Contacts of the helix formed by residues 289 - 295 (chain A) in PDB entry 1WL4
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 GLU 289 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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288A VAL* 1.3 85.7 - - - +
290A PRO* 1.3 74.0 - - + +
291A SER* 4.3 9.2 - - - +
292A ILE* 3.2 39.6 + - + +
293A MET* 3.3 11.1 + - - -
295A ILE* 5.1 0.9 - - - +
387A GLY* 4.2 0.2 - - - -
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Residues in contact with PRO 290 (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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153A ASP* 3.5 29.0 - - - +
155A PHE* 3.7 28.9 - - + -
156A HIS* 4.1 9.6 - - + +
163A THR* 3.7 11.5 - - - +
288A VAL 3.8 5.4 - - - +
289A GLU* 1.3 84.7 - - + +
291A SER* 1.4 63.4 + - - +
292A ILE 3.1 1.0 + - - -
293A MET* 3.2 15.4 + - - +
386A GLY 3.8 22.4 - - - +
387A GLY 4.0 0.9 - - - +
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Residues in contact with SER 291 (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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156A HIS* 4.0 25.8 + - - -
163A THR* 3.4 15.3 - - - -
166A ASN* 2.8 40.9 + - - +
289A GLU* 4.3 7.5 - - - +
290A PRO* 1.4 79.9 - - - +
292A ILE* 1.3 69.5 + - - +
293A MET 3.6 0.2 - - - -
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Residues in contact with ILE 292 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163A THR 4.7 0.4 - - - -
166A ASN* 4.1 13.7 - - + +
167A VAL* 3.8 25.6 - - + +
170A LYS* 5.4 3.1 - - + -
171A TRP* 4.1 20.9 - - + -
289A GLU* 3.5 41.7 - - + +
290A PRO 3.1 0.4 - - - -
291A SER* 1.3 89.1 - - - +
293A MET* 1.3 64.2 + - - +
294A GLY 2.9 5.5 + - - -
295A ILE* 3.1 39.8 + - + +
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Residues in contact with MET 293 (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 MET* 4.0 8.7 - - + -
163A THR* 3.5 25.2 - - - +
288A VAL* 4.1 2.1 - - - +
289A GLU 3.3 6.7 + - - -
290A PRO 3.2 14.1 + - - +
291A SER 3.6 0.4 - - - -
292A ILE* 1.3 77.2 - - - +
294A GLY* 1.3 63.6 + - - +
296A GLY* 2.9 21.9 + - - -
324A PHE* 4.6 11.0 - - + -
327A VAL* 5.3 1.6 - - + -
383A CYS* 3.4 28.1 - - - +
384A ILE 3.4 33.7 - - - +
385A GLY* 3.8 10.1 - - - -
386A GLY 4.3 0.9 - - - +
387A GLY* 3.6 15.5 - - - +
388A MET 3.9 4.5 - - - +
1001A COA 3.6 28.3 - - - -
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Residues in contact with GLY 294 (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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163A THR* 4.8 1.6 + - - -
167A VAL* 4.5 3.6 - - - +
292A ILE 2.9 2.6 + - - -
293A MET* 1.3 90.0 - - - +
295A ILE* 1.4 56.8 + - - +
296A GLY 3.2 0.4 - - - -
297A PRO* 3.2 16.5 - - - +
327A VAL* 3.0 43.1 - - - +
331A ILE* 3.5 3.3 - - - +
383A CYS* 3.5 11.9 - - - +
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Residues in contact with ILE 295 (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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167A VAL* 4.1 22.6 - - + +
171A TRP* 3.8 35.7 - - + -
288A VAL* 4.0 23.6 - - + -
289A GLU* 5.1 0.7 - - - +
292A ILE* 3.1 32.7 + - + +
293A MET 3.1 0.2 + - - -
294A GLY* 1.4 76.0 - - - +
296A GLY* 1.3 65.6 + - - +
297A PRO* 3.2 3.6 - - - -
298A ILE* 2.9 38.3 + - + +
299A PRO* 3.3 12.5 - - + +
327A VAL* 5.4 0.2 - - + -
330A ALA* 4.4 6.7 - - + -
331A ILE* 4.6 5.2 - - + -
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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