Contacts of the helix formed by residues 162 - 177 (chain A) in PDB entry 1JWL
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 SER 162 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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160A ILE 3.7 1.2 + - - -
161A PHE* 1.3 69.0 - - - +
163A HIS* 1.3 57.6 + - - +
164A GLU* 2.9 9.7 + - - +
165A ASP* 2.8 39.8 + - - +
166A GLY* 2.9 23.0 + - - -
273A TYR* 4.3 0.8 + - - -
318A LEU* 4.2 26.3 - - - +
319A LEU 3.0 16.2 + - - -
320A PRO* 5.3 2.0 - - - -
321A VAL* 4.0 8.5 - - - +
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Residues in contact with HIS 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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152A ASP* 3.7 29.4 + - - -
160A ILE* 4.3 8.0 - - + +
161A PHE 3.0 13.9 + - - +
162A SER* 1.3 71.3 - - - +
164A GLU* 1.3 87.8 + - + +
166A GLY 3.8 0.2 - - - -
167A THR* 2.6 38.9 + - - +
196A LEU* 3.7 61.2 + - + +
197A ARG* 4.5 11.9 - - + +
199A ALA* 6.3 0.9 - - + -
200A GLY* 5.2 3.2 - - - -
273A TYR* 3.8 12.8 - - - +
318A LEU* 6.3 1.7 - - + +
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Residues in contact with GLU 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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152A ASP* 4.9 3.5 - - - +
162A SER* 2.9 8.8 - - - +
163A HIS* 1.3 104.7 + - + +
165A ASP* 1.3 63.0 + - - +
167A THR* 3.1 15.4 + - - -
168A ARG* 3.2 15.8 + - - +
200A GLY* 5.6 3.4 - - - -
203A LYS* 2.3 44.6 + - - +
204A TYR* 3.1 25.7 - - + +
318A LEU* 6.1 2.5 - - + -
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Residues in contact with ASP 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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162A SER* 2.8 30.4 + - - +
164A GLU* 1.3 79.6 - - - +
166A GLY* 1.3 61.2 + - - +
168A ARG* 3.4 31.5 + - - +
169A LEU* 3.0 33.7 + - + +
320A PRO* 5.6 3.1 - - - +
321A VAL* 3.9 16.4 - - + +
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Residues in contact with GLY 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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162A SER 2.9 10.7 + - - -
164A GLU 3.3 0.2 - - - -
165A ASP* 1.3 79.2 - - - +
167A THR* 1.3 62.1 + - - +
169A LEU* 3.4 4.4 + - - +
170A GLY* 3.1 17.7 + - - -
273A TYR* 3.5 24.9 - - - -
289A ILE* 3.7 16.5 - - - +
321A VAL* 3.6 13.8 - - - +
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Residues in contact with THR 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 HIS 2.6 25.6 + - - +
164A GLU* 3.1 5.9 + - - -
166A GLY* 1.3 72.6 - - - +
168A ARG* 1.3 61.4 + - - +
170A GLY* 3.4 1.0 + - - +
171A VAL* 2.9 35.3 + - - +
197A ARG* 3.2 41.3 - - + +
200A GLY* 3.3 28.1 + - - -
201A TRP* 3.5 21.8 - - + +
204A TYR* 4.1 2.9 - - - -
273A TYR* 4.3 4.0 + - + -
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Residues in contact with ARG 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 GLU 3.2 15.5 + - - +
165A ASP* 3.4 28.8 + - - +
167A THR* 1.3 82.1 + - - +
169A LEU* 1.3 79.4 + - - +
171A VAL 3.0 1.6 + - - -
172A GLU* 2.6 68.6 + - + +
204A TYR* 3.3 47.4 + - + -
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Residues in contact with LEU 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 ASP* 3.0 24.0 + - + +
166A GLY* 3.5 5.6 - - - +
168A ARG* 1.3 103.1 - - - +
170A GLY* 1.3 62.9 + - - +
172A GLU* 4.1 7.0 - - + +
173A HIS* 3.1 25.5 + - - +
289A ILE* 4.2 8.3 - - + -
321A VAL* 4.3 10.1 - - + +
322A SER* 3.9 13.5 - - - -
323A LEU* 3.9 39.8 - - + +
