Contacts of the helix formed by residues 159 - 172 (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 HIS 159 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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147A LEU* 4.4 16.9 - - + +
151A LEU* 3.4 41.8 - - + +
152A THR* 4.4 4.9 + - - +
158A CYS* 1.3 79.2 - - - +
160A MET* 1.3 77.2 + - - +
161A GLY 3.0 12.2 + - - +
162A ILE* 2.9 21.8 + - + +
163A THR* 3.3 7.1 + - - +
237A TYR* 5.3 2.7 - + - -
238A PHE* 3.0 39.1 - + + -
1001A COA 3.4 32.0 + - - +
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Residues in contact with MET 160 (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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92A CSO 4.8 2.2 - - - +
150A GLY 4.8 1.8 - - - +
151A LEU* 2.8 31.0 + - + +
152A THR 4.2 1.6 - - - -
153A ASP* 3.6 43.5 - - + +
159A HIS* 1.3 78.8 + - - +
161A GLY* 1.3 61.6 + - - +
163A THR* 2.7 30.1 + - + +
164A ALA 3.0 5.7 + - - -
293A MET* 4.0 16.8 - - + +
324A PHE* 3.8 7.8 - - + -
385A GLY* 3.7 30.7 - - - -
386A GLY 4.8 0.9 - - - +
1001A COA 3.7 35.9 - - - +
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Residues in contact with GLY 161 (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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159A HIS* 3.0 11.7 + - - -
160A MET* 1.3 78.8 - - - +
162A ILE* 1.4 55.8 + - - +
164A ALA* 3.2 5.6 + - - +
165A GLU* 3.0 29.1 + - - +
238A PHE* 3.8 23.5 - - - +
246A VAL* 4.2 2.9 - - - +
324A PHE* 3.6 23.2 - - - -
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Residues in contact with ILE 162 (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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158A CYS* 3.9 26.5 - - + -
159A HIS* 2.9 19.7 + - + +
161A GLY* 1.4 72.6 - - - +
163A THR* 1.4 67.4 + - - +
165A GLU* 3.0 8.8 + - + +
166A ASN* 2.9 33.5 + - - +
238A PHE* 3.5 35.9 - - + +
239A LEU* 3.9 23.6 - - + -
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Residues in contact with THR 163 (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* 4.8 2.2 - - + -
158A CYS* 4.1 16.2 - - - -
159A HIS 3.3 10.7 + - - +
160A MET* 2.7 31.8 + - + +
162A ILE* 1.4 76.1 - - - +
164A ALA* 1.3 60.4 + - - +
166A ASN* 3.2 5.4 + - - +
167A VAL* 3.1 26.7 + - - +
290A PRO 3.7 19.1 - - - +
291A SER* 3.4 22.2 - - - +
293A MET* 3.5 27.6 - - + +
294A GLY 4.8 0.2 + - - -
327A VAL* 5.5 0.4 - - - -
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Residues in contact with ALA 164 (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 3.0 7.3 + - - +
161A GLY 3.3 11.2 - - - +
162A ILE 3.1 0.2 - - - -
163A THR* 1.3 73.1 + - - +
165A GLU* 1.3 60.9 + - - +
167A VAL* 3.2 3.1 + - - +
168A ALA* 2.8 28.1 + - - +
246A VAL* 4.2 8.1 - - + -
324A PHE* 3.5 44.9 - - + -
326A ALA* 3.8 7.0 - - + +
327A VAL* 4.1 13.2 - - + -
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Residues in contact with GLU 165 (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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161A GLY 3.0 18.9 + - - +
162A ILE* 3.0 14.1 + - + +
164A ALA* 1.3 77.0 - - - +
166A ASN* 1.3 65.3 + - - +
168A ALA* 3.6 3.8 - - - +
169A LYS* 3.0 32.0 + - - +
236A PRO* 4.8 0.2 - - - +
238A PHE* 5.1 1.5 - - + +
239A LEU* 3.8 41.8 + - + +
243A THR 4.4 1.4 - - - +
244A GLY* 3.5 6.1 - - - -
245A THR* 2.8 49.2 + - - +
246A VAL* 2.9 20.7 + - + +
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Residues in contact with ASN 166 (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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158A CYS* 5.4 2.8 - - - -
162A ILE* 2.9 30.8 + - - +
163A THR* 3.4 5.8 - - - +
165A GLU* 1.3 79.1 - - - +
167A VAL* 1.3 56.7 + - - +
169A LYS* 3.4 16.7 + - - +
170A LYS* 3.0 29.8 + - - +
291A SER* 2.8 42.6 + - - +
292A ILE* 4.1 9.3 - - + +
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Residues in contact with VAL 167 (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 3.1 13.6 + - - +
164A ALA 3.6 6.7 - - - +
166A ASN* 1.3 74.4 - - - +
168A ALA* 1.3 58.0 + - - +
171A TRP* 2.8 45.4 + - + +
292A ILE* 3.8 34.8 - - + +
294A GLY 4.5 6.3 - - - +
295A ILE* 4.1 12.8 - - + +
326A ALA 4.0 8.1 - - - +
327A VAL* 4.2 15.7 - - + -
330A ALA* 3.5 28.9 - - + -
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Residues in contact with ALA 168 (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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164A ALA 2.8 20.8 + - - +
165A GLU* 3.6 7.2 - - - +
167A VAL* 1.3 72.4 - - - +
169A LYS* 1.3 57.1 + - - +
172A GLN* 2.9 23.7 + - - -
173A VAL* 2.9 26.9 + - - +
178A GLN* 3.5 28.3 - - - +
245A THR* 4.0 11.0 - - + +
326A ALA* 3.9 6.7 - - + +
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Residues in contact with LYS 169 (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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165A GLU* 3.0 26.3 + - - +
166A ASN* 3.8 15.9 + - - +
168A ALA* 1.3 77.0 - - - +
170A LYS* 1.3 63.4 + - - +
172A GLN* 3.3 17.7 + - - +
239A LEU* 4.3 21.8 - - - +
243A THR* 4.8 9.5 + - - -
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Residues in contact with LYS 170 (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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166A ASN 3.0 17.4 + - - +
167A VAL 3.3 0.2 + - - -
169A LYS* 1.3 80.1 - - + +
171A TRP* 1.3 89.9 + - + +
172A GLN* 3.3 9.6 + - - +
292A ILE* 5.4 4.3 - - + -
2003A GOL 2.9 52.9 + - - -
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Residues in contact with TRP 171 (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* 2.8 33.2 + - + +
170A LYS* 1.3 98.8 - - + +
172A GLN* 1.3 57.9 + - - +
173A VAL* 3.4 4.9 + - + -
292A ILE* 4.1 25.8 - - + -
295A ILE* 3.8 37.0 - - + -
298A ILE* 4.6 4.4 - - + +
330A ALA* 3.7 35.0 + - + -
333A LYS* 2.8 41.9 + - + +
334A GLU* 3.2 34.5 + - + +
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Residues in contact with GLN 172 (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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168A ALA 2.9 9.2 + - - -
169A LYS* 3.3 13.4 + - - +
170A LYS 3.3 7.4 + - - +
171A TRP* 1.3 79.9 - - - +
173A VAL* 1.3 61.3 + - - +
174A SER* 3.7 3.3 + - - -
177A ASP* 3.7 5.5 - - - +
333A LYS* 3.0 16.2 + - - +
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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