Contacts of the helix formed by residues 203 - 214 (chain A) in PDB entry 4GJ0
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 203 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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171A GLN* 4.6 6.6 + - - -
201A ILE* 4.2 0.2 - - - +
202A HIS* 1.3 80.3 - - - +
204A PRO* 1.3 70.8 - - - +
205A GLU* 3.5 16.0 + - - +
206A GLU* 3.1 24.3 + - - +
207A GLN* 3.0 28.1 + - - +
242A TYR* 3.7 13.2 - - - -
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Residues in contact with PRO 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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203A SER* 1.3 90.9 - - - +
205A GLU* 1.3 66.2 + - - +
207A GLN* 3.3 1.2 + - - +
208A ASP* 2.7 46.2 + - - +
242A TYR* 3.8 28.3 - - + +
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Residues in contact with GLU 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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170A PHE* 3.5 24.1 - - + -
171A GLN* 4.3 10.6 + - - +
203A SER* 3.5 19.8 - - - +
204A PRO* 1.3 89.4 - - - +
206A GLU* 1.3 58.5 + - - +
208A ASP* 3.5 8.7 + - - +
209A PHE 3.1 21.8 + - - -
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Residues in contact with GLU 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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170A PHE* 3.6 15.2 - - + -
171A GLN* 4.9 4.0 - - - +
173A LYS* 2.8 23.8 + - - +
175A TYR* 2.5 35.9 + - + +
200A SER 3.4 10.2 - - - +
201A ILE* 3.5 7.9 - - + -
202A HIS* 2.8 37.6 + - - +
203A SER* 3.1 21.1 + - - +
205A GLU* 1.3 74.3 - - - +
207A GLN* 1.3 65.6 + - - +
209A PHE* 3.3 3.9 + - + +
210A LEU* 3.0 31.4 + - + +
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Residues in contact with GLN 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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201A ILE* 3.7 14.7 - - - +
203A SER 3.0 13.5 + - - +
204A PRO 3.6 2.7 - - - +
206A GLU* 1.3 76.3 - - - +
208A ASP* 1.3 60.6 + - - +
210A LEU* 3.0 4.5 + - - +
211A THR* 2.8 55.5 + - - +
242A TYR* 3.2 28.7 - - + +
244A ASN* 3.4 21.3 - - - +
262A MET* 3.6 18.2 - - - -
266A GLY 3.2 13.9 + - - -
268A TRP* 2.9 28.4 + - - -
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Residues in contact with ASP 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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204A PRO* 2.7 31.2 + - - +
205A GLU* 3.7 9.1 - - - +
207A GLN* 1.3 74.9 - - - +
209A PHE* 1.3 61.3 + - - +
211A THR* 3.4 6.3 + - - -
212A LYS* 2.8 51.7 + - - +
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Residues in contact with PHE 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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168A ILE* 3.8 28.0 - - + -
169A ASN 4.1 3.1 - - - -
170A PHE* 3.7 45.3 - + + -
175A TYR* 3.6 32.3 - + - -
177A PHE* 3.8 17.9 - + - -
205A GLU 3.1 15.0 + - - +
206A GLU 3.5 8.3 - - - +
208A ASP* 1.3 76.4 - - - +
210A LEU* 1.3 71.6 + - + +
212A LYS* 3.2 11.1 + - + +
213A HIS* 3.1 50.8 + + - -
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Residues in contact with LEU 210 (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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175A TYR* 3.8 26.9 - - + -
177A PHE* 3.9 20.3 - - + -
199A VAL* 4.1 12.8 - - + -
201A ILE* 3.5 43.3 - - + -
206A GLU* 3.0 23.3 + - + +
207A GLN* 3.5 11.7 - - - +
209A PHE* 1.3 80.9 - - + +
211A THR* 1.3 62.7 + - - +
213A HIS* 3.0 3.3 + - - +
214A ALA* 2.8 32.2 + - - +
262A MET* 4.2 11.0 - - + -
281A VAL* 4.3 8.7 - - + -
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Residues in contact with THR 211 (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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207A GLN* 2.8 40.3 + - - +
208A ASP* 3.7 9.5 + - - -
210A LEU* 1.3 72.3 - - - +
212A LYS* 1.3 65.1 + - + +
213A HIS 3.3 0.5 + - - -
214A ALA* 3.5 18.9 + - - +
244A ASN* 5.2 0.2 + - - -
262A MET* 5.4 0.2 - - - -
264A GLY 4.0 8.5 - - - +
265A SER* 3.5 26.6 + - - +
266A GLY* 3.5 8.3 - - - -
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Residues in contact with LYS 212 (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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208A ASP* 2.8 47.4 + - - +
209A PHE* 3.3 12.3 - - - +
210A LEU 3.2 0.2 - - - -
211A THR* 1.3 81.8 - - + +
213A HIS* 1.3 72.5 + - + +
214A ALA 5.2 0.6 - - - +
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Residues in contact with HIS 213 (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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168A ILE* 4.2 23.4 - - + +
177A PHE* 3.5 42.5 - + + +
179A LYS* 5.0 4.2 + - - -
209A PHE* 3.1 50.1 + + - -
210A LEU 3.0 2.9 + - - +
212A LYS* 1.3 86.3 - - + +
214A ALA* 1.3 66.6 + - - +
215A SER* 3.7 1.2 + - - -
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Residues in contact with ALA 214 (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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177A PHE* 4.8 4.9 - - - -
179A LYS* 5.0 0.2 - - - -
210A LEU 2.8 16.1 + - - +
211A THR* 3.5 16.5 + - - +
212A LYS 3.5 0.9 - - - +
213A HIS* 1.3 80.7 - - - +
215A SER* 1.3 68.6 + - - +
216A HIS* 3.5 2.3 + - - -
219A SER* 4.9 1.1 - - - +
262A MET* 3.9 24.7 - - + +
263A ARG 4.6 9.9 - - - +
264A GLY* 4.7 5.6 - - - +
266A GLY* 5.6 0.2 - - - -
281A VAL* 5.9 0.4 - - - -
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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