Contacts of the strand formed by residues 174 - 181 (chain B) in PDB entry 4JF7
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 TRP 174 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151B PHE* 3.8 12.8 - + - -
167B PHE* 3.8 23.8 - + + -
168B SER 3.0 11.0 - - - +
169B LEU* 3.9 10.1 - - + -
173B HIS* 1.3 79.4 - - - +
175B CYS* 1.3 72.5 + - - +
176B TYR* 4.0 7.0 - - + -
196B SER* 3.6 21.3 - - - -
197B MET* 3.3 20.3 - - - +
198B GLY* 2.9 47.0 + - - -
199B ILE* 3.0 28.5 + - - +
200B ILE* 4.0 5.6 - - + -
210B PHE* 3.2 37.3 - + + -
211B ARG 3.5 24.0 - - - -
212B THR* 3.7 19.3 - - - -
231B THR* 4.1 0.2 - - - -
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Residues in contact with CYS 175 (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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167B PHE* 3.4 7.1 - - - -
168B SER* 2.7 37.1 + - - +
173B HIS* 3.9 2.7 - - - -
174B TRP* 1.3 78.6 - - - +
176B TYR* 1.3 59.6 + - - +
196B SER 3.5 5.2 - - - -
229B ILE* 3.7 21.0 - - + +
231B THR* 3.8 16.2 - - + +
235B GLY 3.3 13.0 - - - -
236B CYS* 2.0 49.8 - - - -
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Residues in contact with TYR 176 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151B PHE* 3.8 26.7 - + + -
152B ILE* 3.4 35.4 - - + +
153B PRO* 5.1 0.2 - - + -
165B PRO* 3.6 20.2 - - + +
166B SER 3.5 9.6 - - - -
167B PHE* 4.2 13.7 - + + -
174B TRP* 4.0 4.0 - - + -
175B CYS* 1.3 74.8 - - - +
177B THR* 1.3 79.6 + - - +
178B HIS* 2.6 43.1 + + - +
194B PHE* 4.1 11.7 - + - -
195B VAL* 3.3 5.0 - - - +
196B SER* 2.7 55.1 + - - +
229B ILE* 4.2 2.4 - - - +
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Residues in contact with THR 177 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164B ILE 5.3 0.4 - - - +
165B PRO* 3.3 1.4 - - - +
166B SER* 3.0 49.8 + - - +
176B TYR* 1.3 88.6 - - - +
178B HIS* 1.3 61.7 + - - +
193B GLN* 2.7 30.9 + - - +
194B PHE 2.6 21.1 + - - -
195B VAL* 3.6 2.5 - - - +
227B CYS* 4.5 5.4 - - + +
229B ILE* 3.9 18.6 - - + -
238B MET* 3.4 17.1 - - - -
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Residues in contact with HIS 178 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149A PRO* 5.8 0.6 - - - +
152B ILE* 3.8 11.6 - - + +
153B PRO* 3.6 35.6 + - + +
162B THR* 3.7 24.3 - - - +
163B ARG 3.4 12.1 - - - +
164B ILE 3.6 8.3 - - - +
165B PRO* 3.9 4.3 - - + -
176B TYR* 2.6 28.3 + + - +
177B THR* 1.3 76.9 + - - +
179B ASN* 1.3 71.6 + - - +
180B VAL* 3.9 13.2 - - + +
193B GLN* 3.1 13.0 + - - +
194B PHE* 2.9 39.6 + + + +
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Residues in contact with ASN 179 (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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161B CYS 3.6 1.1 - - - +
162B THR* 3.3 5.2 - - - -
163B ARG* 2.8 42.5 + - + +
164B ILE* 4.1 11.6 + - + -
178B HIS* 1.3 74.6 - - - +
180B VAL* 1.3 60.4 + - - +
181B ILE* 3.4 20.4 - - - +
191B SER* 3.0 23.1 + - - -
192B ASN 3.3 6.2 + - - -
193B GLN* 3.1 22.1 + - - +
224B ARG 3.2 11.5 + - - -
225B LYS* 3.4 29.1 + - - +
226B SER 6.1 1.3 - - - +
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Residues in contact with VAL 180 (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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147A ASN* 3.9 24.7 - - - +
149A PRO* 4.5 12.3 - - + -
161B CYS 3.4 7.0 - - - +
162B THR* 4.3 9.4 - - + -
178B HIS* 3.9 21.1 - - + +
179B ASN* 1.3 77.9 - - - +
181B ILE* 1.3 63.8 + - - +
182B LEU* 4.3 6.2 + - + -
191B SER* 3.3 5.0 - - - -
192B ASN* 2.7 43.4 + - - +
194B PHE* 4.5 4.5 - - + -
217B TYR* 3.5 39.3 - - + +
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Residues in contact with ILE 181 (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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160B GLY* 4.0 0.5 - - - -
161B CYS* 2.9 41.1 + - + +
163B ARG* 6.3 1.8 - - + -
179B ASN* 3.4 17.3 - - - +
180B VAL* 1.3 75.9 - - - +
182B LEU* 1.3 65.1 + - - +
183B ASN 3.5 5.1 + - - +
184B GLY 3.1 20.2 - - - +
185B CYS* 3.8 25.4 - - - +
186B GLN 4.5 0.7 - - - +
187B ASP* 3.8 34.3 - - + +
190B SER 4.4 2.5 - - - +
191B SER* 3.9 11.2 - - - +
225B LYS* 3.4 23.6 - - - +
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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
------------------------------------------------------------
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