Contacts of the helix formed by residues 185 - 194 (chain D) in PDB entry 2JG1
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 ASN 185 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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183D LYS* 3.8 2.2 + - - +
184D PRO* 1.3 76.4 - - - +
186D ILE* 1.3 66.1 + - + +
187D SER* 3.4 11.9 + - - -
188D GLU* 2.8 59.7 + - - +
189D LEU* 3.0 19.2 + - - +
221D VAL* 4.0 2.0 - - - -
222D SER* 3.4 21.1 - - - +
1312D ANP 2.6 35.3 + - - +
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Residues in contact with ILE 186 (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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185D ASN* 1.3 73.4 - - + +
187D SER* 1.3 65.6 + - - +
189D LEU* 3.2 3.1 + - - +
190D TYR* 3.2 37.7 + - + -
197D LEU* 4.1 14.8 - - + -
198D ASP 3.9 14.8 - - - +
199D GLU* 4.0 25.8 - - + -
204D LEU* 3.8 24.2 - - + -
221D VAL* 3.8 9.4 - - + +
222D SER 3.1 8.3 + - - +
223D LEU* 3.7 34.1 - - + -
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Residues in contact with SER 187 (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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185D ASN* 3.3 11.6 + - - -
186D ILE* 1.3 82.5 - - - +
188D GLU* 1.3 57.4 + - - +
190D TYR* 3.5 1.4 + - - +
191D GLN* 3.0 55.7 + - - +
197D LEU* 3.7 20.1 - - - +
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Residues in contact with GLU 188 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163D ASP* 4.4 7.3 - - - +
164D CYS 4.9 3.1 - - - +
165D SER* 3.8 33.1 + - - -
166D GLY 5.6 2.4 + - - -
169D LEU* 5.6 3.0 - - + +
183D LYS* 4.2 4.5 + - - +
184D PRO* 3.4 14.9 - - + +
185D ASN* 2.8 52.3 + - - +
187D SER* 1.3 70.7 - - - +
189D LEU* 1.3 66.4 + - - +
191D GLN* 3.8 14.3 - - - +
192D LEU* 3.1 25.8 + - - +
1311D MG 4.3 7.3 - - - -
1312D ANP 4.9 1.4 + - - -
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Residues in contact with LEU 189 (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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184D PRO* 4.0 19.7 - - + +
185D ASN 3.0 11.9 + - - +
186D ILE* 3.2 8.3 + - - +
188D GLU* 1.3 78.3 - - - +
190D TYR* 1.3 67.8 + - + +
192D LEU* 3.4 8.4 - - - +
193D LEU* 3.3 24.9 + - + +
204D LEU* 3.9 28.0 - - + -
207D ALA* 4.0 20.0 - - + -
208D VAL* 4.1 17.0 - - + -
213D PHE* 3.7 34.1 - - + -
219D ILE* 5.2 1.1 - - + -
221D VAL* 4.1 16.6 - - + -
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Residues in contact with TYR 190 (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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186D ILE* 3.2 38.2 + - + +
187D SER* 4.2 2.5 - - - +
189D LEU* 1.3 80.6 - - + +
191D GLN* 1.3 59.6 + - - +
193D LEU* 3.1 7.9 + - + -
194D ASN 2.9 24.6 + - - -
195D GLN* 3.1 49.5 + - + +
196D PRO 3.4 19.5 - - - -
197D LEU* 3.9 16.4 - - + -
198D ASP 2.7 34.7 + - - -
203D SER* 2.8 34.3 + - - -
204D LEU* 3.5 13.1 + - + -
207D ALA* 4.2 13.0 - - + -
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Residues in contact with GLN 191 (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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165D SER* 6.0 0.9 - - - -
166D GLY* 6.3 1.6 - - - -
187D SER* 3.0 39.5 + - - +
188D GLU* 3.8 15.9 - - - +
190D TYR* 1.3 75.0 - - - +
192D LEU* 1.3 63.9 + - - +
194D ASN* 3.2 15.5 + - - +
195D GLN 5.2 0.2 - - - -
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Residues in contact with LEU 192 (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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166D GLY* 3.5 34.7 - - - +
169D LEU* 3.8 18.8 - - + -
170D GLN* 3.7 41.7 - - + +
173D LEU* 3.8 13.0 - - + -
188D GLU 3.1 13.9 + - - +
189D LEU* 3.4 11.2 - - - +
191D GLN* 1.3 75.6 - - - +
193D LEU* 1.3 59.5 + - - +
194D ASN* 3.3 2.0 + - - +
212D LEU* 4.1 8.6 - - + +
213D PHE* 3.7 37.2 - - + -
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Residues in contact with LEU 193 (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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189D LEU* 3.3 15.8 + - + +
190D TYR* 3.1 12.3 + - + +
192D LEU* 1.3 77.0 - - + +
194D ASN* 1.3 69.0 + - - +
195D GLN* 3.2 23.3 + - + +
207D ALA* 3.7 30.7 - - + +
210D GLN* 3.5 35.0 - - - +
212D LEU* 4.1 17.5 - - + -
213D PHE* 3.7 29.6 - - + -
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Residues in contact with ASN 194 (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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190D TYR 2.9 5.6 + - - -
191D GLN* 3.2 13.8 + - - +
192D LEU 3.3 1.9 - - - +
193D LEU* 1.3 78.9 - - - +
195D GLN* 1.3 59.3 + - - +
196D PRO* 4.6 2.1 - - - +
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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