Contacts of the strand formed by residues 220 - 225 (chain A) in PDB entry 4Z2A
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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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146A GLY* 4.5 18.1 + - - +
147A ILE 2.9 12.2 + - - +
148A VAL* 3.5 24.9 - - + +
149A VAL* 3.0 27.9 + - - +
166A ASN* 3.3 14.1 - - - +
167A TYR 5.4 1.3 - - - +
168A ASP* 3.6 27.6 + - + +
218A ASN 5.3 2.0 - - - +
219A ALA* 1.3 78.0 - - - +
221A ILE* 1.3 60.4 + - - +
246A HIS* 3.5 25.1 - - - -
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Residues in contact with ILE 221 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149A VAL* 3.3 37.0 - - + +
151A ILE* 4.1 12.8 - - + -
156A ILE* 4.5 6.1 - - + -
163A LEU* 4.5 18.8 - - + +
166A ASN* 2.9 25.0 + - + +
167A TYR* 3.4 8.4 - - - +
168A ASP* 2.8 26.2 + - - -
171A ALA* 4.4 0.2 - - - -
199A ALA* 3.9 25.1 - - + +
202A VAL* 4.1 15.9 - - + -
203A ALA* 3.6 18.6 - - + -
220A ARG* 1.3 75.7 - - - +
222A GLY* 1.3 66.8 + - - +
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Residues in contact with GLY 222 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149A VAL 2.9 10.0 + - - +
150A SER* 3.3 2.8 - - - -
151A ILE* 2.9 26.7 + - - +
156A ILE* 4.1 9.5 - - - +
167A TYR* 4.5 0.7 - - - -
168A ASP 3.9 0.4 - - - -
171A ALA* 3.7 18.9 - - - +
172A SER* 3.0 15.5 - - - -
221A ILE* 1.3 76.7 - - - +
223A GLY* 1.3 59.2 + - - -
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Residues in contact with GLY 223 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150A SER* 3.9 1.6 - - - -
151A ILE* 3.3 12.6 - - - -
155A GLY 5.5 1.1 - - - -
156A ILE* 3.7 20.5 - - - +
171A ALA 3.6 0.8 + - - -
172A SER* 2.9 29.7 + - - -
173A PHE 3.1 2.8 + - - -
182A PRO* 3.4 9.7 - - - +
222A GLY* 1.3 75.6 - - - -
224A VAL* 1.3 65.3 + - - -
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Residues in contact with VAL 224 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150A SER* 3.8 4.7 - - - +
151A ILE 2.8 9.0 + - - +
152A LEU* 3.4 30.3 - - + -
153A ASP 3.1 28.4 + - - +
155A GLY* 4.1 3.6 + - - -
173A PHE* 3.1 10.5 - - + +
175A VAL* 3.7 17.7 - - + -
223A GLY* 1.3 75.8 - - - +
225A ARG* 1.3 61.1 + - - +
226A MET* 3.3 19.6 + - + -
239A SER* 3.7 14.4 - - - +
242A LEU* 3.6 34.3 - - + -
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Residues in contact with ARG 225 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153A ASP 3.8 3.4 - - - -
154A ASP 3.8 16.1 + - - +
155A GLY* 3.8 11.4 - - - +
173A PHE 2.8 8.7 + - - +
174A ASP* 2.9 37.0 + - - +
175A VAL 2.8 29.6 + - - -
176A ASN* 3.2 16.8 + - - +
177A ASP* 3.1 28.9 + - - -
182A PRO* 3.9 11.6 - - + +
183A GLN 3.4 24.9 + - - -
184A PRO* 4.4 3.8 - - - +
185A ARG* 3.1 29.6 - - - +
223A GLY 4.0 1.4 + - - -
224A VAL* 1.3 69.1 - - - +
226A MET* 1.3 59.3 + - - +
228A ASP* 2.9 40.5 + - + +
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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