Contacts of the strand formed by residues 170 - 176 (chain A) in PDB entry 4JYY
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 LEU 170 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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129A LEU* 3.9 9.0 - - + -
132A ALA* 3.7 25.4 - - + -
133A ILE* 3.8 30.3 - - + +
136A ASP* 2.8 30.2 + - - +
137A PHE* 3.8 18.3 - - + -
162A LEU* 4.2 9.9 - - + -
163A VAL 3.3 13.7 - - - +
164A ALA* 3.8 7.6 - - + -
168A GLY 4.1 4.7 - - - +
169A LYS* 1.3 82.9 - - - +
171A SER* 1.3 64.3 + - - +
189A ILE* 4.1 10.8 - - + -
227A TYR* 3.7 24.0 - - + -
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Residues in contact with SER 171 (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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137A PHE* 3.8 10.5 - - - -
162A LEU* 3.5 4.9 - - - +
163A VAL* 2.9 46.6 + - - +
165A THR* 5.9 2.6 - - - +
169A LYS* 5.2 1.4 + - - -
170A LEU* 1.3 77.4 - - - +
172A ILE* 1.3 68.2 + - - +
173A MET* 5.5 1.4 - - - +
186A LEU* 5.6 2.3 - - - +
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Residues in contact with ILE 172 (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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137A PHE* 3.8 15.4 - - + -
143A PHE* 3.7 29.2 - - + +
146A GLU* 3.8 26.9 + - + +
147A PHE* 3.4 37.9 - - + +
150A SER* 3.5 34.0 + - - +
160A ALA* 5.6 0.2 - - + -
161A TRP 3.3 14.1 - - - +
162A LEU* 4.3 0.9 - - + -
171A SER* 1.3 83.3 - - - +
173A MET* 1.3 68.3 + - - +
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Residues in contact with MET 173 (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* 5.8 0.2 - - - -
160A ALA* 3.8 0.2 - - - -
161A TRP* 2.8 33.6 + - + +
163A VAL* 3.9 20.4 - - + -
171A SER* 4.2 1.3 + - - +
172A ILE* 1.3 77.7 - - - +
174A THR* 1.3 83.9 + - - +
175A THR* 3.9 13.2 - - + -
181A PRO* 3.9 20.2 - - + -
184A LYS* 4.4 26.5 - - + +
186A LEU* 3.8 27.6 - - + -
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Residues in contact with THR 174 (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 25.8 - - - +
154A VAL* 3.5 28.4 - - + +
159A TRP 3.1 13.0 - - - +
160A ALA* 4.2 4.5 - - - -
161A TRP* 4.2 0.7 - - - -
173A MET* 1.3 90.3 - - - +
175A THR* 1.3 70.9 + - - +
176A PRO* 4.6 1.2 - - - +
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Residues in contact with THR 175 (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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154A VAL* 4.7 3.4 - - - +
158A GLY* 3.2 2.9 - - - -
159A TRP* 2.9 35.8 + - - +
161A TRP* 2.8 26.3 + - + +
173A MET* 3.9 16.8 - - + -
174A THR* 1.3 82.7 - - - +
176A PRO* 1.3 68.9 - - + +
179A ASP* 2.6 37.0 + - + +
180A SER 4.1 1.6 - - - -
181A PRO* 4.1 11.2 - - + -
184A LYS* 6.1 2.9 - - + +
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Residues in contact with PRO 176 (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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102A ARG* 5.6 0.2 - - - +
154A VAL* 5.8 1.3 - - + -
157A SER 3.6 7.9 - - - +
174A THR 4.6 1.3 - - - +
175A THR* 1.3 88.0 - - + +
177A ASN* 1.3 82.4 + - - +
178A GLN 3.1 0.2 + - - -
179A ASP* 2.9 39.7 + - + +
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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