Contacts of the strand formed by residues 191 - 201 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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189D GLU 3.6 3.0 + - - -
190D THR* 1.3 78.1 - - - +
192D TYR* 1.4 66.6 + - - -
193D PHE* 3.5 10.3 - - - -
252D LYS* 3.6 2.9 - - - +
253D LEU 2.8 35.7 + - - +
283D LYS* 4.2 10.8 - - - -
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Residues in contact with TYR 192 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191D GLY* 1.4 79.1 - - - -
193D PHE* 1.3 61.6 + - - +
250D ILE* 4.5 1.3 - - + -
251D ALA 3.5 4.3 - - - +
252D LYS* 3.1 47.2 + - + -
283D LYS* 3.9 3.4 - - - +
284D LEU* 3.0 49.7 + - + +
146E CYS* 4.0 2.7 - - - -
172E PHE* 3.8 29.8 - + + -
173E LYS 4.4 4.9 + - - -
174E ARG* 3.4 56.2 - - + +
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Residues in contact with PHE 193 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177D ALA* 4.4 3.4 - - + -
178D LEU* 3.7 32.1 - - + -
187D VAL* 3.7 10.3 - - + -
189D GLU 3.2 27.1 - - - -
191D GLY 3.5 27.1 - - - -
192D TYR* 1.3 73.6 - - - +
194D PHE* 1.4 61.3 + - - +
195D ILE* 3.6 12.2 - - + +
250D ILE* 3.3 6.7 - - - +
251D ALA 2.7 42.3 + - - +
253D LEU* 3.6 36.3 - - + -
281D ALA* 4.7 2.2 - - + -
282D LEU 3.3 5.6 - - - +
283D LYS* 3.6 42.0 - - + -
284D LEU* 4.6 0.2 - - - -
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Residues in contact with PHE 194 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193D PHE* 1.4 68.7 - - - +
195D ILE* 1.3 58.0 + - - +
196D TYR* 3.9 22.1 - + + -
246D TYR* 4.0 5.4 - - - -
248D ALA* 3.6 27.4 - - + -
249D GLY* 3.4 18.6 - - - -
250D ILE* 4.4 12.8 - - + +
281D ALA* 3.3 2.1 - - - -
282D LEU* 2.8 62.2 + - + +
284D LEU* 4.3 17.6 - - + +
194E PHE* 3.6 35.2 - + - -
196E TYR* 5.1 2.7 - + - -
246E TYR* 4.0 6.3 - - - -
282E LEU* 5.3 3.6 - - + -
194F PHE* 3.9 24.2 - + - -
246F TYR* 6.0 0.2 - - - -
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Residues in contact with ILE 195 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193D PHE* 3.6 16.8 - - + +
194D PHE* 1.3 76.2 - - - +
196D TYR* 1.3 63.7 + - - +
212D ILE* 3.6 29.6 - - + -
229D LEU* 4.4 7.9 - - + -
230D PHE* 4.3 8.2 - - + -
248D ALA* 3.1 5.1 - - - +
249D GLY 2.9 33.4 + - - +
251D ALA* 3.3 34.5 - - + +
253D LEU* 3.8 16.4 - - + -
259D LEU* 3.9 23.3 - - + -
279D PHE* 4.2 8.1 - - + -
280D GLY 3.6 10.8 - - - +
281D ALA* 4.2 3.1 - - + -
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Residues in contact with TYR 196 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147D LEU 4.3 0.9 + - - -
148D GLN* 2.7 40.5 + - - +
194D PHE* 3.9 22.9 - + + -
195D ILE* 1.3 73.0 - - - +
197D GLY* 1.3 60.0 + - - +
212D ILE* 3.9 6.1 - - - -
246D TYR* 3.4 23.6 - - + +
247D SER 3.6 6.5 - - - -
248D ALA* 3.7 5.4 - - + -
278D PHE* 4.2 22.9 - + - -
279D PHE* 3.3 7.4 - - - -
280D GLY* 2.9 61.4 + - - +
281D ALA* 3.7 6.3 - - - -
282D LEU 4.8 0.2 - - - -
194F PHE* 5.3 2.7 - + - -
248F ALA 4.3 4.9 - - - -
249F GLY* 4.2 10.5 - - - -
250F ILE* 3.3 32.4 - - + +
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Residues in contact with GLY 197 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196D TYR* 1.3 79.5 - - - +
198D GLN* 1.3 59.8 + - - -
210D HIS* 3.6 10.6 + - - -
212D ILE* 3.8 9.1 - - - +
246D TYR* 3.4 6.3 - - - -
247D SER 3.1 32.6 + - - +
261D LEU* 4.3 7.2 - - - -
278D PHE* 3.4 11.9 - - - -
279D PHE* 4.2 2.2 - - - -
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Residues in contact with GLN 198 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197D GLY* 1.3 73.2 - - - +
199D VAL* 1.3 74.9 + - - +
210D HIS* 4.3 0.2 - - - -
244D SER* 3.9 15.0 + - - -
245D CYS 3.2 17.3 - - - +
246D TYR* 3.7 17.7 + - + +
261D LEU* 4.7 0.4 - - - +
276D VAL 3.0 19.1 + - - +
277D THR* 3.2 2.1 - - - +
278D PHE* 2.9 57.8 + - + +
231F ARG 2.9 27.5 + - - -
246F TYR 3.9 2.1 - - - +
247F SER* 2.7 29.8 + - - -
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Residues in contact with VAL 199 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166D VAL* 4.7 0.7 - - + -
198D GLN* 1.3 80.8 - - - +
200D LEU* 1.4 63.9 + - - +
201D TYR* 3.5 38.5 - - + +
210D HIS* 3.5 18.2 - - + +
244D SER* 3.3 1.4 - - - -
245D CYS 2.9 27.8 + - - -
261D LEU* 3.6 27.1 - - + -
263D ILE* 4.1 6.1 - - + -
270D ILE* 3.8 21.8 - - + -
276D VAL 3.9 3.6 - - - -
277D THR* 3.7 18.8 - - + +
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Residues in contact with LEU 200 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199D VAL* 1.4 71.9 - - - +
201D TYR* 1.3 63.5 + - - +
202D THR* 4.3 9.4 - - + -
242D ASN* 3.9 11.9 - - - +
243D ASN 3.6 32.8 - - - +
244D SER* 3.7 7.4 - - - +
270D ILE* 3.3 7.3 - - - +
271D SER* 2.9 48.8 + - - +
276D VAL* 3.6 39.2 + - + +
277D THR* 3.3 7.3 + - - -
231F ARG* 4.3 4.9 - - - +
233F ILE* 3.8 25.8 - - + -
29L VAL 5.9 1.3 - - - +
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Residues in contact with TYR 201 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199D VAL* 3.5 32.8 - - + +
200D LEU* 1.3 71.6 - - - +
202D THR* 1.3 62.7 + - - +
203D ASP 3.5 0.7 - - - -
208D MET* 3.6 36.8 - - + -
209D GLY* 3.0 36.3 - - - -
210D HIS* 2.6 33.8 + - - +
234D GLN* 5.2 2.2 - - + -
236D MET* 3.4 20.0 - - + +
242D ASN* 3.4 5.2 - - - -
243D ASN 2.8 44.7 + - - +
245D CYS* 4.2 13.5 - - + -
263D ILE* 3.9 7.0 - - + +
269D GLN 3.8 2.2 - - - +
270D ILE* 3.5 19.3 - - + -
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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