Contacts of the helix formed by residues 203 - 214 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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171D GLN* 4.9 3.6 + - - -
201D ILE* 4.2 0.5 - - - +
202D HIS* 1.3 82.4 - - - +
204D PRO* 1.3 70.8 - - - +
205D GLU* 3.3 20.7 + - - +
206D GLU* 3.2 25.4 + - - +
207D GLN* 2.9 26.9 + - - +
242D TYR* 3.7 12.9 - - - +
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Residues in contact with PRO 204 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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203D SER* 1.3 81.8 - - - +
205D GLU* 1.3 76.3 + - - +
207D GLN* 3.2 2.4 + - - +
208D ASP* 2.8 29.7 + - - +
242D TYR* 3.5 31.6 - - + +
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Residues in contact with GLU 205 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170D PHE* 3.6 18.1 - - + -
171D GLN* 3.8 25.9 + - - +
203D SER* 3.3 19.3 + - - +
204D PRO* 1.3 90.7 - - - +
206D GLU* 1.3 63.5 + - - +
208D ASP* 3.3 8.5 + - - +
209D PHE 3.0 18.5 + - - -
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Residues in contact with GLU 206 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170D PHE* 3.6 15.7 - - + -
171D GLN* 5.4 2.2 - - - +
173D LYS* 2.8 24.6 + - - +
175D TYR* 2.6 34.8 + - + +
200D SER 3.4 9.6 - - - +
201D ILE* 3.4 7.3 - - + -
202D HIS* 2.7 35.4 + - - +
203D SER* 3.2 21.6 + - - +
205D GLU* 1.3 75.9 - - - +
207D GLN* 1.3 65.9 + - - +
209D PHE* 3.3 3.6 + - - +
210D LEU* 3.1 26.6 + - + +
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Residues in contact with GLN 207 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201D ILE* 3.7 12.7 - - + +
203D SER 2.9 7.1 + - - -
204D PRO 3.2 5.4 + - - +
206D GLU* 1.3 75.5 - - - +
208D ASP* 1.3 65.2 + - - +
210D LEU* 3.0 5.8 + - - +
211D THR* 2.8 50.4 + - - +
242D TYR* 3.2 33.7 - - + +
244D ASN* 3.5 21.0 + - - +
262D MET* 3.4 18.2 - - - -
266D GLY 3.4 9.7 + - - -
268D TRP* 2.8 32.6 + - - -
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Residues in contact with ASP 208 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204D PRO 2.8 17.4 + - - +
205D GLU* 3.4 13.7 - - - +
206D GLU 3.2 0.2 - - - -
207D GLN* 1.3 73.3 - - - +
209D PHE* 1.3 62.1 + - - +
211D THR* 3.4 8.4 + - - +
212D LYS* 3.1 54.3 + - - +
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Residues in contact with PHE 209 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168D ILE* 3.9 23.6 - - + -
169D ASN 3.9 8.1 - - - -
170D PHE* 3.7 46.7 - + + -
175D TYR* 3.3 36.6 - + - -
177D PHE* 4.1 14.8 - + - -
205D GLU 3.0 13.2 + - - +
206D GLU 3.5 7.9 - - - +
208D ASP* 1.3 77.2 - - - +
210D LEU* 1.3 73.8 + - + +
212D LYS* 3.1 12.1 + - - +
213D HIS* 2.9 55.4 + + - -
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Residues in contact with LEU 210 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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175D TYR* 3.6 32.5 - - + -
177D PHE* 4.1 19.0 - - + -
199D VAL* 4.1 10.8 - - + -
201D ILE* 3.6 44.4 - - + -
206D GLU* 3.1 21.6 + - + +
207D GLN* 3.0 12.0 + - - +
209D PHE* 1.3 83.3 - - + +
211D THR* 1.3 55.2 + - - +
213D HIS 3.0 2.4 + - - -
214D ALA* 2.7 38.2 + - - +
262D MET* 4.3 12.8 - - + -
281D VAL* 4.2 8.7 - - + -
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Residues in contact with THR 211 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207D GLN* 2.8 35.8 + - - +
208D ASP* 3.6 10.2 - - - +
210D LEU* 1.3 77.5 - - - +
212D LYS* 1.3 63.1 + - + +
213D HIS 3.3 0.3 + - - -
214D ALA* 3.7 15.6 + - - +
244D ASN* 5.2 0.2 + - - -
262D MET* 5.5 0.2 - - - -
264D GLY 4.0 9.7 - - - +
265D SER* 3.5 28.0 + - - +
266D GLY* 3.3 11.4 - - - -
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Residues in contact with LYS 212 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208D ASP* 3.1 46.3 + - - +
209D PHE* 3.1 12.1 + - - +
211D THR* 1.3 79.1 - - + +
213D HIS* 1.3 73.7 + - + +
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Residues in contact with HIS 213 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168D ILE* 3.9 26.1 - - + +
177D PHE* 3.3 42.8 - + + +
209D PHE* 2.9 49.4 + + - +
210D LEU 3.0 2.8 + - - -
212D LYS* 1.3 91.6 - - + +
214D ALA* 1.3 64.7 + - - +
215D SER 3.9 0.5 + - - -
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Residues in contact with ALA 214 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177D PHE* 4.2 8.7 - - + -
210D LEU 2.7 18.7 + - - +
211D THR* 3.7 12.8 + - - +
212D LYS 5.4 0.2 - - - -
213D HIS* 1.3 80.5 - - - +
215D SER* 1.3 72.3 + - - +
216D HIS* 3.6 12.8 + - - -
219D SER* 4.7 4.3 - - - +
262D MET* 4.0 23.6 - - + +
263D ARG 4.8 8.5 - - - +
264D GLY 5.1 3.9 - - - +
281D VAL* 5.7 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