Contacts of the strand formed by residues 200 - 212 (chain B) in PDB entry 6ZGI
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 200 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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355A ARG* 3.0 27.0 + - - -
394A ASN* 5.4 2.0 + - + +
396A TYR* 4.0 18.3 - + - -
464A PHE* 4.9 8.0 - + + -
514A SER* 4.4 8.5 + - - -
196B ASN* 3.4 6.1 + - - -
197B ILE 2.9 36.3 + - - +
198B ASP* 3.3 27.4 - - + -
199B GLY* 1.3 78.1 - - - +
201B PHE* 1.3 60.5 + - - +
202B LYS* 3.8 13.4 + - + +
228B ASP* 3.1 31.2 - - - +
229B LEU 3.3 8.1 - - - -
230B PRO* 4.0 23.1 - - + -
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Residues in contact with PHE 201 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86B PHE* 4.3 16.2 - + - -
106B PHE* 3.9 21.1 - + - -
117B LEU* 4.2 8.7 - - + -
119B ILE* 4.2 9.9 - - + -
194B PHE* 3.7 24.5 - + + -
195B LYS 3.4 12.8 - - - -
196B ASN* 4.1 5.2 - - - +
199B GLY 4.1 0.6 + - - -
200B TYR* 1.3 70.1 - - - +
202B LYS* 1.3 60.7 + - - +
203B ILE* 3.6 34.6 - - + +
227B VAL 3.9 1.0 - - - +
228B ASP* 3.5 1.4 - - - -
229B LEU* 2.9 47.5 + - + +
231B ILE* 3.6 21.5 - - + +
235B ILE* 3.8 30.3 - - + -
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Residues in contact with LYS 202 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193B VAL 3.5 0.9 - - - +
194B PHE* 3.5 4.9 - - - -
195B LYS* 2.9 56.0 + - + +
197B ILE* 4.9 20.9 - - + +
200B TYR* 4.4 16.4 - - - +
201B PHE* 1.3 73.8 - - - +
203B ILE* 1.3 63.0 + - - +
204B TYR* 4.3 27.9 + - + +
227B VAL 3.6 4.9 - - - +
228B ASP* 3.5 32.5 - - - +
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Residues in contact with ILE 203 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119B ILE* 4.1 17.5 - - + -
128B ILE* 5.9 2.2 - - + -
192B PHE* 4.3 6.7 - - + -
193B VAL 3.4 2.0 - - - -
194B PHE* 3.7 22.9 - - + -
201B PHE* 3.6 32.5 - - + -
202B LYS* 1.3 76.6 - - - +
204B TYR* 1.3 74.1 + - - +
225B PRO* 4.3 0.2 - - - +
226B LEU* 2.9 41.8 + - + +
227B VAL* 2.9 41.0 + - + +
229B LEU* 4.5 3.6 - - + -
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Residues in contact with TYR 204 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B TYR* 3.7 35.1 - + + -
38B TYR 3.9 10.3 - - - -
39B PRO 4.7 8.1 + - - -
192B PHE* 3.3 4.3 - - - +
193B VAL* 2.9 52.2 + - + +
195B LYS* 4.0 26.9 + - + -
202B LYS* 4.3 28.2 + - + +
203B ILE* 1.3 78.7 - - - +
205B SER* 1.3 64.5 + - - +
223B LEU* 4.1 15.0 - - + -
224B GLU 3.4 8.5 - - - +
225B PRO* 3.5 34.8 - - + -
226B LEU 4.1 0.4 - - - +
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Residues in contact with SER 205 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191B GLU 3.2 7.2 - - - -
192B PHE* 3.6 30.0 - - - +
204B TYR* 1.3 77.1 - - - +
206B LYS* 1.3 66.6 + - - +
207B HIS* 5.0 9.0 + - - -
223B LEU* 4.1 6.4 - - - +
224B GLU* 3.2 26.4 + - - +
226B LEU* 3.7 26.2 - - - +
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Residues in contact with LYS 206 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189B LEU 4.0 0.5 - - - +
190B ARG* 3.6 2.1 - - - -
191B GLU* 2.9 36.0 + - - +
192B PHE* 6.1 0.2 - - - -
205B SER* 1.3 78.6 - - - +
207B HIS* 1.3 80.3 + - - +
208B THR* 4.1 6.0 + - - +
221B SER* 3.2 27.8 - - - +
222B ALA 3.2 20.6 - - - +
223B LEU* 3.6 17.0 - - + +
224B GLU* 4.4 25.6 + - - -
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Residues in contact with HIS 207 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188B ASN* 6.2 1.8 - - - +
189B LEU 3.6 3.4 - - - +
190B ARG* 3.5 46.8 + - + +
192B PHE* 4.6 14.7 - + - -
205B SER* 5.0 9.0 + - - -
206B LYS* 1.3 87.1 + - - +
208B THR* 1.3 67.5 + - - +
209B PRO* 4.5 2.5 - - - +
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Residues in contact with THR 208 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34B ARG* 5.7 2.8 + - - +
188B ASN* 3.7 7.7 + - - +
189B LEU* 2.9 50.3 + - + +
191B GLU* 6.0 1.7 - - - -
206B LYS* 4.1 10.7 + - - +
207B HIS* 1.3 77.0 + - - +
209B PRO* 1.3 83.8 - - + +
210B ILE* 4.2 9.0 - - + -
221B SER* 4.4 12.4 + - - -
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Residues in contact with PRO 209 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187B LYS 3.8 8.5 - - - +
188B ASN* 4.7 4.7 - - - +
207B HIS 4.5 2.5 - - - +
208B THR* 1.3 93.6 - - + +
210B ILE* 1.3 65.2 + - - +
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Residues in contact with ILE 210 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34B ARG* 6.1 0.4 - - - +
95B THR* 4.2 14.8 - - + -
186B PHE* 3.9 9.9 - - + +
187B LYS* 3.2 39.4 + - - +
188B ASN 3.7 12.3 - - - +
189B LEU* 3.9 36.1 - - + -
208B THR* 4.2 8.5 - - + +
209B PRO* 1.3 79.0 - - - +
211B ASN* 1.3 63.7 + - - +
212B LEU* 3.9 33.4 - - + -
217B PRO* 4.8 4.7 - - + -
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Residues in contact with ASN 211 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185B ASN* 2.8 38.2 + - - +
186B PHE 3.6 3.7 - - - +
187B LYS* 5.3 4.2 - - - +
210B ILE* 1.3 75.4 - - - +
212B LEU* 1.3 62.3 + - - +
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Residues in contact with LEU 212 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95B THR* 4.8 7.6 - - + -
185B ASN* 3.2 6.2 - - - +
186B PHE* 3.0 40.4 + - + +
210B ILE* 3.9 28.9 - - + -
211B ASN* 1.3 76.5 + - - +
213B VAL* 1.3 69.0 + - - +
214B ARG* 3.8 22.7 - - - +
215B ASP 4.0 7.9 - - - +
217B PRO* 3.6 40.4 - - + -
266B TYR* 6.0 0.4 - - - +
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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