Contacts of the strand formed by residues 189 - 201 (chain B) in PDB entry 4ZPK
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 THR 189 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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173B LYS* 3.7 1.4 - - - -
174B CYS* 2.9 51.1 + - - +
177B THR* 3.6 33.8 + - + +
187B SER 3.2 5.9 + - - +
188B ALA* 1.3 73.7 - - - +
190B TRP* 1.3 65.6 + - - +
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Residues in contact with TRP 190 (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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134B PHE 3.8 3.4 - - - -
135B THR 4.2 2.2 - - - -
136B HIS* 3.2 65.3 - + + -
137B PRO* 4.6 6.1 - - + -
171B ARG* 4.1 15.9 - - + -
172B MET 3.6 19.3 - - - -
173B LYS* 3.5 42.2 - - + -
188B ALA* 4.7 9.4 + - + -
189B THR* 1.3 77.0 - - - +
191B LYS* 1.3 58.8 + - - +
192B VAL* 4.3 4.8 + - + +
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Residues in contact with LYS 191 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118B PHE* 3.8 15.7 - - - +
119B MET* 3.9 17.5 - - + -
171B ARG* 4.6 1.3 - - - -
172B MET* 2.9 36.0 + - - +
174B CYS* 3.7 35.4 - - + -
176B VAL* 6.4 1.1 - - - -
178B ASN* 6.2 0.2 - - - -
189B THR 3.6 1.0 + - - -
190B TRP* 1.3 73.8 - - - +
192B VAL* 1.3 70.0 + - - +
193B LEU* 4.3 1.8 - - - +
228B PRO* 3.3 25.8 - - + +
229B ILE 4.1 13.5 + - - -
230B GLN* 5.7 1.2 - - - +
301B GLN* 5.6 2.9 + - - +
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Residues in contact with VAL 192 (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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169B PHE* 4.7 10.3 - - + -
170B MET 3.7 9.0 - - - +
171B ARG* 4.5 10.8 - - + +
190B TRP* 5.0 4.0 - - + +
191B LYS* 1.3 79.7 - - - +
193B LEU* 1.3 64.9 + - - +
194B HIS 4.3 0.2 - - - -
228B PRO* 3.4 22.5 - - - +
229B ILE* 3.8 9.1 + - + -
299B LYS* 4.5 18.8 - - + -
300B GLY* 4.1 12.6 - - - +
301B GLN* 3.8 55.6 + - + +
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Residues in contact with LEU 193 (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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98B PHE* 3.5 41.1 - - + -
119B MET* 3.8 14.4 - - + -
169B PHE* 3.1 12.4 - - - -
170B MET* 2.9 43.2 + - + +
172B MET* 3.6 31.9 - - + -
191B LYS 4.3 3.8 - - - +
192B VAL* 1.3 80.9 - - - +
194B HIS* 1.3 60.7 + - - +
195B CYS* 3.4 12.9 - - - -
226B CYS* 3.9 9.9 - - + -
227B GLU 3.8 4.0 - - - -
228B PRO 3.6 23.8 - - - -
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Residues in contact with HIS 194 (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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342A ARG* 5.5 0.6 + - - -
344A GLN* 5.9 3.0 + - - -
167B ASP* 3.0 30.7 + - - -
168B PHE 3.6 4.4 + - - -
169B PHE* 3.2 37.6 - + + -
192B VAL 4.3 0.4 + - - -
193B LEU* 1.3 68.9 - - - +
195B CYS* 1.3 58.9 + - - +
196B THR* 3.7 17.8 + - + +
225B MET 3.3 3.3 - - - +
226B CYS* 3.3 2.3 - - - -
227B GLU* 2.9 70.1 + - + +
229B ILE* 3.9 8.4 - - + +
303B VAL* 4.6 21.6 - - + +
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Residues in contact with CYS 195 (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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166B ARG 4.6 0.2 - - - -
167B ASP* 3.3 4.9 - - - -
168B PHE* 2.8 57.2 + - + +
170B MET* 3.3 36.6 - - - -
193B LEU* 3.4 22.4 - - - -
194B HIS* 1.3 72.6 + - - +
196B THR* 1.3 64.0 + - - +
224B ILE* 3.7 23.6 - - + -
225B MET 3.5 4.5 - - - -
226B CYS* 4.2 4.7 - - - -
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Residues in contact with THR 196 (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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171A ALA 3.4 9.1 - - - +
342A ARG* 3.6 24.2 + - - +
166B ARG 3.4 4.9 - - - -
167B ASP* 3.4 24.5 - - - +
194B HIS* 3.7 25.5 + - + +
195B CYS* 1.3 80.5 - - - +
197B GLY* 1.3 57.3 + - - +
224B ILE* 4.1 2.2 - - - +
225B MET* 2.9 42.0 + - - +
227B GLU* 5.2 1.2 + - - -
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Residues in contact with GLY 197 (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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171A ALA 3.5 12.8 - - - -
165B GLU* 3.6 4.3 - - - +
166B ARG* 2.9 35.1 + - - +
196B THR* 1.3 75.2 - - - +
198B GLN* 1.3 68.0 + - - +
223B ILE 3.2 13.2 - - - -
224B ILE* 3.8 5.0 - - - +
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Residues in contact with GLN 198 (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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170A GLU* 3.7 27.5 + - + +
171A ALA* 5.3 2.9 - - - -
173A ASP* 5.4 5.9 + - - -
164B THR* 3.3 22.1 + - - -
165B GLU* 2.7 38.2 + - + +
166B ARG 4.7 0.2 - - - +
197B GLY* 1.3 78.0 - - - +
199B VAL* 1.3 67.9 + - - +
200B ARG* 4.1 17.7 + - + +
222B LEU* 3.2 9.1 - - - +
223B ILE* 2.9 31.7 + - + -
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Residues in contact with VAL 199 (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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146B ASN 4.4 3.4 - - - +
147B LEU 4.3 10.1 - - - +
148B THR* 5.5 0.7 - - - -
149B LEU 5.1 11.0 - - - +
164B THR* 3.5 30.5 + - - +
166B ARG* 3.8 20.2 - - + +
198B GLN* 1.3 87.6 + - - +
200B ARG* 1.3 60.4 + - - +
201B VAL* 3.9 6.9 + - + +
220B SER* 3.5 26.0 - - - +
221B CYS 3.3 13.9 - - - +
222B LEU* 3.6 18.4 - - + +
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Residues in contact with ARG 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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170A GLU* 2.4 45.0 + - + +
69B LEU* 4.2 12.1 - - + -
72B SER 5.9 0.2 - - - -
73B VAL* 3.7 27.8 - - + +
198B GLN* 4.1 14.6 + - - +
199B VAL* 1.3 77.1 - - - +
201B VAL* 1.3 80.0 + - - +
220B SER* 3.2 2.6 - - - -
221B CYS* 2.9 31.9 + - - +
223B ILE* 3.8 18.1 - - + +
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Residues in contact with VAL 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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69B LEU* 4.0 3.5 - - - +
72B SER 4.7 5.9 - - - +
199B VAL* 4.3 6.7 - - + +
200B ARG* 1.3 91.8 - - - +
202B TYR* 1.3 71.5 + - - +
203B ASN* 4.3 3.8 - - + +
219B LEU 3.5 13.9 - - - +
220B SER* 3.5 21.5 - - - +
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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