Contacts of the helix formed by residues 194 - 206 (chain l) in PDB entry 5GJQ
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 l).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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40l ILE* 3.3 29.3 - - + +
42l THR* 3.9 12.8 - - - +
47l CYS* 3.9 11.4 - - - -
189l MET* 3.6 14.7 - - + +
190l THR 4.0 0.8 - - - -
191l LEU* 3.7 17.8 - - + -
192l LYS 3.2 0.4 - - - -
193l GLU* 1.3 76.1 + - - +
195l ILE* 1.3 60.2 + - - +
197l SER 3.4 0.5 + - - -
198l SER* 2.9 34.1 + - - -
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Residues in contact with ILE 195 (chain l).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47l CYS* 4.1 20.6 - - + -
191l LEU* 4.1 24.9 - - + -
192l LYS* 3.4 9.9 + - - +
194l ALA* 1.3 77.1 - - - +
196l LYS* 1.3 62.8 + - - +
198l SER* 3.2 7.2 + - - -
199l LEU* 2.9 34.2 + - + +
217l LEU* 4.0 23.6 - - + -
219l THR* 3.9 21.8 - - + -
229l PHE* 4.1 15.7 - - + -
237l VAL* 4.1 26.9 - - + -
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Residues in contact with LYS 196 (chain l).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192l LYS 2.8 18.8 + - - +
193l GLU* 4.1 7.9 - - - -
195l ILE* 1.3 77.4 - - - +
197l SER* 1.3 63.6 + - - +
199l LEU* 3.2 5.2 + - - +
200l ILE* 2.9 41.0 + - + +
237l VAL* 5.2 10.5 - - + +
240l ASP* 3.5 44.4 + - - +
241l ILE* 5.3 4.5 - - - -
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Residues in contact with SER 197 (chain l).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40l ILE* 4.3 10.8 - - - -
184l VAL* 4.5 22.1 + - - +
189l MET* 3.6 10.7 - - - +
193l GLU* 3.4 17.3 + - - -
194l ALA* 3.5 7.4 - - - -
195l ILE 3.4 0.2 - - - -
196l LYS* 1.3 78.0 - - - +
198l SER* 1.3 63.5 + - - +
200l ILE* 3.0 13.4 + - - +
201l ILE* 2.9 31.6 + - - +
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Residues in contact with SER 198 (chain l).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38l ILE* 3.7 23.7 - - - +
40l ILE* 3.1 19.1 - - - +
47l CYS* 3.4 12.4 - - - -
49l ALA* 4.4 16.8 - - - -
194l ALA 2.9 22.6 + - - -
195l ILE* 3.4 7.6 - - - -
197l SER* 1.3 73.3 - - - +
199l LEU* 1.3 62.1 + - - +
201l ILE* 3.4 3.1 + - - +
202l LEU* 2.9 30.5 + - - +
217l LEU* 5.2 0.7 - - - -
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Residues in contact with LEU 199 (chain l).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49l ALA* 4.6 4.7 - - - +
195l ILE* 2.9 25.0 + - + +
196l LYS* 3.8 4.5 - - - +
198l SER* 1.3 82.9 - - - +
200l ILE* 1.3 56.0 + - - +
202l LEU* 3.6 4.2 - - + +
203l LYS* 2.9 30.7 + - - +
210l LEU* 3.6 14.2 - - + +
215l ILE* 3.5 28.5 - - + -
217l LEU* 4.5 19.1 - - + -
234l LEU* 5.1 6.5 - - + -
237l VAL* 3.5 33.9 - - + -
238l ILE* 4.4 18.4 - - + +
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Residues in contact with ILE 200 (chain l).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196l LYS* 2.9 39.6 + - + +
197l SER* 3.3 12.1 - - - +
199l LEU* 1.3 72.5 - - - +
201l ILE* 1.3 63.7 + - + +
203l LYS* 3.1 20.3 + - - +
204l GLN* 2.9 47.0 + - + +
241l ILE 5.0 12.3 - - - +
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Residues in contact with ILE 201 (chain l).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38l ILE* 3.9 11.2 - - + -
177l ALA* 3.7 34.8 - - + -
180l SER* 3.6 21.5 - - - +
181l LEU* 3.6 48.2 - - + +
184l VAL* 4.2 10.1 - - + -
197l SER* 2.9 17.2 + - - +
198l SER* 4.8 0.2 - - - -
200l ILE* 1.3 79.5 - - + +
202l LEU* 1.3 63.8 + - - +
204l GLN* 3.1 14.6 + - - +
205l VAL* 3.0 27.9 + - + +
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Residues in contact with LEU 202 (chain l).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36l THR* 4.4 20.4 - - - +
38l ILE* 4.2 17.2 - - + +
49l ALA* 4.0 24.9 - - - +
50l VAL* 4.1 9.9 - - - +
51l GLU* 4.6 4.3 - - + +
198l SER 2.9 16.4 + - - +
199l LEU* 3.6 7.2 - - + +
200l ILE 3.2 0.2 - - - -
201l ILE* 1.3 76.6 - - - +
203l LYS* 1.3 57.4 + - - +
205l VAL* 3.1 15.0 + - + +
206l MET* 2.8 52.2 + - + +
210l LEU* 5.3 1.8 - - + -
215l ILE* 3.6 32.3 - - + -
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Residues in contact with LYS 203 (chain l).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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369H ARG* 5.4 2.3 + - - -
199l LEU 2.9 17.1 + - - +
200l ILE* 3.1 19.9 + - - +
202l LEU* 1.3 76.1 - - - +
204l GLN* 1.3 69.4 + - - +
205l VAL 3.5 0.3 + - - -
206l MET* 3.8 17.2 + - - +
209l LYS* 5.9 4.0 - - + -
210l LEU* 3.7 33.3 - - + +
241l ILE* 3.8 38.1 - - + -
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Residues in contact with GLN 204 (chain l).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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369H ARG* 4.9 7.3 + - - -
372H LEU* 5.7 1.4 - - - +
180l SER* 3.6 21.4 + - - -
200l ILE* 2.9 37.6 + - + +
201l ILE* 3.1 19.5 + - - +
203l LYS* 1.3 86.5 - - - +
205l VAL* 1.3 65.3 + - + +
206l MET 4.2 2.9 - - - +
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Residues in contact with VAL 205 (chain l).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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372H LEU* 4.8 1.1 - - - -
375H ARG* 2.2 41.2 + - - +
36l THR* 4.1 23.1 - - + +
38l ILE* 5.6 0.2 - - + -
173l ALA* 3.6 23.3 - - + -
176l GLY* 5.1 2.7 - - - -
177l ALA* 4.4 23.1 - - + +
180l SER* 5.9 0.2 - - - +
201l ILE* 3.0 20.8 + - + +
202l LEU* 3.3 19.1 - - + +
204l GLN* 1.3 82.2 - - + +
206l MET* 1.3 62.3 + - - +
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Residues in contact with MET 206 (chain l).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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369H ARG* 3.9 14.9 + - - -
372H LEU* 4.5 1.7 - - - +
51l GLU* 2.6 36.8 - - + +
202l LEU* 2.8 37.1 + - + +
203l LYS* 3.9 13.1 - - - +
204l GLN 3.5 1.3 - - - +
205l VAL* 1.3 79.6 - - - +
207l GLU* 1.3 63.9 - - - +
208l GLU 4.4 9.1 - - - +
210l LEU* 4.1 19.7 - - - +
214l ASN* 3.3 35.7 - - - +
215l ILE* 3.5 32.3 - - + -
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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