4.0 - - - +
200A GLN* 1.3 71.7 - - - +
202A ILE* 1.3 60.6 + - - +
204A LEU* 3.0 6.3 + - - +
205A ASN* 2.8 31.5 + - - +
211A LEU* 4.1 12.7 - - + +
172B PRO 5.5 0.2 - - - -
175B THR* 3.7 22.7 - - + +
176B SER* 4.1 4.3 - - - +
179B ALA* 3.6 20.2 - - + -
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Residues in contact with ILE 202 (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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198A LEU 2.8 30.6 + - - +
199A ARG* 3.8 4.7 - - - +
201A ALA* 1.3 71.8 - - - +
203A ARG* 1.3 66.0 + - + +
205A ASN 4.2 7.0 - - - +
206A PRO* 3.4 20.1 - - + +
208A ASN 5.8 0.2 - - - +
211A LEU* 3.9 28.3 - - + +
212A LYS* 4.0 35.9 - - + +
215A LEU* 3.4 43.5 - - + -
235A LEU* 5.1 3.4 - - + -
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Residues in contact with ARG 203 (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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199A ARG* 3.0 51.0 + - - +
200A GLN* 3.3 22.5 - - - +
202A ILE* 1.3 80.0 - - + +
204A LEU* 1.3 64.4 + - + +
206A PRO* 3.9 8.3 - - - +
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Residues in contact with LEU 204 (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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200A GLN* 3.1 10.2 + - + +
201A ALA 3.0 6.7 + - - +
203A ARG* 1.3 79.3 - - + +
205A ASN* 1.3 79.8 + - - +
206A PRO* 3.4 7.6 - - - +
170B LYS* 3.9 24.0 - - + +
171B ASN 3.1 28.5 - - - +
172B PRO* 3.7 14.1 - - + +
175B THR* 3.5 27.8 - - + +
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Residues in contact with ASN 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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201A ALA 2.8 15.5 + - - +
202A ILE* 3.4 10.9 - - - +
204A LEU* 1.3 106.1 + - - +
206A PRO* 1.3 67.4 - - - +
207A ASP* 3.3 14.1 - - - +
208A ASN* 3.4 27.2 + - + +
211A LEU* 4.5 4.9 - - + +
212A LYS* 4.7 0.5 + - - -
172B PRO* 2.9 42.5 - - - +
173B GLU* 4.0 2.6 + - - -
176B SER* 4.3 10.9 + - - -
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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