Contacts of the strand formed by residues 185 - 189 (chain A) in PDB entry 1JEH
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 185 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183A PRO* 3.6 6.6 - - - +
184A LYS* 1.3 86.8 - - - +
186A LEU* 1.3 60.5 + - - +
187A THR* 4.0 1.3 - - - +
208A LYS* 3.5 28.3 - - + +
258A VAL* 3.5 2.4 - - - +
275A GLU* 3.2 54.6 + - - +
276A ALA* 3.8 12.3 - - + +
277A GLU* 3.0 56.5 + - - -
278A VAL 3.4 8.8 + - - +
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Residues in contact with LEU 186 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171A VAL* 5.4 0.9 - - + -
176A ALA* 5.9 1.1 - - + -
179A LEU* 4.9 4.5 - - + -
183A PRO* 3.9 13.2 - - + -
185A ARG* 1.3 73.8 - - - +
187A THR* 1.3 64.3 + - - +
188A ILE* 4.2 17.5 - - + -
198A MET 4.0 9.6 - - - +
202A TYR* 3.7 38.6 - - + -
207A SER* 4.0 9.0 - - - -
208A LYS 3.3 8.9 + - - -
209A VAL* 3.2 13.2 - - + +
210A THR 3.2 19.8 + - - -
278A VAL* 3.5 36.3 - - + +
280A LEU* 4.6 15.5 - - + -
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Residues in contact with THR 187 (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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185A ARG* 5.4 1.2 - - - +
186A LEU* 1.3 74.0 + - - +
188A ILE* 1.3 65.5 + - - +
189A ILE* 5.1 0.9 - - + -
210A THR* 3.5 17.8 + - - +
212A VAL* 4.0 26.0 - - + -
261A ILE* 3.7 24.1 - - + +
274A LEU* 4.4 11.2 - - + +
275A GLU 4.9 1.9 + - - -
276A ALA* 3.2 17.1 - - - +
278A VAL 3.1 6.9 + - - +
279A LEU* 3.4 17.9 - - + -
280A LEU* 2.8 25.3 + - - +
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Residues in contact with ILE 188 (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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186A LEU* 4.2 11.0 - - + +
187A THR* 1.3 80.7 - - - +
189A ILE* 1.3 67.0 + - - +
190A GLY 3.6 20.6 - - - +
195A GLY* 3.4 33.9 - - - +
198A MET 4.1 1.3 - - - -
199A GLY* 3.6 23.8 - - - +
209A VAL* 3.9 10.8 - - + -
210A THR 2.9 11.9 + - - +
211A VAL* 3.5 7.8 - - + -
212A VAL* 2.8 29.8 + - - +
280A LEU* 3.5 27.1 - - + +
282A ALA* 4.3 7.9 - - + -
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Residues in contact with ILE 189 (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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160A PHE* 5.2 0.7 - - + -
163A ILE* 3.8 28.9 - - + -
187A THR* 5.1 1.6 - - + -
188A ILE* 1.3 76.3 - - - +
190A GLY* 1.3 59.0 + - - +
212A VAL* 3.5 16.2 - - + +
213A GLU* 6.0 0.4 - - - -
247A VAL* 3.7 34.5 - - + -
261A ILE* 5.9 0.7 - - + -
279A LEU* 3.7 27.4 - - + -
280A LEU 2.8 15.9 + - - +
281A VAL* 4.1 12.1 - - + -
282A ALA* 2.8 32.9 + - - -
283A VAL* 3.2 22.2 + - + -
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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