Contacts of the helix formed by residues 160 - 170 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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385C ASN* 6.1 0.3 - - - +
153D ASN* 4.5 4.9 - - - +
155D GLY* 3.6 19.0 + - - +
156D ILE 4.2 2.5 - - - -
157D GLY 3.0 9.2 + - - +
158D GLY 3.1 1.4 - - - -
159D SER* 1.3 82.3 - - - +
161D LEU* 1.3 87.3 + - - +
162D GLY 3.4 2.0 + - - -
163D PRO* 3.5 3.6 - - - +
164D LEU* 3.0 36.3 + - - +
182D TYR* 3.6 27.8 - - - +
183D VAL 4.6 1.2 + - - +
184D SER* 3.6 29.0 + - - -
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Residues in contact with LEU 161 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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385C ASN* 5.6 8.3 - - + +
389C ALA* 5.2 9.6 - - + -
157D GLY* 3.0 19.8 + - - +
158D GLY* 5.3 0.2 - - - -
160D ASP* 1.3 92.1 + - - +
162D GLY* 1.3 56.7 + - - +
164D LEU* 3.7 9.9 - - + +
165D MET* 2.8 34.3 + - + +
346D ARG* 4.8 8.7 - - - +
349D ALA* 3.9 16.2 - - + +
350D TYR* 3.7 39.7 - - + +
353D GLN* 3.7 21.5 - - + +
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Residues in contact with GLY 162 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158D GLY 4.4 5.1 + - - -
161D LEU* 1.3 78.0 - - - +
163D PRO* 1.3 69.9 - - - +
165D MET* 3.1 2.3 + - - +
166D VAL* 2.8 31.0 + - - +
275D LEU* 3.9 13.0 - - - -
350D TYR* 3.2 27.2 - - - -
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Residues in contact with PRO 163 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153D ASN* 5.2 1.3 - - - +
158D GLY 4.0 11.9 - - - +
159D SER 4.5 5.8 - - - +
160D ASP 3.5 11.9 - - - +
162D GLY* 1.3 87.6 - - - +
164D LEU* 1.3 56.7 + - - +
166D VAL* 4.0 0.2 - - - +
167D THR* 2.8 32.9 + - - +
182D TYR* 3.3 13.3 + - + -
275D LEU* 4.3 6.3 - - + -
279D ILE* 3.5 32.1 - - + +
280D GLY* 4.4 4.7 - - - -
282D SER* 3.4 22.9 - - - +
283D ILE* 3.8 14.8 - - + -
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Residues in contact with LEU 164 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160D ASP* 3.0 31.7 + - - +
161D LEU* 3.7 9.9 - - + +
163D PRO* 1.3 77.8 - - - +
165D MET* 1.3 65.5 + - - +
167D THR* 3.1 8.3 + - - -
168D GLU* 3.0 37.0 + - + +
182D TYR* 3.7 38.7 - - + +
346D ARG* 3.9 32.8 - - + +
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Residues in contact with MET 165 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161D LEU* 2.8 23.7 + - + +
162D GLY 3.7 1.3 - - - +
164D LEU* 1.3 78.4 - - + +
166D VAL* 1.3 73.6 + - + +
168D GLU* 3.4 3.3 + - - +
169D ALA* 3.0 27.8 + - - +
275D LEU* 4.9 0.9 - - + -
343D TYR 4.7 0.7 - - - +
344D LEU* 5.6 1.7 - - - -
346D ARG* 3.3 39.0 - - + +
347D PHE* 3.9 21.3 - - + +
350D TYR* 3.9 34.3 - - + -
486D LEU* 4.5 10.3 - - + -
490D VAL* 4.1 24.5 - - + -
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Residues in contact with VAL 166 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162D GLY 2.8 20.1 + - - +
165D MET* 1.3 87.6 - - + +
167D THR* 1.3 62.8 + - - +
169D ALA* 3.1 1.9 + - - -
170D LEU* 2.9 46.9 + - + +
275D LEU* 4.0 21.5 - - + -
283D ILE* 3.7 38.6 - - + -
295D LEU* 3.9 14.6 - - + -
486D LEU* 4.0 13.9 - - + -
490D VAL* 5.7 1.1 - - + -
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Residues in contact with THR 167 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163D PRO 2.8 20.5 + - - +
164D LEU 3.1 7.8 + - - -
166D VAL* 1.3 76.4 - - - +
168D GLU* 1.3 64.6 + - - +
170D LEU* 3.8 3.7 - - - +
171D LYS* 3.2 29.9 + - - -
180D VAL* 4.2 6.5 - - + +
182D TYR* 3.2 33.7 - - - +
282D SER 4.3 0.4 - - - +
283D ILE* 3.7 29.2 - - + -
286D HIS* 3.8 28.1 + - + +
287D VAL* 5.4 2.2 - - + -
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Residues in contact with GLU 168 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193C LYS* 5.6 4.2 + - - -
164D LEU* 3.0 38.0 + - + +
165D MET* 3.6 6.5 - - - +
167D THR* 1.3 81.4 + - - +
169D ALA* 1.3 60.9 + - - +
170D LEU 3.5 0.3 + - - -
171D LYS* 3.5 28.9 + - - +
180D VAL* 6.0 0.2 - - - +
182D TYR* 6.0 2.1 - - + -
343D TYR* 3.4 28.4 - - - +
345D HIS* 2.6 41.3 + - + +
346D ARG* 4.7 1.8 - - + -
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Residues in contact with ALA 169 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165D MET* 3.0 21.3 + - - +
166D VAL 3.6 3.8 - - - +
168D GLU* 1.3 78.9 - - - +
170D LEU* 1.3 62.3 + - - +
171D LYS 3.4 1.6 + - - -
172D PRO* 4.2 2.6 - - - +
173D TYR* 5.5 0.2 - - - -
343D TYR* 3.1 27.7 + - - +
344D LEU* 3.5 28.0 - - + -
412D GLN* 6.0 0.9 - - - +
481D LEU* 3.8 10.1 - - + +
486D LEU* 4.0 17.7 - - + -
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Residues in contact with LEU 170 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166D VAL* 2.9 37.2 + - + +
167D THR 3.8 2.9 - - - -
169D ALA* 1.3 82.2 - - - +
171D LYS* 1.3 64.4 - - - +
172D PRO* 3.1 6.3 - - - -
173D TYR* 2.8 27.7 + - + +
283D ILE* 5.2 1.1 - - + -
287D VAL* 3.6 27.2 - - + +
291D ASN 5.5 0.4 - - - +
295D LEU* 4.8 5.8 - - + -
481D LEU* 3.7 24.0 - - + +
482D THR 4.1 0.9 - - - -
483D PRO* 3.9 42.4 - - + -
486D LEU* 3.8 13.5 - - + -
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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