Contacts of the strand formed by residues 220 - 225 (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 ARG 220 (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* 5.7 5.6 - - - +
147F ILE 2.9 17.1 + - - +
148F VAL* 3.5 10.0 - - + -
149F VAL* 3.0 28.8 + - - +
164F ALA 5.4 0.2 + - - -
165F GLY 3.5 23.6 + - - -
166F ASN* 3.4 8.5 + - - +
167F TYR 2.8 28.4 + - - -
168F ASP* 3.8 31.3 + - + +
169F PRO* 4.6 4.9 - - - +
218F ASN 5.0 4.5 - - - +
219F ALA* 1.3 78.5 - - - +
221F ILE* 1.3 59.7 + - - +
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Residues in contact with ILE 221 (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* 3.4 30.7 - - + +
151F ILE* 3.9 22.9 - - + -
156F ILE* 4.3 8.7 - - + -
163F LEU* 4.5 13.2 - - + +
166F ASN* 2.9 30.4 + - + +
167F TYR* 3.3 9.2 - - - +
168F ASP* 2.8 26.9 + - - -
199F ALA* 4.2 20.0 - - + +
202F VAL* 4.1 16.2 - - + -
203F ALA* 3.9 15.3 - - + +
219F ALA 3.9 0.2 + - - -
220F ARG* 1.3 75.6 - - - +
222F GLY* 1.3 64.7 + - - +
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Residues in contact with GLY 222 (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 2.8 10.3 + - - -
150F SER* 3.4 0.6 - - - -
151F ILE* 2.9 30.4 + - - +
156F ILE* 4.1 6.1 - - - +
167F TYR* 4.5 2.0 - - - -
168F ASP 3.8 1.1 - - - -
171F ALA* 3.5 20.5 - - - +
172F SER* 3.2 14.8 - - - -
221F ILE* 1.3 76.9 - - - +
223F GLY* 1.3 58.7 + - - -
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Residues in contact with GLY 223 (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* 4.2 0.2 - - - -
151F ILE* 3.3 12.1 - - - -
155F GLY 5.5 0.4 - - - -
156F ILE* 3.6 22.4 - - - +
171F ALA 3.4 1.0 + - - -
172F SER* 3.0 30.3 + - - -
173F PHE 3.2 3.3 + - - -
182F PRO* 3.3 10.5 - - - +
222F GLY* 1.3 75.2 - - - -
224F VAL* 1.3 64.8 + - - -
225F ARG 4.0 0.7 - - - -
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Residues in contact with VAL 224 (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* 3.6 7.4 - - - +
151F ILE 2.9 7.3 + - - +
152F LEU* 3.3 30.3 - - + -
153F ASP 3.0 27.2 + - - +
155F GLY 4.3 2.5 + - - -
173F PHE* 3.2 8.7 - - + +
175F VAL* 3.7 20.4 - - + -
182F PRO* 4.9 0.2 - - - -
223F GLY* 1.3 73.7 - - - +
225F ARG* 1.3 61.6 + - - +
226F MET* 3.2 6.4 + - + +
239F SER* 3.5 29.6 - - - +
242F LEU* 3.5 31.0 - - + -
247F ILE* 5.7 0.2 - - + -
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Residues in contact with ARG 225 (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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153F ASP 3.7 3.6 - - - -
154F ASP 4.0 16.9 + - - +
155F GLY* 3.8 11.4 - - - +
173F PHE 2.9 9.6 + - - +
174F ASP* 2.8 35.7 + - - +
175F VAL 2.9 24.8 + - - -
176F ASN* 3.2 20.2 + - - +
177F ASP* 2.7 34.9 + - - -
182F PRO* 4.1 9.3 - - + +
183F GLN 3.6 23.6 + - - -
185F ARG* 3.6 23.1 - - - +
223F GLY 4.0 1.4 + - - -
224F VAL* 1.3 70.0 - - - +
226F MET* 1.3 58.7 + - - +
228F ASP* 2.7 40.1 + - + +
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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