Contacts of the helix formed by residues 187 - 196 (chain C) in PDB entry 1JLH
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 ASP 187 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185C ASN* 2.9 26.7 + - + +
186C ILE* 1.3 78.2 - - - +
188C GLY* 1.3 63.1 + - - +
189C THR* 2.9 34.4 + - - +
190C HIS* 2.9 20.8 + - - +
191C ILE* 4.3 1.0 + - - +
341D ASP* 3.3 12.7 - - - +
342D GLN* 2.8 28.7 + - + +
411D THR* 4.5 5.4 + - - -
420D HIS* 4.8 0.6 - - - -
421D HIS* 5.0 1.7 + - - -
424D LEU* 3.7 28.9 - - + +
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Residues in contact with GLY 188 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186C ILE 3.0 5.1 + - - -
187C ASP* 1.3 73.6 + - - +
189C THR* 1.3 56.7 + - - +
190C HIS 3.2 0.2 - - - -
191C ILE* 3.3 5.1 - - - +
192C ALA* 2.9 33.1 + - - +
411D THR* 5.6 1.1 + - - -
413D HIS* 4.3 9.4 - - - -
415D ILE* 3.7 8.7 - - - +
420D HIS* 3.5 33.1 - - - +
421D HIS* 5.0 1.4 - - - +
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Residues in contact with THR 189 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187C ASP* 2.9 18.8 + - - +
188C GLY* 1.3 73.7 - - - +
190C HIS* 1.3 64.0 + - - +
192C ALA* 4.1 0.2 - - - -
193C LYS* 2.9 37.1 + - - +
341D ASP* 5.3 3.1 - - - +
342D GLN* 3.4 23.7 - - - +
343D TYR* 3.8 28.7 + - + -
411D THR* 4.1 12.8 - - - +
412D GLN* 4.9 2.5 - - + +
413D HIS* 3.4 33.2 + - + +
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Residues in contact with HIS 190 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160C ASP* 5.8 0.2 - - - -
164C LEU* 6.6 0.2 - - + -
182C TYR 3.1 21.6 + - - -
183C VAL* 4.3 5.4 - - + -
184C SER* 3.1 31.7 + - - -
185C ASN* 3.1 33.1 + - + +
187C ASP 2.9 14.5 + - - +
189C THR* 1.3 84.9 + - - +
191C ILE* 1.3 61.6 + - - +
193C LYS* 3.7 12.6 - - - +
194C THR* 2.8 30.9 + - - -
342D GLN* 4.0 33.3 + - + -
385D ASN* 4.9 1.1 - - - -
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Residues in contact with ILE 191 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152C ILE* 5.4 0.2 - - + -
154C ILE* 4.5 6.1 - - + -
183C VAL* 4.0 25.9 - - + +
187C ASP 4.3 0.4 + - - -
188C GLY* 3.3 13.2 - - - +
190C HIS* 1.3 78.6 - - - +
192C ALA* 1.3 73.7 + - - +
194C THR* 3.2 2.8 + - + -
195C LEU* 2.9 56.1 + - + +
205C PHE* 5.0 1.1 - - + -
220C ASN* 3.7 37.0 + - + +
223C THR* 4.0 12.6 - - + -
224C ALA* 4.4 7.6 - - + -
415D ILE* 3.6 20.0 - - + -
420D HIS* 4.1 6.3 - - - +
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Residues in contact with ALA 192 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188C GLY 2.9 18.7 + - - +
189C THR 3.9 0.2 - - - +
191C ILE* 1.3 85.4 - - - +
193C LYS* 1.3 62.0 + - - +
195C LEU* 3.5 6.4 + - - +
196C ALA* 3.2 21.3 + - - +
413D HIS* 3.9 30.5 - - + +
415D ILE* 4.3 15.5 - - + -
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Residues in contact with LYS 193 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189C THR* 2.9 29.5 + - - +
190C HIS* 3.7 13.3 - - - +
192C ALA* 1.3 73.7 - - - +
194C THR* 1.3 64.4 + - - +
196C ALA* 3.9 8.1 + - - +
197C GLN* 2.8 33.1 + - - +
168D GLU* 5.6 4.0 + - - -
171D LYS* 5.8 3.6 - - + +
342D GLN* 4.4 23.8 - - - +
343D TYR* 3.7 39.0 - - + +
345D HIS* 6.6 0.4 - - - -
413D HIS* 4.9 4.9 - - + +
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Residues in contact with THR 194 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152C ILE* 4.5 2.9 - - + -
181C TRP* 4.0 29.1 - - + +
182C TYR 5.2 0.9 + - - -
183C VAL* 3.7 24.9 - - + +
190C HIS* 2.8 27.2 + - - -
191C ILE 3.2 4.5 + - - -
192C ALA 3.1 0.4 - - - -
193C LYS* 1.3 79.7 + - - +
195C LEU* 1.3 71.3 + - + +
197C GLN* 3.0 21.5 + - - +
198C LEU* 3.3 30.9 - - + +
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Residues in contact with LEU 195 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191C ILE* 2.9 51.4 + - + +
192C ALA* 3.9 5.8 - - - +
194C THR* 1.3 78.6 - - + +
196C ALA* 1.3 58.1 + - - +
197C GLN 2.8 6.6 + - - -
198C LEU* 2.8 34.3 + - + +
205C PHE* 3.9 27.4 - - + -
223C THR* 4.5 6.3 - - + +
224C ALA* 4.4 6.3 - - - -
227C TRP* 3.5 52.7 + - + +
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Residues in contact with ALA 196 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192C ALA 3.2 14.2 + - - +
193C LYS* 3.9 10.8 - - - +
194C THR 3.2 1.2 - - - -
195C LEU* 1.3 77.6 - - - +
197C GLN* 1.3 60.8 + - + +
198C LEU 5.0 1.1 - - - +
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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