Contacts of the helix formed by residues 195 - 214 (chain A) in PDB entry 3UON
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 PHE 195 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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111A VAL* 5.0 1.3 - - + -
191A ALA 2.7 16.0 + - - +
193A ALA 3.6 0.2 - - - -
194A ALA* 1.3 72.9 - - - +
196A TYR* 1.3 82.0 + + - +
198A PRO* 3.0 16.5 - - - +
199A VAL* 3.1 33.6 - - + +
396A PHE* 3.4 26.5 - + - -
397A ILE* 5.1 7.0 - - + -
400A TRP* 3.3 56.8 - + + -
401A ALA* 4.1 8.7 - - + -
404A ASN* 3.4 29.6 - - + +
1162A QNB 3.0 19.5 - + + +
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Residues in contact with TYR 196 (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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188A PHE* 4.1 19.5 - + - -
191A ALA* 3.2 16.5 + - + -
192A ILE* 3.1 38.1 + - + +
195A PHE* 1.3 92.0 - + - +
197A LEU* 1.3 60.2 + - - +
199A VAL* 3.1 8.5 + - + +
200A ILE* 2.8 38.8 + - + +
404A ASN* 3.0 39.6 + - + -
405A VAL* 3.6 9.0 + - - +
408A LEU* 4.0 13.1 - - + +
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Residues in contact with LEU 197 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192A ILE* 2.8 35.1 + - + +
193A ALA* 4.3 15.7 - - + +
196A TYR* 1.3 72.3 - - - +
198A PRO* 1.3 63.9 - - + +
200A ILE* 3.0 25.7 + - + +
201A ILE* 2.8 37.9 + - + +
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Residues in contact with PRO 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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111A VAL* 5.3 9.9 - - + -
115A LEU* 3.6 32.4 - - + +
193A ALA 3.6 13.2 - - - +
194A ALA 3.1 20.2 - - - +
195A PHE* 3.0 21.5 - - - +
197A LEU* 1.3 95.4 - - + +
199A VAL* 1.3 53.9 + - + +
201A ILE* 3.4 6.5 + - + +
202A MET* 2.9 39.5 + - + +
396A PHE* 6.5 0.4 - - + -
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Residues in contact with VAL 199 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195A PHE* 3.1 32.5 + - + +
196A TYR* 3.1 12.2 + - + +
198A PRO* 1.3 75.6 - - + +
200A ILE* 1.3 62.5 + - + +
202A MET* 3.2 14.0 + - + +
203A THR* 2.9 38.9 + - - +
396A PHE* 3.9 28.3 - - + -
397A ILE* 5.2 17.7 - - + -
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Residues in contact with ILE 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 TYR* 2.8 27.0 + - + +
197A LEU* 3.4 31.0 - - + +
199A VAL* 1.3 74.5 - - + +
201A ILE* 1.3 66.5 + - + +
203A THR* 3.0 11.1 + - - -
204A VAL* 2.9 32.6 + - + +
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Residues in contact with ILE 201 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115A LEU* 5.3 4.5 - - + -
119A PHE* 4.4 15.7 - - + -
197A LEU* 2.8 28.1 + - + +
198A PRO* 3.7 8.1 - - + +
200A ILE* 1.3 76.6 - - + +
202A MET* 1.3 65.9 + - + +
204A VAL* 3.2 7.9 + - - +
205A LEU* 3.1 38.9 + - + +
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Residues in contact with MET 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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111A VAL* 5.4 1.8 - - + +
114A LEU* 3.8 22.2 - - + +
115A LEU* 3.4 24.5 - - + -
118A SER* 3.4 23.3 - - - +
198A PRO* 2.9 17.4 + - + +
199A VAL* 3.5 36.8 - - + +
201A ILE* 1.3 75.4 - - + +
203A THR* 1.3 62.8 + - - +
205A LEU* 3.9 8.5 - - - +
206A TYR* 2.9 35.4 + - + +
393A LEU* 4.3 14.6 - - + -
396A PHE* 4.2 18.2 - - + -
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Residues in contact with THR 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 VAL* 2.9 23.7 + - - +
200A ILE* 3.1 13.1 - - + +
202A MET* 1.3 77.3 - - - +
204A VAL* 1.3 62.0 - - + +
206A TYR* 3.3 4.1 + - - +
207A TRP* 2.8 30.5 + - + +
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Residues in contact with VAL 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 ILE* 2.9 28.6 + - + +
201A ILE* 3.7 8.3 - - - +
203A THR* 1.3 81.0 - - + +
205A LEU* 1.3 60.2 + - - +
207A TRP* 3.0 27.5 - - + +
208A HIS* 3.0 28.0 + - + +
