Contacts of the helix formed by residues 163 - 174 (chain A) in PDB entry 6WYG
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 163 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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158A MET 4.5 3.8 + - - -
159A GLY* 3.0 20.2 + - - +
160A ALA* 4.3 0.2 - - - -
161A PRO 3.7 6.7 - - - +
162A GLU* 1.3 77.3 - - - +
164A GLY* 1.3 61.3 + - - +
165A LEU* 3.7 12.8 + - - +
166A ALA* 3.3 34.0 + - - +
167A GLU* 3.7 7.3 + - - +
165B LEU* 5.7 1.7 - - - +
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Residues in contact with GLY 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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161A PRO 4.1 4.7 + - - -
162A GLU 3.4 6.9 + - - -
163A SER* 1.3 70.5 - - - +
165A LEU* 1.3 64.4 + - - +
166A ALA 3.2 0.2 - - - -
167A GLU* 3.5 8.3 + - - +
168A TYR* 3.0 23.7 + - - +
157C CYS* 3.5 35.0 + - - +
158C MET* 4.6 0.2 - - - +
205C RFT 5.0 6.8 + - - -
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Residues in contact with LEU 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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163A SER* 3.2 9.6 - - - +
164A GLY* 1.3 74.5 - - - +
166A ALA* 1.3 67.3 + - - +
168A TYR* 3.4 1.9 + - - +
169A LEU* 2.9 50.4 + - + +
165B LEU* 3.9 21.8 - - + -
157C CYS 3.7 5.7 + - - -
158C MET* 3.9 36.6 - - + +
163C SER* 5.1 2.5 - - - +
165C LEU* 4.5 16.8 - - + -
166C ALA* 4.6 12.1 - - + +
169C LEU* 4.5 16.8 - - + -
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Residues in contact with ALA 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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155A LEU* 5.0 0.4 - - - -
158A MET* 3.3 54.8 - - + +
160A ALA* 4.1 10.1 - - + +
163A SER* 3.3 19.3 + - - +
164A GLY 3.2 0.6 - - - -
165A LEU* 1.3 82.4 - - - +
167A GLU* 1.3 57.3 + - - +
169A LEU* 3.1 2.0 + - - -
170A PHE* 2.9 27.8 + - - +
165B LEU* 4.9 2.2 - - + -
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Residues in contact with GLU 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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48A LEU* 4.2 16.9 - - + +
51A PHE* 3.7 11.3 - - + -
95A SER* 3.9 10.9 - - - -
96A GLY* 2.9 24.4 + - - -
97A LEU* 3.0 26.3 + - - +
155A LEU* 4.3 13.2 - - + +
160A ALA* 3.6 26.7 - - + +
161A PRO* 4.0 8.2 - - + +
163A SER 3.7 8.0 + - - +
164A GLY* 3.5 8.8 + - - +
165A LEU 3.4 0.2 - - - -
166A ALA* 1.3 74.6 - - - +
168A TYR* 1.3 63.0 + - - +
170A PHE* 3.4 0.3 + - - +
171A ASP* 3.0 24.8 + - - +
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Residues in contact with TYR 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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48A LEU* 4.0 11.8 - - + +
164A GLY 3.0 18.1 + - - +
165A LEU 3.5 3.6 - - - +
167A GLU* 1.3 75.8 - - - +
169A LEU* 1.3 80.5 + - + +
171A ASP* 3.0 13.9 + - - +
172A LYS* 3.1 46.7 + - + +
154C ASN* 3.5 23.6 - - - +
157C CYS* 6.4 0.2 - - + -
158C MET* 3.5 47.8 - - + -
169C LEU 4.6 0.2 - - - -
170C PHE* 3.4 14.5 - + - -
173C HIS* 3.1 24.9 - + + +
174C THR* 2.7 29.2 + - - -
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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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158A MET* 4.0 10.1 - - + -
165A LEU* 2.9 43.4 + - + +
166A ALA 3.1 2.9 + - - +
168A TYR* 1.3 91.1 - - + +
170A PHE* 1.3 57.5 + - - +
172A LYS* 3.2 2.5 + - - +
173A HIS* 2.9 43.1 + - + +
203A FE 3.9 19.1 - - - -
165B LEU* 4.2 5.6 - - + -
168B TYR* 4.5 0.2 - - - -
169B LEU* 4.2 27.1 - - + -
169C LEU* 4.2 18.4 - - + -
173C HIS* 4.0 17.0 - - + +
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Residues in contact with PHE 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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51A PHE* 3.7 22.9 - + - -
100A MET* 5.4 0.7 - - - -
151A HIS* 3.7 32.3 - + + -
154A ASN* 3.8 22.4 - - + -
155A LEU* 3.7 22.0 - - + -
158A MET* 3.6 19.6 - - + +
166A ALA 2.9 16.1 + - - +
167A GLU 3.8 3.6 - - - +
169A LEU* 1.3 76.5 - - - +
171A ASP* 1.3 58.3 + - - +
174A THR* 3.0 50.8 + - + -
175A LEU* 3.3 31.0 + - + -
168B TYR* 3.5 17.9 - + - -
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Residues in contact with ASP 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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48A LEU* 3.3 21.5 - - + +
49A LYS* 4.5 2.3 + - - +
50A ASN* 2.8 58.7 + - - +
51A PHE* 3.0 24.1 + - + -
167A GLU 3.0 14.1 + - - +
168A TYR 3.0 9.2 + - - +
170A PHE* 1.3 79.1 - - - +
172A LYS* 1.3 80.3 + - - +
175A LEU* 4.4 5.4 - - - -
176A GLY 3.0 15.8 + - - -
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Residues in contact with LYS 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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47A ALA 5.8 1.0 + - - -
48A LEU* 5.0 2.6 - - - +
50A ASN* 4.3 7.6 - - - +
168A TYR* 3.1 65.1 + - + +
169A LEU* 3.2 6.7 + - - +
171A ASP* 1.3 103.5 + - - +
173A HIS* 1.3 60.3 + - + +
176A GLY* 3.1 23.2 - - - -
154C ASN* 5.1 1.4 + - - -
173C HIS* 3.8 39.3 - - + +
174C THR* 3.8 9.4 - - - +
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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* 2.9 32.7 + - + +
172A LYS* 1.3 75.4 - - + +
174A THR* 1.3 64.6 + - - +
176A GLY 4.3 4.3 + - - -
203A FE 3.1 21.5 - - - -
168B TYR* 3.3 15.9 - + - +
169B LEU* 4.2 16.3 - - + +
172B LYS* 3.8 34.2 + - + +
173B HIS* 3.5 28.9 + + - -
173C HIS* 3.5 22.4 + + - -
173D HIS* 5.0 0.2 - + - -
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Residues in contact with THR 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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151A HIS* 3.7 30.7 - - + +
154A ASN* 5.7 1.2 + - - +
170A PHE* 3.0 27.0 + - + -
173A HIS* 1.3 76.6 - - - +
175A LEU* 1.3 67.8 + - + +
176A GLY* 3.2 3.3 + - - -
168B TYR* 2.5 29.6 + - - -
172B LYS* 3.3 18.4 + - - +
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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