Contacts of the strand formed by residues 148 - 153 (chain F) in PDB entry 4RYD
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 VAL 148 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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146F GLY 4.6 2.9 - - - +
147F ILE* 1.3 77.2 - - - +
149F VAL* 1.3 63.6 + - - +
168F ASP* 3.9 11.7 - - - +
171F ALA* 3.5 30.5 - - + -
220F ARG* 3.5 13.9 - - + +
246F HIS* 3.5 39.5 - - + +
247F ILE* 3.8 13.9 - - + -
248F HIS* 2.6 43.5 + - + +
249F ILE 3.1 8.0 + - - +
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Residues in contact with VAL 149 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147F ILE* 4.5 2.5 - - + -
148F VAL* 1.3 80.8 - - - +
150F SER* 1.3 70.0 + - - +
151F ILE* 4.5 6.7 - - + -
171F ALA* 4.3 1.9 - - - +
202F VAL* 3.9 24.9 - - + -
219F ALA* 4.9 4.7 - - + -
220F ARG 3.0 9.1 + - - +
221F ILE* 3.4 17.6 - - + +
222F GLY* 2.8 24.1 + - - -
247F ILE* 4.7 0.2 - - - -
249F ILE* 3.3 40.6 - - + +
251F SER* 4.9 1.1 - - - -
375F ALA* 4.5 7.6 - - + +
379F ALA* 4.2 15.9 - - + -
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Residues in contact with SER 150 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149F VAL* 1.3 75.8 - - - +
151F ILE* 1.3 64.4 + - - +
152F LEU* 3.7 2.1 + - - +
171F ALA* 2.8 26.4 + - - -
222F GLY 3.4 5.1 + - - -
224F VAL* 3.6 19.4 - - - +
247F ILE* 3.8 26.1 - - - +
249F ILE 2.9 7.8 + - - -
250F TYR* 3.5 10.6 - - - +
251F SER* 3.0 25.8 + - - -
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Residues in contact with ILE 151 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149F VAL* 4.5 1.8 - - + -
150F SER* 1.3 74.3 + - - +
152F LEU* 1.3 58.5 + - - +
153F ASP* 3.3 26.3 + - + +
155F GLY 5.7 1.7 - - - +
156F ILE* 5.7 1.6 - - + -
195F GLY* 3.9 16.8 - - - +
198F CYS* 4.1 14.4 - - + +
199F ALA* 3.8 25.1 - - + +
202F VAL* 4.0 23.6 - - + -
221F ILE* 3.9 10.5 - - + -
222F GLY 2.9 18.6 + - - +
223F GLY* 3.3 4.0 - - - -
224F VAL 2.9 23.6 + - - +
251F SER* 3.8 26.9 - - - +
253F SER 6.3 0.2 - - - +
372F PRO* 5.3 0.2 - - + -
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Residues in contact with LEU 152 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150F SER* 4.0 10.3 - - - +
151F ILE* 1.3 69.6 - - - +
153F ASP* 1.3 63.1 + - - +
224F VAL* 3.3 35.0 - - + -
226F MET* 3.9 9.6 - - + -
239F SER* 3.8 27.4 - - - +
240F LEU* 3.5 33.2 - - + +
250F TYR* 4.2 18.6 - - + -
251F SER 3.0 18.5 + - - +
252F ALA* 4.2 4.8 - - + -
253F SER 4.5 0.2 + - - -
254F TRP* 2.8 42.0 + - + +
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Residues in contact with ASP 153 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151F ILE* 3.3 12.7 + - + +
152F LEU* 1.3 77.7 - - - +
154F ASP* 1.3 69.5 + - - +
155F GLY 3.3 5.6 - - - +
194F HIS* 2.7 38.3 + - - -
195F GLY* 3.1 27.4 + - - -
198F CYS* 4.5 2.9 - - - -
224F VAL 3.0 9.2 + - - +
226F MET* 2.8 31.8 + - - -
227F LEU* 2.9 28.9 + - - +
253F SER* 4.1 11.6 + - - +
254F TRP* 4.3 0.2 - - - -
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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