Contacts of the strand formed by residues 178 - 185 (chain A) in PDB entry 2JIL
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 178 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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167A ARG* 5.0 1.1 - - - +
168A GLY* 4.6 0.7 - - - -
169A GLY* 2.9 29.7 + - - +
177A SER* 1.3 83.1 - - - +
179A PRO* 1.3 78.7 - - + +
180A VAL 3.6 0.2 + - - -
1244A SCN 3.8 34.2 - - - +
195B GLY 4.3 0.7 - - - +
196B THR* 2.7 40.5 + - - +
198B LYS* 3.6 20.2 - - + +
199B PRO 5.6 0.6 + - - -
201B ASP* 2.7 39.4 + - - -
236B TYR* 3.2 33.9 - - - +
237B ASP 5.3 0.4 + - - -
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Residues in contact with PRO 179 (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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167A ARG* 4.2 3.5 + - - +
168A GLY* 3.6 9.9 - - - -
177A SER 4.7 0.9 - - - +
178A ARG* 1.3 90.8 - - + +
180A VAL* 1.3 63.4 + - - +
181A VAL* 3.5 15.3 + - + +
202A ARG* 3.5 44.4 - - + +
211A LEU 5.9 2.0 - - - +
194B GLU 4.4 5.4 - - - +
195B GLY* 3.1 36.8 - - - +
196B THR* 4.4 2.7 - - - +
198B LYS* 5.6 0.4 - - - +
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Residues in contact with VAL 180 (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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166A ILE* 3.9 32.8 - - + -
167A ARG 3.3 10.5 - - - +
168A GLY 4.2 4.3 - - - +
169A GLY* 4.0 21.8 - - - +
179A PRO* 1.3 70.9 - - - +
181A VAL* 1.3 63.7 + - - +
202A ARG* 3.5 5.9 - - - +
203A LEU* 2.9 47.8 + - + +
211A LEU* 4.2 35.3 + - + +
214A THR* 5.1 1.6 - - - +
219A ALA* 4.4 10.1 - - + -
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Residues in contact with VAL 181 (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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166A ILE* 3.4 3.4 - - - -
167A ARG* 2.9 72.5 + - + +
179A PRO* 3.6 20.4 - - + +
180A VAL* 1.3 80.8 - - - +
182A ILE* 1.3 77.3 + - - +
183A THR* 3.5 1.1 + - + -
200A GLY* 3.9 18.2 - - - +
201A ASP 3.5 11.7 - - - +
202A ARG* 4.6 6.5 - - + -
194B GLU* 5.6 3.4 - - - +
196B THR* 4.9 4.0 - - - +
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Residues in contact with ILE 182 (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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164A PHE* 3.7 34.3 - - + -
165A VAL 3.3 8.7 - - - +
166A ILE* 4.2 5.6 - - + -
181A VAL* 1.3 76.2 - - - +
183A THR* 1.3 59.5 + - - +
184A SER 3.8 17.0 - - - +
185A VAL* 4.2 4.0 - - + -
197A ILE* 3.5 44.9 - - + -
198A LYS 4.1 10.3 - - - +
200A GLY 2.7 31.0 + - - -
201A ASP* 2.9 18.0 + - + +
203A LEU* 4.4 18.6 - - + -
234A ILE* 4.5 11.0 - - + -
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Residues in contact with THR 183 (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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165A VAL* 2.8 26.0 + - - +
167A ARG* 3.5 49.1 - - + +
181A VAL* 3.8 2.7 - - + +
182A ILE* 1.3 75.6 - - - +
184A SER* 1.3 62.1 + - - +
199A PRO* 3.8 15.1 - - - +
200A GLY 4.9 0.2 - - - +
149B ARG* 3.8 15.0 + - - +
240B GLU* 2.7 26.6 + - - +
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Residues in contact with SER 184 (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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164A PHE* 3.2 7.8 - - - +
165A VAL* 2.9 45.5 + - - +
182A ILE* 3.7 3.6 - - - +
183A THR* 1.3 82.0 + - - +
185A VAL* 1.3 71.1 + - - +
186A ARG* 5.5 0.3 - - - -
199A PRO* 4.2 7.4 - - - +
240B GLU* 5.7 0.2 - - - -
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Residues in contact with VAL 185 (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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163A GLY 3.6 7.0 - - - +
164A PHE* 4.3 3.6 - - + -
182A ILE* 4.2 4.7 - - + -
184A SER* 1.3 85.4 + - - +
186A ARG* 1.3 64.3 + - - +
187A PRO* 3.4 9.2 - - - +
191A ALA* 4.2 3.8 - - + -
192A ASP* 3.7 41.5 - - + +
197A ILE* 3.7 40.8 - - + +
198A LYS* 5.8 0.4 - - + -
199A PRO* 4.3 16.4 - - + +
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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