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Residues in contact with GLY 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 GLY 3.1 11.6 + - - -
167A THR* 3.8 2.7 - - - -
168A ARG 3.1 0.6 - - - -
169A LEU* 1.3 78.9 - - - +
171A VAL* 1.3 64.5 + - - +
173A HIS* 3.3 5.6 + - - +
174A LEU* 3.1 28.4 + - - +
201A TRP* 5.8 1.1 - - - -
243A LEU* 4.0 16.1 - - - +
271A VAL* 4.8 9.2 - - - +
289A ILE* 4.3 10.3 - - - +
323A LEU* 5.4 1.1 - - - -
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Residues in contact with VAL 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 THR 2.9 22.1 + - - +
168A ARG 3.7 1.8 - - - +
170A GLY* 1.3 73.7 - - - +
172A GLU* 1.3 68.2 + - + +
174A LEU* 3.3 5.7 + - - +
175A VAL* 3.0 33.4 + - + +
182A ILE* 5.6 0.4 - - + -
201A TRP* 4.1 15.9 - - + +
204A TYR* 3.9 26.2 - - + +
205A LEU* 3.4 39.3 - - + -
208A ASN* 4.8 3.4 - - - +
243A LEU* 4.0 16.6 - - + -
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Residues in contact with GLU 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 ARG* 2.6 58.4 + - + +
169A LEU* 4.4 6.3 - - - +
171A VAL* 1.3 75.4 - - + +
173A HIS* 1.3 55.5 + - - +
175A VAL* 3.9 5.9 - - - +
176A ALA* 3.0 30.5 + - - +
204A TYR* 5.0 4.1 - - + -
208A ASN* 5.1 13.5 - - - +
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Residues in contact with HIS 173 (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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169A LEU 3.1 22.1 + - - +
170A GLY* 3.5 5.6 - - - +
171A VAL 3.1 0.6 - - - -
172A GLU* 1.3 74.1 - - - +
174A LEU* 1.3 66.5 + - - +
176A ALA* 3.4 7.4 + - - +
177A LEU* 3.2 39.2 + - + +
271A VAL* 4.6 5.2 - - + -
287A THR* 4.4 7.7 - - + +
323A LEU* 3.8 21.9 - - + +
325A LYS* 4.1 27.3 - - + +
329A THR* 2.8 46.2 + - + -
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Residues in contact with LEU 174 (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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170A GLY 3.1 9.9 + - - +
171A VAL* 3.7 4.5 - - - +
173A HIS* 1.3 80.1 - - + +
175A VAL* 1.3 61.0 + - - +
177A LEU* 3.3 2.0 + - + -
178A GLY 3.3 2.8 + - - -
179A HIS* 2.9 42.4 + - + -
182A ILE* 4.1 19.3 - - + -
241A ALA* 3.5 31.6 - - + -
242A MET 4.5 4.3 - - - +
243A LEU* 3.0 46.0 - - + -
269A SER* 4.4 9.4 - - - -
271A VAL* 4.2 17.3 - - + -
329A THR* 4.6 6.1 - - + -
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Residues in contact with VAL 175 (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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171A VAL* 3.0 32.3 + - + +
172A GLU* 3.9 5.4 - - - +
174A LEU* 1.3 73.2 - - - +
176A ALA* 1.3 59.9 + - - +
177A LEU 3.0 2.0 - - - -
178A GLY* 2.5 27.4 + - - -
179A HIS 4.1 7.9 - - - +
182A ILE* 5.0 3.8 - - + -
208A ASN* 3.8 27.1 - - + +
210A ILE* 3.6 29.8 - - + -
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Residues in contact with ALA 176 (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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172A GLU 3.0 19.2 + - - +
173A HIS* 3.7 7.6 - - - +
175A VAL* 1.3 78.2 - - - +
177A LEU* 1.3 65.4 + - + +
178A GLY* 3.0 1.1 + - - -
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Residues in contact with LEU 177 (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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173A HIS* 3.2 47.7 + - + +
174A LEU* 3.4 11.0 - - + +
175A VAL 3.0 0.8 - - - -
176A ALA* 1.3 82.5 - - + +
178A GLY* 1.3 59.4 + - - +
179A HIS* 3.5 19.0 + - + +
329A THR* 3.8 21.1 - - + +
330A LEU* 3.6 22.5 - - - +
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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