Contacts of the helix formed by residues 160 - 170 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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385A ASN* 6.0 0.2 - - - -
153B ASN* 4.4 5.4 - - - +
155B GLY 3.4 20.1 - - - +
156B ILE 4.1 2.5 - - - -
157B GLY 3.1 6.0 + - - +
158B GLY 3.2 1.4 + - - -
159B SER* 1.3 79.8 - - - +
161B LEU* 1.3 89.2 + - - +
162B GLY 3.4 2.0 - - - -
163B PRO* 3.3 5.7 - - - +
164B LEU* 3.0 29.5 + - - +
182B TYR* 3.5 30.9 - - - +
183B VAL 4.6 1.2 + - - +
184B SER* 3.5 27.9 + - - -
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Residues in contact with LEU 161 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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381A GLU* 6.5 0.7 - - + -
385A ASN* 5.8 7.2 - - + +
389A ALA* 5.3 9.0 - - + -
157B GLY* 3.0 16.7 + - - +
158B GLY* 5.2 0.4 - - - -
160B ASP* 1.3 92.4 + - - +
162B GLY* 1.3 55.9 + - - +
164B LEU* 3.8 9.8 - - + +
165B MET* 2.9 34.0 + - + +
346B ARG* 4.7 10.5 - - + +
349B ALA* 4.0 13.2 - - + +
350B TYR* 3.4 42.4 - - + +
353B GLN* 3.8 20.6 - - + +
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Residues in contact with GLY 162 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158B GLY* 4.6 5.9 + - - -
161B LEU* 1.3 79.2 - - - +
163B PRO* 1.3 68.8 - - - +
165B MET* 3.7 0.7 - - - +
166B VAL* 2.9 32.4 + - - +
275B LEU* 3.8 13.0 - - - -
350B TYR* 3.3 26.4 - - - -
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Residues in contact with PRO 163 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153B ASN* 5.1 2.0 - - - +
158B GLY 4.5 2.2 - - - +
159B SER 4.6 4.9 - - - +
160B ASP* 3.3 15.0 - - - +
162B GLY* 1.3 88.3 - - - +
164B LEU* 1.3 56.0 + - - +
167B THR* 2.8 33.6 + - - +
182B TYR* 3.3 14.1 + - + -
275B LEU* 4.3 6.7 - - + -
279B ILE* 3.4 36.3 - - + +
280B GLY* 4.5 0.2 - - - -
282B SER* 3.3 22.9 - - - +
283B ILE* 3.8 18.4 - - + -
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Residues in contact with LEU 164 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160B ASP* 3.0 25.8 + - - +
161B LEU* 3.8 10.8 - - + +
163B PRO* 1.3 76.7 - - - +
165B MET* 1.3 67.0 + - - +
167B THR* 3.1 6.1 + - - +
168B GLU* 3.0 44.6 + - + +
182B TYR* 3.4 39.6 - - + -
346B ARG* 3.8 33.7 - - + +
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Residues in contact with MET 165 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161B LEU* 2.9 20.3 + - + +
162B GLY 3.7 0.4 - - - +
164B LEU* 1.3 82.3 - - - +
166B VAL* 1.3 76.5 + - + +
168B GLU* 3.6 2.5 - - - +
169B ALA* 3.0 28.7 + - - +
275B LEU* 4.8 0.7 - - + -
343B TYR 4.7 1.0 - - - +
344B LEU* 4.9 2.2 - - + -
346B ARG* 3.4 39.8 - - + +
347B PHE* 3.9 20.4 - - + +
350B TYR* 3.8 37.0 - - + -
486B LEU* 4.5 10.3 - - - -
490B VAL* 3.9 23.6 - - + -
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Residues in contact with VAL 166 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162B GLY 2.9 22.3 + - - +
163B PRO 4.0 2.2 - - - +
165B MET* 1.3 93.9 - - + +
167B THR* 1.3 60.3 + - - +
169B ALA* 3.2 1.0 + - - -
170B LEU* 2.9 53.1 + - + +
275B LEU* 4.0 19.7 - - + -
283B ILE* 4.0 19.5 - - + -
295B LEU* 4.0 20.0 - - + -
486B LEU* 3.9 12.6 - - + -
490B VAL* 5.6 1.6 - - + -
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Residues in contact with THR 167 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163B PRO 2.8 22.9 + - - +
164B LEU* 3.1 8.7 + - - +
166B VAL* 1.3 71.7 - - - +
168B GLU* 1.3 62.5 + - - +
170B LEU* 3.6 4.1 - - - +
171B LYS* 3.1 30.7 + - - -
180B VAL* 4.1 6.9 - - + +
182B TYR* 3.1 34.7 + - - +
282B SER 4.2 0.2 - - - +
283B ILE* 3.8 28.7 - - + -
286B HIS* 3.8 29.3 + - + +
287B VAL* 5.5 2.9 - - + -
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Residues in contact with GLU 168 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193A LYS* 5.9 0.9 + - - -
164B LEU* 3.0 45.2 + - + +
165B MET* 3.6 5.8 - - - +
167B THR* 1.3 80.0 + - - +
169B ALA* 1.3 61.6 + - - +
170B LEU 3.4 0.2 + - - -
171B LYS* 3.5 28.5 + - - +
343B TYR* 3.3 28.6 - - - +
345B HIS* 2.7 40.1 + - + +
346B ARG* 4.8 1.3 - - + -
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Residues in contact with ALA 169 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165B MET* 3.0 19.2 + - - +
166B VAL 3.2 4.7 + - - +
168B GLU* 1.3 78.3 - - - +
170B LEU* 1.3 58.1 + - - +
171B LYS 3.4 1.0 + - - -
172B PRO* 4.1 3.3 - - - +
173B TYR* 5.5 0.5 - - - -
343B TYR* 3.2 28.2 + - + +
344B LEU* 3.6 30.5 - - + -
412B GLN* 5.9 1.0 - - - +
481B LEU* 3.8 14.6 - - + +
486B LEU* 3.8 16.8 - - + -
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Residues in contact with LEU 170 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166B VAL* 2.9 39.0 + - + +
167B THR 3.6 3.4 - - - +
169B ALA* 1.3 75.7 - - - +
171B LYS* 1.3 65.4 - - - +
172B PRO* 3.1 5.6 - - - -
173B TYR* 2.8 25.3 + - + -
283B ILE* 5.2 0.9 - - + -
287B VAL* 3.5 31.5 - - + +
291B ASN 5.6 0.4 - - - +
295B LEU* 4.7 6.5 - - + -
481B LEU* 3.8 26.9 - - + +
482B THR 4.0 0.9 - - - -
483B PRO* 3.9 42.2 - - + -
486B LEU* 3.8 13.9 - - + -
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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