Contacts of the strand formed by residues 191 - 201 (chain E) in PDB entry 3V56
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 GLY 191 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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190E THR* 1.3 78.0 - - - +
192E TYR* 1.4 65.9 + - - -
193E PHE* 3.4 13.0 - - - -
252E LYS* 3.3 8.7 - - - +
253E LEU 2.7 34.7 + - - -
283E LYS* 4.4 8.3 - - - -
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Residues in contact with TYR 192 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191E GLY* 1.4 75.7 - - - -
193E PHE* 1.3 63.6 + - - +
250E ILE* 4.3 7.9 - - + -
251E ALA 3.4 3.6 - - - -
252E LYS* 3.7 44.1 + - + +
283E LYS* 3.7 2.6 - - - +
284E LEU* 2.9 51.9 + - + +
146F CYS* 5.1 0.2 - - - -
172F PHE* 3.7 40.6 - + + +
173F LYS 4.8 5.4 + - - -
174F ARG* 3.4 48.1 - - + +
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Residues in contact with PHE 193 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177E ALA* 4.2 4.7 - - + -
178E LEU* 3.9 31.6 - - + -
187E VAL* 3.9 6.7 - - + -
189E GLU 3.2 27.6 - - - -
191E GLY 3.4 28.9 - - - -
192E TYR* 1.3 74.3 - - - +
194E PHE* 1.3 61.1 + - - +
195E ILE* 3.7 11.0 + - + +
250E ILE* 3.3 7.0 - - - -
251E ALA 2.8 33.8 + - - +
253E LEU* 3.6 37.7 - - + -
281E ALA* 4.9 1.6 - - + -
282E LEU 3.3 7.9 - - - +
283E LYS* 3.5 43.7 - - + -
284E LEU* 4.6 1.1 - - - -
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Residues in contact with PHE 194 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194D PHE* 3.6 33.0 - + - -
193E PHE* 1.3 69.7 - - - +
195E ILE* 1.4 58.2 + - - +
196E TYR* 3.9 21.4 - + + -
246E TYR* 4.0 5.6 - - - -
248E ALA* 3.6 27.1 - - + -
249E GLY* 3.5 19.5 - - - -
250E ILE* 4.2 13.2 - - + +
281E ALA* 3.3 2.1 - - - -
282E LEU* 2.8 63.0 + - + +
284E LEU* 4.3 14.5 - - + +
194F PHE* 3.8 27.1 - + - -
196F TYR* 5.4 2.2 - + - -
246F TYR* 4.4 3.6 - - - -
282F LEU* 5.6 3.1 - - + -
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Residues in contact with ILE 195 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193E PHE* 3.8 20.2 - - + +
194E PHE* 1.4 76.0 - - - +
196E TYR* 1.3 62.3 + - - +
212E ILE* 3.6 29.8 - - + -
229E LEU* 4.4 9.4 - - + -
230E PHE* 4.3 9.1 - - + -
248E ALA* 3.1 5.0 - - - +
249E GLY 2.9 33.5 + - - +
251E ALA* 3.8 25.1 - - + +
253E LEU* 3.8 18.2 - - + -
259E LEU* 3.8 23.6 - - + -
279E PHE* 4.1 8.1 - - + -
280E GLY 3.6 11.0 - - - +
281E ALA* 4.2 3.6 - - + -
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Residues in contact with TYR 196 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194D PHE* 5.1 1.3 - + - -
248D ALA 4.4 4.9 - - - -
249D GLY* 4.1 9.6 - - - -
250D ILE* 3.2 37.9 - - + +
147E LEU 4.3 0.3 + - - -
148E GLN* 2.6 40.9 + - - +
194E PHE* 3.9 22.2 - + + -
195E ILE* 1.3 73.2 - - - +
197E GLY* 1.3 60.6 + - - +
212E ILE* 3.8 5.4 - - - -
246E TYR* 3.4 24.2 - - + +
247E SER 3.6 5.8 - - - -
248E ALA* 3.7 5.4 - - + -
278E PHE* 4.2 22.2 - + - -
279E PHE* 3.3 7.6 - - - -
280E GLY* 2.9 62.0 + - - +
281E ALA* 3.7 3.8 - - - -
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Residues in contact with GLY 197 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196E TYR* 1.3 79.0 - - - +
198E GLN* 1.4 60.0 + - - -
210E HIS* 3.6 10.8 + - - -
212E ILE* 3.7 10.0 - - - +
246E TYR* 3.4 6.4 - - - -
247E SER 3.1 32.4 + - - +
261E LEU* 4.3 7.4 - - - -
278E PHE* 3.4 11.2 - - - -
279E PHE* 4.2 2.2 - - - -
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Residues in contact with GLN 198 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231D ARG 2.9 27.7 + - - -
246D TYR 4.0 1.9 - - - +
247D SER* 2.7 29.9 + - - -
197E GLY* 1.4 74.8 - - - +
199E VAL* 1.4 75.1 + - - +
210E HIS* 4.2 0.2 - - - -
244E SER* 3.9 15.4 + - - -
245E CYS 3.2 17.0 - - - +
246E TYR* 3.7 16.0 + - + +
261E LEU* 4.6 0.4 - - - +
276E VAL 3.0 18.6 + - - +
277E THR* 3.2 1.9 - - - +
278E PHE* 2.9 57.6 + - + +
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Residues in contact with VAL 199 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166E VAL* 4.8 0.2 - - + -
168E TRP* 5.4 0.2 - - + -
198E GLN* 1.4 81.2 - - - +
200E LEU* 1.3 62.4 + - - +
201E TYR* 3.5 38.0 - - + +
210E HIS* 3.5 17.2 - - + +
244E SER* 3.2 1.2 - - - -
245E CYS 2.9 28.6 + - - -
261E LEU* 3.6 28.0 - - + -
263E ILE* 4.2 5.4 - - + -
270E ILE* 3.8 21.8 - - + -
276E VAL 3.9 3.6 - - - -
277E THR* 3.7 18.6 - - + +
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Residues in contact with LEU 200 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231D ARG* 4.4 5.2 - - - +
233D ILE* 3.6 31.9 - - + -
199E VAL* 1.3 71.1 - - - +
201E TYR* 1.3 65.6 - - - +
202E THR* 4.3 9.6 - - + -
242E ASN* 3.9 10.3 - - - +
243E ASN 3.6 29.8 - - - +
244E SER* 3.8 7.4 - - - +
270E ILE* 3.2 7.6 - - - +
271E SER* 2.9 48.7 + - - +
276E VAL* 3.6 32.6 + - + -
277E THR* 3.3 8.1 + - - -
29J VAL 5.8 1.8 - - - +
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Residues in contact with TYR 201 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199E VAL* 3.5 33.0 - - + +
200E LEU* 1.3 71.4 - - - +
202E THR* 1.3 61.1 + - - +
203E ASP 3.5 0.9 - - - -
208E MET* 3.6 38.1 - - + -
209E GLY* 3.0 35.8 - - - -
210E HIS* 2.5 35.2 + - - +
234E GLN* 5.2 2.7 - - + -
236E MET* 3.4 19.7 - - + +
242E ASN* 3.4 6.8 - - - -
243E ASN 2.8 43.2 + - - +
245E CYS* 4.2 12.1 - - + -
263E ILE* 4.0 6.6 - - + +
269E GLN 3.8 1.6 - - - +
270E ILE* 3.5 18.4 - - + -
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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