Contacts of the helix formed by residues 160 - 170 (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 160 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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153C ASN* 4.6 5.1 - - - +
155C GLY* 3.5 19.5 - - - +
156C ILE 4.2 2.7 - - - -
157C GLY 2.9 9.0 + - - +
158C GLY 3.2 0.8 - - - -
159C SER* 1.3 80.2 - - - +
161C LEU* 1.3 81.5 + - - +
162C GLY 3.4 1.6 - - - -
163C PRO* 3.3 5.0 - - - +
164C LEU* 2.9 36.7 + - - +
182C TYR* 3.5 30.4 - - - +
183C VAL 4.6 0.7 + - - +
184C SER* 3.6 26.6 + - - -
385D ASN* 5.9 0.3 - - - -
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Residues in contact with LEU 161 (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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157C GLY* 3.0 16.7 + - - +
158C GLY* 5.2 0.4 - - - -
160C ASP* 1.3 91.5 + - - +
162C GLY* 1.3 57.5 + - - +
164C LEU* 4.4 7.2 - - + -
165C MET* 2.8 35.8 + - + +
346C ARG* 4.5 13.7 - - + +
349C ALA* 4.0 13.9 - - + +
350C TYR* 3.6 40.6 - - + +
353C GLN* 3.9 20.0 - - + +
385D ASN* 5.8 7.2 - - + +
389D ALA* 5.2 9.2 - - + -
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Residues in contact with GLY 162 (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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158C GLY 4.5 5.6 + - - -
161C LEU* 1.3 78.7 - - - +
163C PRO* 1.3 66.2 - - - +
165C MET* 3.7 0.5 - - - +
166C VAL* 2.9 37.0 + - - +
275C LEU* 3.7 15.0 - - - -
350C TYR* 3.4 25.9 - - - -
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Residues in contact with PRO 163 (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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153C ASN* 5.2 1.3 - - - +
158C GLY 4.3 9.2 - - - +
159C SER 4.5 6.1 - - - +
160C ASP 3.3 11.4 - - - +
162C GLY* 1.3 89.4 - - - +
164C LEU* 1.3 48.8 + - - +
167C THR* 2.7 38.8 + - - +
182C TYR* 3.2 14.9 + - + -
275C LEU* 4.3 6.5 - - + -
279C ILE* 3.4 33.2 - - + +
280C GLY* 4.5 3.6 - - - -
282C SER* 3.5 22.2 - - - +
283C ILE* 3.6 16.2 - - + +
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Residues in contact with LEU 164 (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* 2.9 34.7 + - - +
161C LEU* 3.7 9.0 - - + +
163C PRO* 1.3 74.7 - - - +
165C MET* 1.3 67.6 + - + +
167C THR* 3.1 7.1 + - - -
168C GLU* 3.1 36.2 + - + +
182C TYR* 3.7 39.2 - - + +
190C HIS* 6.6 0.2 - - + -
346C ARG* 3.9 32.8 - - + +
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Residues in contact with MET 165 (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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161C LEU* 2.8 23.2 + - + +
162C GLY 3.7 0.9 - - - +
164C LEU* 1.3 78.6 - - - +
166C VAL* 1.3 74.1 + - + +
168C GLU* 3.3 4.1 + - - +
169C ALA* 2.9 27.9 + - - +
275C LEU* 5.1 0.2 - - + -
343C TYR 4.6 1.0 - - - +
344C LEU* 5.3 2.2 - - - -
346C ARG* 3.2 41.2 - - + +
347C PHE* 3.8 26.7 - - + +
350C TYR* 3.7 35.7 - - + -
486C LEU* 4.5 10.1 - - - -
490C VAL* 4.0 19.5 - - + -
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Residues in contact with VAL 166 (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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162C GLY 2.9 21.9 + - - +
165C MET* 1.3 87.9 - - + +
167C THR* 1.3 59.5 + - - +
169C ALA* 3.1 1.2 + - - -
170C LEU* 2.8 53.1 + - + +
275C LEU* 4.1 20.2 - - + -
283C ILE* 3.6 35.4 - - + -
295C LEU* 4.1 9.2 - - + -
486C LEU* 3.8 15.5 - - + -
490C VAL* 5.7 1.6 - - + -
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Residues in contact with THR 167 (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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163C PRO 2.7 21.3 + - - +
164C LEU 3.1 7.4 + - - -
166C VAL* 1.3 76.8 - - - +
168C GLU* 1.3 62.1 + - - +
170C LEU* 3.9 3.4 - - - +
171C LYS* 3.3 30.2 + - - -
180C VAL* 4.1 7.0 - - + +
182C TYR* 3.2 33.7 + - - +
282C SER 4.2 3.1 - - - +
283C ILE* 3.8 28.5 - - + -
286C HIS* 3.9 23.8 + - + +
287C VAL* 5.6 3.4 - - + -
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Residues in contact with GLU 168 (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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164C LEU* 3.1 35.7 + - + +
165C MET* 3.6 6.3 - - - +
167C THR* 1.3 81.1 + - - +
169C ALA* 1.3 61.8 + - - +
170C LEU 3.4 0.5 + - - -
171C LYS* 3.4 28.1 + - - +
180C VAL* 5.9 0.5 - - - +
182C TYR* 6.0 2.5 - - + -
343C TYR* 3.3 29.8 - - - +
345C HIS* 2.7 40.2 + - + +
346C ARG* 4.7 1.8 - - + -
193D LYS* 5.9 0.9 + - - -
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Residues in contact with ALA 169 (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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165C MET* 2.9 19.4 + - - +
166C VAL 3.6 4.0 - - - +
168C GLU* 1.3 78.3 - - - +
170C LEU* 1.3 58.4 + - - +
171C LYS 3.4 0.7 + - - -
172C PRO* 4.1 3.1 - - - +
173C TYR* 5.6 0.3 - - - -
343C TYR* 3.1 27.5 + - - +
344C LEU* 3.3 28.9 - - + -
412C GLN* 5.9 1.0 - - - +
481C LEU* 3.6 15.0 - - + +
486C LEU* 4.0 18.6 - - + -
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Residues in contact with LEU 170 (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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166C VAL* 2.8 35.9 + - + +
167C THR* 3.9 2.9 - - - -
169C ALA* 1.3 75.6 - - - +
171C LYS* 1.3 64.6 + - - +
172C PRO* 3.1 6.1 - - - -
173C TYR* 2.8 29.6 + - + +
283C ILE* 5.3 1.3 - - + -
287C VAL* 3.6 27.5 - - + +
291C ASN 6.1 0.2 - - - -
295C LEU* 4.7 5.4 - - + -
481C LEU* 3.7 26.7 - - + -
482C THR 3.9 1.8 - - - +
483C PRO* 3.7 47.6 - - + -
486C LEU* 3.9 10.3 - - + -
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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