Contacts of the strand formed by residues 202 - 206 (chain B) in PDB entry 3FZ7
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 202 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141B TRP* 3.9 8.8 - - - -
144B ARG* 5.3 2.6 + - - -
156B ASN* 2.6 22.9 + - - +
158B VAL* 4.0 13.0 - - + -
197B ALA 4.0 0.3 + - - -
198B CYS* 3.4 7.5 - - - -
199B ASP* 2.7 38.6 + - - +
200B GLU 3.3 0.7 - - - +
201B ASN* 1.3 74.9 - - - +
203B ILE* 1.3 62.7 - - - +
204B GLY 3.6 25.1 - - - +
238B ILE* 3.8 29.6 - - + +
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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
----------------------------------------------------------
134B GLY 4.1 4.0 - - - +
137B MET* 3.8 40.1 - - + +
138B LYS* 3.9 20.0 - - + +
140B ARG* 5.2 1.9 + - - -
141B TRP* 3.7 36.1 - - + +
155B PRO* 3.6 31.4 - - + -
156B ASN 2.7 18.5 + - - +
157B LEU* 3.8 22.7 - - + -
169B PHE* 4.2 11.9 - - + -
175B VAL* 4.3 7.6 - - + -
201B ASN 4.0 0.4 - - - +
202B THR* 1.3 73.0 - - - +
204B GLY* 1.3 59.9 + - - +
238B ILE* 5.4 0.7 - - - -
239B ASP* 4.9 5.2 + - - +
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Residues in contact with GLY 204 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137B MET* 3.7 15.3 - - - -
157B LEU* 4.0 5.8 - - - +
158B VAL 3.3 21.5 + - - +
202B THR* 3.2 8.7 - - - +
203B ILE* 1.3 82.8 - - - +
205B VAL* 1.3 65.1 + - - -
238B ILE* 4.1 6.5 - - - -
239B ASP 3.2 14.1 - - - -
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Residues in contact with VAL 205 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158B VAL* 3.2 22.2 - - + +
189B MET* 3.8 20.9 - - + -
194B MET* 3.6 28.7 - - - -
198B CYS* 4.0 14.8 - - - -
202B THR* 4.6 0.2 - - + -
204B GLY* 1.3 77.9 - - - +
206B VAL* 1.3 66.4 + - - +
207B PRO* 3.4 11.8 - - + +
227B LEU* 4.2 9.2 - - + -
238B ILE* 3.9 16.8 - - + -
239B ASP 2.9 9.6 + - - +
240B MET* 3.3 9.3 - - + -
241B HIS 3.2 22.3 + - - -
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Residues in contact with VAL 206 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137B MET* 3.7 28.0 - - + -
157B LEU* 3.8 20.6 - - + -
158B VAL 2.8 13.5 + - - +
159B CYS* 3.6 18.2 - - + +
160B GLY 4.0 2.3 + - - -
162B VAL* 4.7 4.9 - - + -
166B TRP* 3.8 39.3 - - + +
189B MET* 3.9 4.5 - - - +
205B VAL* 1.3 78.3 - - - +
207B PRO* 1.3 67.6 - - - +
208B THR* 3.8 3.5 + - - -
241B HIS 3.3 14.1 - - - +
243B ASP* 4.2 4.5 - - + -
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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