Contacts of the strand formed by residues 199 - 209 (chain B) in PDB entry 4ZCH
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 199 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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197B GLU 3.8 0.6 + - - -
198B THR* 1.3 78.0 - - - +
200B TYR* 1.3 68.0 + - - -
201B PHE* 3.3 9.2 - - - -
260B LYS* 3.6 11.5 - - - +
261B LEU 2.8 31.6 + - - +
291B LYS* 4.5 7.6 - - - -
294B GLY 5.4 5.2 - - - -
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Residues in contact with TYR 200 (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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199B GLY* 1.3 76.1 - - - -
201B PHE* 1.3 60.9 + - - +
258B ILE* 4.1 5.2 - - + -
259B ALA 3.5 4.9 - - - -
260B LYS* 3.7 39.6 - - + +
291B LYS* 3.9 4.4 - - - +
292B LEU* 2.9 47.0 + - + +
294B GLY 5.7 0.4 + - - -
305B CYS* 5.0 0.2 - - - -
331B PHE* 3.4 46.5 - + + +
332B LYS 4.7 5.4 + - - -
333B ARG* 3.6 44.3 - - + +
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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
----------------------------------------------------------
185B ALA* 4.2 3.6 - - + -
186B LEU* 3.7 35.7 - - + -
195B VAL* 3.8 16.8 - - + -
197B GLU 3.1 28.7 - - - -
199B GLY 3.3 26.0 - - - -
200B TYR* 1.3 73.8 - - - +
202B PHE* 1.4 61.0 + - - +
203B ILE* 3.7 10.5 + - + +
258B ILE* 3.3 7.6 - - - -
259B ALA 3.1 27.8 + - - -
261B LEU* 3.5 29.4 - - + -
289B ALA* 4.6 2.0 - - + -
290B LEU 3.2 8.3 - - - +
291B LYS* 3.6 42.0 - - + -
292B LEU* 4.6 0.4 - - - -
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Residues in contact with PHE 202 (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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56B LEU* 4.1 22.4 - - + -
106B ALA* 6.1 0.4 - - + -
201B PHE* 1.4 68.3 - - - +
203B ILE* 1.3 57.7 + - - +
204B TYR* 3.6 26.2 - + + -
254B TYR* 4.0 7.6 - - - -
256B ALA* 3.7 27.1 - - + -
257B GLY* 3.6 13.7 - - - -
258B ILE* 4.3 18.2 - - + -
289B ALA* 3.3 2.8 - - - -
290B LEU* 2.8 63.3 + - + +
292B LEU* 4.3 12.4 - - + +
353B PHE* 4.1 28.9 - + - -
355B TYR* 5.2 4.9 - + - -
405B TYR* 4.6 3.4 - - - -
441B LEU* 5.2 6.7 - - + -
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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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201B PHE* 3.9 14.1 - - + +
202B PHE* 1.3 77.6 - - - +
204B TYR* 1.4 64.5 + - - +
220B ILE* 3.7 26.2 - - + -
237B LEU* 4.0 15.0 - - + -
238B PHE* 4.4 7.6 - - + -
256B ALA* 3.2 5.2 - - - +
257B GLY 2.8 33.6 + - - +
259B ALA* 4.0 24.5 - - + +
261B LEU* 3.9 23.1 - - + -
267B LEU* 4.0 22.2 - - + -
287B PHE* 4.1 7.0 - - + -
288B GLY 3.5 12.6 - - - +
289B ALA* 4.6 1.6 - - + -
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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
----------------------------------------------------------
56B LEU* 5.5 0.7 - - + -
106B ALA 4.3 7.6 - - - -
107B GLY* 4.4 1.6 - - - -
108B VAL* 3.7 30.4 - - + +
155B LEU 4.3 1.9 + - - -
156B GLN* 2.9 40.7 + - + +
202B PHE* 3.6 23.3 - + - -
203B ILE* 1.4 75.7 - - - +
205B GLY* 1.3 59.3 + - - +
220B ILE* 3.7 7.9 - - - -
254B TYR* 3.5 24.2 - + + +
255B SER 3.5 7.0 - - - +
256B ALA* 3.6 5.2 - - + -
286B PHE* 4.0 28.3 - + - -
287B PHE* 3.2 5.9 - - - -
288B GLY* 2.8 61.0 + - - +
289B ALA* 4.1 7.4 + - - -
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Residues in contact with GLY 205 (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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204B TYR* 1.3 78.6 - - - +
206B GLN* 1.3 60.7 + - - -
218B HIS* 3.5 9.2 + - - -
220B ILE* 3.6 6.3 - - - +
254B TYR* 3.4 7.1 - - - -
255B SER 3.1 30.9 + - - +
269B LEU* 4.1 15.0 - - - -
286B PHE* 3.5 10.8 - - - -
287B PHE* 4.1 0.4 - - - -
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Residues in contact with GLN 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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87B ARG 3.0 24.6 + - - +
88B CYS* 4.8 0.2 - - - -
104B TYR 4.2 1.4 - - - +
105B SER* 2.8 26.6 + - - -
176B TRP* 4.8 0.2 - - - -
205B GLY* 1.3 74.3 - - - +
207B VAL* 1.3 74.3 + - - +
218B HIS* 4.1 0.4 - - - -
252B SER* 4.0 14.1 + - - -
253B CYS 3.2 15.7 - - - +
254B TYR* 3.6 15.0 - - + +
269B LEU* 4.5 0.4 - - - +
284B VAL* 2.8 27.9 + - - +
285B THR* 3.4 1.2 - - - +
286B PHE* 2.9 61.0 + - + +
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Residues in contact with VAL 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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174B VAL* 4.8 0.9 - - + -
176B TRP* 5.3 0.2 - - + -
206B GLN* 1.3 80.2 - - - +
208B LEU* 1.3 63.7 + - - +
209B TYR* 3.5 29.7 - - + +
218B HIS* 3.5 24.2 - - + +
252B SER* 3.3 1.9 - - - -
253B CYS* 2.8 33.0 + - - -
269B LEU* 3.6 27.4 - - + -
271B ILE* 4.2 7.2 - - + -
278B ILE* 3.8 20.9 - - + -
284B VAL 4.1 3.4 - - - -
285B THR* 3.8 16.6 - - + -
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Residues in contact with LEU 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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87B ARG* 6.2 0.7 - - - +
89B ILE* 3.9 19.3 - - + -
207B VAL* 1.3 73.0 - - - +
209B TYR* 1.3 60.1 + - - +
210B THR* 4.8 1.8 - - + -
250B ASN* 3.4 27.4 - - - +
251B ASN 3.5 29.8 - - - +
252B SER* 3.5 5.2 - - - +
278B ILE* 3.3 7.4 - - - +
279B SER* 2.8 52.8 + - - +
284B VAL* 3.6 36.5 + - + -
285B THR* 3.1 10.0 + - - +
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Residues in contact with TYR 209 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207B VAL* 3.5 20.6 - - + -
208B LEU* 1.3 74.9 - - - +
210B THR* 1.3 66.3 + - - +
211B ASP 3.6 1.3 - - - +
216B MET* 3.5 40.6 - - + -
217B GLY* 2.8 44.8 - - - -
218B HIS* 2.8 21.3 + - - +
242B GLN* 5.0 2.2 - - + -
244B MET* 3.6 15.4 - - + +
250B ASN* 3.7 1.9 - - - -
251B ASN 3.1 38.6 + - - +
253B CYS* 3.5 24.4 - - + +
271B ILE* 4.4 7.4 - - + -
277B GLN 3.7 4.0 - - - +
278B ILE* 3.5 18.6 - - + -
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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