Contacts of the strand formed by residues 198 - 209 (chain C) in PDB entry 2JIF
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 TYR 198 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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194C LYS* 3.7 2.3 - - - -
195C GLU* 2.8 70.4 + - + +
196C GLY 3.3 3.0 + - - +
197C ASP* 1.3 91.1 - - - +
199C TYR* 1.3 73.1 + - - +
200C VAL* 3.4 26.5 - - + +
269C LYS* 3.6 40.5 + - + -
270C VAL 3.3 18.2 - - - +
271C PRO* 4.1 2.9 - - + -
272C GLU* 3.8 2.9 - - - +
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Residues in contact with TYR 199 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192C ALA* 4.1 8.3 - - + -
193C ASP 3.2 5.2 - - - -
194C LYS* 3.5 51.7 - - + +
198C TYR* 1.3 79.9 - - - +
200C VAL* 1.3 58.4 + - - +
201C LEU* 3.8 8.7 + - + -
223C VAL* 4.2 19.5 - - + -
235C PHE* 3.8 32.8 - + + -
268C VAL 3.3 3.5 - - - +
269C LYS* 3.4 2.4 - - - -
270C VAL* 2.8 38.1 + - + +
272C GLU* 4.2 22.0 - - + -
275C ILE* 3.5 21.2 - - + +
279C ILE* 3.6 24.3 - - + +
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Residues in contact with VAL 200 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191C ARG* 3.5 1.9 - - - +
192C ALA* 3.3 2.9 - - - -
193C ASP* 2.8 46.1 + - + +
195C GLU* 3.6 23.1 - - + +
198C TYR* 3.4 28.9 - - + +
199C TYR* 1.3 71.9 - - - +
201C LEU* 1.3 62.8 + - - +
202C ASN* 3.6 11.0 + - - +
267C ASN* 3.4 41.3 - - + +
268C VAL 3.4 3.6 - - - -
269C LYS* 4.9 3.4 - - + -
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Residues in contact with LEU 201 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190C THR* 4.7 1.8 - - + -
191C ARG 3.2 8.3 - - - +
192C ALA* 3.7 18.2 - - + -
199C TYR* 4.0 11.9 - - + +
200C VAL* 1.3 76.2 - - - +
202C ASN* 1.3 59.7 + - - +
219C VAL* 4.0 31.9 - - + -
221C ALA* 4.2 12.3 - - + -
235C PHE* 4.4 10.3 - - + -
237C VAL* 4.4 7.0 - - + -
265C PHE* 3.7 19.2 - - + +
267C ASN* 3.3 6.8 + - - -
268C VAL* 2.7 43.2 + - + +
270C VAL* 4.0 28.7 - - + -
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Residues in contact with ASN 202 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189C LYS 4.0 1.2 - - - +
190C THR* 3.3 6.0 - - - +
191C ARG* 2.9 74.3 + - + +
193C ASP* 4.9 5.1 + - - -
200C VAL* 3.6 19.2 + - - +
201C LEU* 1.3 73.6 - - - +
203C GLY* 1.3 58.5 + - - +
265C PHE 3.4 6.1 - - - +
266C GLU* 3.7 4.0 - - - +
267C ASN* 2.8 45.5 + - - +
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Residues in contact with GLY 203 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189C LYS 5.2 1.6 - - - -
190C THR* 3.8 11.9 - - - -
191C ARG* 5.5 1.3 - - - -
202C ASN* 1.3 74.3 - - - +
204C SER* 1.3 64.0 + - - -
264C THR* 3.6 2.8 - - - -
265C PHE* 2.8 35.5 + - - +
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Residues in contact with SER 204 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178C GLU* 3.3 21.4 + - - +
179C ALA* 5.4 5.2 + - - +
190C THR* 3.1 15.4 + - - -
203C GLY* 1.3 76.2 - - - -
205C LYS* 1.3 67.6 + - - +
263C LEU 3.2 14.4 - - - -
264C THR* 4.2 11.9 - - - +
265C PHE* 4.5 1.8 - - - -
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Residues in contact with LYS 205 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175C CYS* 3.6 21.5 + - + +
176C LEU 2.8 24.2 + - - +
177C SER 3.3 16.4 - - - +
178C GLU* 2.8 25.5 + - + -
179C ALA 5.3 0.4 - - - -
188C LEU* 3.8 8.3 - - - +
190C THR* 3.6 8.0 + - - -
204C SER* 1.3 79.5 - - - +
206C MET* 1.3 65.0 + - - +
208C ILE* 3.8 19.1 - - + -
219C VAL* 4.3 7.0 - - - -
220C MET 2.9 28.3 + - - -
262C PRO* 3.7 4.7 - - - +
263C LEU* 2.9 34.5 + - + +
265C PHE* 3.9 17.0 - - + -
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Residues in contact with MET 206 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177C SER* 2.9 15.6 + - - +
178C GLU 4.0 1.3 - - - -
179C ALA* 3.8 38.8 - - + +
205C LYS* 1.3 76.4 - - - +
207C TRP* 1.3 114.3 + - + +
208C ILE* 3.3 13.6 - - - +
250C GLU* 4.3 14.4 - - - +
262C PRO* 4.1 24.0 - - + -
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Residues in contact with TRP 207 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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391A GLY* 3.3 23.8 - - - -
392A VAL* 3.4 34.1 - - + -
395A THR* 3.7 23.3 - - + -
177C SER* 4.3 6.5 - - - -
178C GLU 4.9 5.1 + - - -
179C ALA* 5.4 1.6 - - - +
182C GLY* 6.0 0.4 - - - -
206C MET* 1.3 112.3 - - + +
208C ILE* 1.3 61.5 + - - +
209C SER 3.1 0.2 + - - -
250C GLU* 4.3 17.0 + - + -
252C LYS* 6.3 1.3 - - + -
260C THR* 3.6 23.6 - - + +
261C CYS 3.8 6.2 + - - +
1433C FAD 2.9 95.1 + + + +
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Residues in contact with ILE 208 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173C SER* 3.6 31.0 - - - +
174C PHE 3.9 4.5 - - - +
175C CYS* 3.8 25.6 - - - -
177C SER 4.2 2.0 - - - +
205C LYS* 3.8 24.2 - - + -
206C MET 3.3 16.4 - - - +
207C TRP* 1.3 75.7 - - - +
209C SER* 1.3 63.3 + - - +
211C ALA* 3.6 16.4 + - + +
259C SER 3.6 0.3 - - - +
260C THR* 3.4 1.8 - - - -
261C CYS 3.0 40.7 + - - +
263C LEU* 3.9 12.6 - - + -
1433C FAD 3.8 24.0 - - - +
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Residues in contact with SER 209 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137C VAL* 5.4 1.4 - - - +
141C ILE* 3.3 28.5 - - - +
173C SER* 2.9 24.9 + - - -
174C PHE 4.8 0.2 + - - -
207C TRP 3.1 1.2 + - - -
208C ILE* 1.3 72.9 - - - +
210C SER* 1.3 63.3 + - - +
211C ALA 3.2 0.7 - - - -
255C LEU* 5.9 0.7 - - - +
258C SER* 4.3 8.5 + - - -
259C SER 3.1 8.9 + - - -
260C THR* 4.4 1.3 + - - +
413C TYR* 5.3 2.6 - - - -
1433C FAD 2.9 52.3 + - - +
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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