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Residues in contact with LEU 205 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118A SER* 3.4 39.3 - - - +
119A PHE* 3.7 38.6 - - + -
122A TYR* 4.0 18.4 - - + -
201A ILE* 3.1 28.4 + - + +
202A MET* 3.9 2.5 - - + +
204A VAL* 1.3 76.8 - - + +
206A TYR* 1.3 74.3 + - + +
208A HIS* 3.3 10.6 + - - +
209A ILE* 2.8 37.5 + - + +
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Residues in contact with TYR 206 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A ILE* 4.1 3.6 - - - +
118A SER* 3.0 40.7 + - - -
121A ARG* 3.9 11.5 - - + +
202A MET* 2.9 31.2 + - + +
203A THR* 3.8 4.3 - - - +
205A LEU* 1.3 83.1 - - + +
207A TRP* 1.3 61.1 + - - +
209A ILE* 3.6 26.4 - - + +
210A SER* 2.8 28.6 + - - -
389A ILE* 3.0 30.3 - - + +
393A LEU* 3.7 26.6 - - + +
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Residues in contact with TRP 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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203A THR* 2.8 17.6 + - + +
204A VAL* 3.0 17.3 - - + +
206A TYR* 1.3 76.3 - - - +
208A HIS* 1.3 110.0 + + - +
210A SER* 3.2 9.6 + - - -
211A ARG* 2.9 65.1 + - + +
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Residues in contact with HIS 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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122A TYR* 3.9 27.3 - + + -
126A THR* 5.7 2.6 - - + +
204A VAL* 3.0 30.1 + - + +
205A LEU* 3.5 9.5 - - - +
207A TRP* 1.3 110.0 - + - +
209A ILE* 1.3 64.4 + - - +
211A ARG* 3.2 7.7 + - + +
212A ALA* 3.0 25.9 + - - +
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Residues in contact with ILE 209 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A ARG* 3.5 18.8 - - + +
122A TYR* 3.5 39.7 - - + +
125A VAL* 3.9 25.8 - - + -
126A THR* 6.0 0.9 - - + -
205A LEU* 2.8 33.7 + - + +
206A TYR* 3.6 28.9 - - + +
207A TRP 3.3 0.2 - - - -
208A HIS* 1.3 75.0 - - - +
210A SER* 1.3 63.3 + - - +
212A ALA* 3.5 0.9 + - - +
213A SER* 3.0 33.4 + - - +
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Residues in contact with SER 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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206A TYR 2.8 14.5 + - - -
207A TRP* 3.2 13.7 + - - -
209A ILE* 1.3 74.5 - - - +
211A ARG* 1.3 68.3 + - - +
213A SER* 3.1 13.2 + - - -
214A LYS* 3.1 16.1 + - - +
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Residues in contact with ARG 211 (chain A).
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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207A TRP* 2.9 66.5 + - + +
208A HIS* 3.5 9.0 - - + +
210A SER* 1.3 80.2 + - - +
212A ALA* 1.3 62.7 + - - +
213A SER 3.4 0.2 + - - -
214A LYS* 3.6 41.3 - - - +
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Residues in contact with ALA 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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125A VAL* 3.5 29.3 - - + +
126A THR* 5.3 7.6 - - + -
208A HIS 3.0 14.6 + - - +
211A ARG* 1.3 77.8 - - - +
213A SER* 1.3 60.7 + - - +
214A LYS* 3.5 2.0 + - - +
215A SER 5.1 3.6 + - - +
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Residues in contact with SER 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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125A VAL* 3.4 24.6 - - - +
209A ILE* 3.0 21.4 + - - +
210A SER* 3.1 5.7 + - - -
212A ALA* 1.3 76.6 - - - +
214A LYS* 1.3 66.9 + - - +
215A SER 3.2 2.5 - - - -
216A ARG* 3.1 33.5 + - - +
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Residues in contact with LYS 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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210A SER 3.1 9.6 + - - +
211A ARG* 3.6 34.3 - - - +
212A ALA 3.5 2.2 - - - +
213A SER* 1.3 77.3 - - - +
215A SER* 1.3 69.7 + - - +
216A ARG 3.7 1.2 + - - -
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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