Contacts of the strand formed by residues 196 - 207 (chain A) in PDB entry 5E67
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 196 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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186A LEU* 4.2 11.0 - - + -
187A LYS 3.3 24.9 - - - +
188A LYS* 3.7 40.6 - - + -
189A SER* 4.2 1.1 - - - -
192A ILE* 3.5 21.7 - - - +
194A VAL* 3.3 20.4 - - - +
195A GLY* 1.3 80.1 - - - +
197A GLN* 1.3 63.4 + - - +
198A SER 4.1 1.2 + - - -
281A HIS 5.0 1.9 - - - +
282A LEU* 5.6 0.5 - - - +
287A LEU* 4.0 26.0 - - + +
291A ARG* 3.9 30.5 - - - -
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Residues in contact with GLN 197 (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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185A ILE 3.4 2.3 - - - +
186A LEU* 3.3 7.4 - - - -
187A LYS* 2.9 50.2 + - + +
189A SER* 4.0 4.8 - - - -
192A ILE* 3.5 21.6 - - + +
196A PHE* 1.3 72.1 - - - +
198A SER* 1.3 63.9 + - - +
199A ILE* 3.5 26.6 + - + +
287A LEU* 5.8 0.2 - - - -
3B T 3.4 35.7 + - + +
4B A 3.0 48.1 + - - -
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Residues in contact with SER 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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184A SER* 5.2 1.4 + - - -
185A ILE 3.4 5.9 + - - -
186A LEU* 3.8 16.4 - - - +
196A PHE 4.1 2.0 + - - -
197A GLN* 1.3 77.3 + - - +
199A ILE* 1.3 63.9 + - - +
200A LEU* 5.4 0.2 - - - +
272A ILE* 4.2 2.9 - - - +
276A MET* 3.1 38.7 - - - +
281A HIS* 4.2 19.0 - - - -
287A LEU* 5.3 3.1 - - - +
290A ILE* 3.7 24.8 - - - +
3B T 4.9 2.1 + - - -
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Residues in contact with ILE 199 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183A LYS 3.8 0.2 - - - +
184A SER* 3.6 3.6 + - - -
185A ILE* 2.8 48.9 + - + +
187A LYS* 3.7 19.7 - - + -
197A GLN* 3.5 43.3 - - + +
198A SER* 1.3 78.5 + - - +
200A LEU* 1.3 69.2 + - - +
201A VAL* 3.8 20.5 + - + -
240A THR* 5.0 14.4 - - + +
276A MET* 4.8 0.7 - - - -
4B A 4.5 4.0 - - + +
5B C 4.2 17.5 - - - +
20C T 5.1 3.4 - - + +
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Residues in contact with LEU 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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183A LYS 3.4 3.8 - - - +
184A SER* 4.4 5.8 - - - -
198A SER 4.3 0.8 + - - -
199A ILE* 1.3 81.9 - - - +
201A VAL* 1.3 63.8 + - - +
202A PHE 4.2 0.2 - - - -
239A VAL 3.8 7.1 - - - +
240A THR* 4.1 8.8 - - - +
242A PHE* 4.2 14.7 - - + -
245A ILE* 4.2 22.7 - - + +
269A TRP* 3.7 39.5 - - + +
272A ILE* 3.4 26.7 - - + -
273A ALA* 3.6 39.0 - - + +
276A MET* 4.0 12.8 - - + +
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Residues in contact with VAL 201 (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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181A SER 3.7 1.0 - - - +
183A LYS* 2.8 66.3 + - + +
185A ILE* 4.5 13.7 - - + -
199A ILE* 3.8 18.6 - - + -
200A LEU* 1.3 80.0 - - - +
202A PHE* 1.3 72.2 + - - +
203A GLN* 4.7 2.2 - - + +
238A THR* 3.9 18.6 - - + -
239A VAL 3.4 7.9 - - - +
240A THR* 4.1 10.5 - - + -
269A TRP* 3.8 4.9 + - - -
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Residues in contact with PHE 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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176A VAL* 3.7 21.3 - - + -
181A SER 3.7 6.3 - - - -
182A PHE* 3.5 40.4 - + - -
201A VAL* 1.3 75.1 - - - +
203A GLN* 1.3 69.5 + - - +
204A ILE* 3.9 13.5 - - + -
221A LEU* 4.3 7.2 - - + -
237A TYR* 3.9 25.1 - + - -
238A THR* 3.4 4.0 - - - -
239A VAL* 2.8 36.4 + - + +
245A ILE* 4.0 19.7 - - + +
249A ILE* 3.7 22.7 - - + -
253A PHE* 3.5 28.9 - + - -
269A TRP* 4.1 3.8 - - + -
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Residues in contact with GLN 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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179A ASP 4.7 0.2 - - - -
180A GLY* 3.1 4.7 - - - -
181A SER* 2.7 46.3 + - - +
183A LYS* 2.8 38.5 + - - -
201A VAL* 4.7 3.8 - - + +
202A PHE* 1.3 79.9 - - - +
204A ILE* 1.3 72.9 + - - +
205A THR* 3.0 22.4 + - - +
236A TYR* 3.5 25.2 - - + -
237A TYR 3.2 10.8 - - - +
238A THR* 4.6 4.9 + - - +
17C A 3.2 25.0 + - - +
18C G 4.9 0.7 - - - +
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Residues in contact with ILE 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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172A LEU* 4.2 11.9 - - + -
175A PHE* 3.7 27.6 - - + -
176A VAL* 3.6 26.0 - - + -
179A ASP 3.5 9.6 - - - +
180A GLY* 4.3 1.8 - - - -
202A PHE* 3.9 22.2 - - + -
203A GLN* 1.3 78.4 - - - +
205A THR* 1.3 64.1 + - - +
214A MET* 3.3 18.3 - - + +
217A LEU* 3.9 19.7 - - + -
221A LEU* 5.0 1.3 - - + -
236A TYR* 3.5 1.4 - - - -
237A TYR* 2.9 44.8 + - + +
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Residues in contact with THR 205 (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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179A ASP* 3.0 23.6 + - - +
181A SER* 5.2 0.5 + - - -
203A GLN* 3.0 26.9 + - - +
204A ILE* 1.3 72.5 - - - +
206A GLN* 1.3 81.0 + - - +
214A MET* 4.2 0.2 - - - -
234A TRP* 5.4 0.7 - - + -
235A LEU 3.5 4.9 - - - +
236A TYR* 3.6 20.9 - - + -
15C T 3.7 32.5 - - + -
16C C 3.3 28.2 + - + +
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Residues in contact with GLN 206 (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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18A ASP 4.8 3.2 + - - -
101A THR* 4.3 10.6 + - + +
175A PHE* 3.6 23.2 - - + -
179A ASP* 2.3 31.5 - - - +
205A THR* 1.3 80.7 - - - +
207A HIS* 1.3 73.1 + - - +
209A ARG* 5.6 3.6 - - - +
210A ASP* 3.9 23.9 + - + +
213A LEU* 5.4 1.1 - - + -
214A MET* 3.7 28.1 - - + +
234A TRP* 3.6 3.1 - - - +
235A LEU* 2.9 34.3 + - - +
15C T 4.5 9.1 + - - -
16C C 4.8 1.9 + - - -
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Residues in contact with HIS 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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206A GLN* 1.3 91.1 - - - +
208A ALA* 1.3 74.9 + - - +
209A ARG* 3.3 63.3 + - + +
210A ASP* 3.1 22.6 + - - +
233A PRO* 3.4 39.5 + - + +
234A TRP* 4.5 0.4 - - - -
235A LEU* 4.5 1.8 - - - +
15C T 3.1 36.3 + - - +
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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