Contacts of the helix formed by residues 166 - 181 (chain B) in PDB entry 1W5B
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 GLY 166 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162B PHE 5.0 1.9 - - - +
163B VAL* 3.1 15.6 + - - +
164B MET 3.2 2.9 - - - -
165B GLU* 1.3 81.8 - - - +
167B LYS* 1.3 65.9 + - - -
168B VAL 3.4 2.6 + - - -
169B ARG* 3.7 2.0 + - - +
170B MET* 3.5 19.6 + - - +
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Residues in contact with LYS 167 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166B GLY* 1.3 71.4 - - - -
168B VAL* 1.3 61.6 + - + +
170B MET* 3.5 6.1 + - - +
171B LYS* 2.8 30.8 + - - +
348B ASP* 4.9 21.3 + - + +
349B THR* 5.3 13.0 - - + -
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Residues in contact with VAL 168 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166B GLY 3.4 0.6 - - - -
167B LYS* 1.3 76.1 - - + +
169B ARG* 1.3 59.8 + - + +
171B LYS* 3.1 11.8 + - + +
172B ASN* 2.8 51.2 + - - +
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Residues in contact with ARG 169 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99B GLY* 4.1 16.2 - - - -
132B GLY* 3.4 28.0 + - - +
133B GLY* 3.6 15.4 - - - -
161B PRO* 4.0 10.1 - - + -
165B GLU* 3.3 39.1 + - + +
166B GLY 3.7 6.4 + - - +
167B LYS 3.4 0.4 - - - -
168B VAL* 1.3 80.4 - - + +
170B MET* 1.3 58.3 + - - +
172B ASN* 3.4 1.9 + - - +
173B ALA* 2.8 28.8 + - - +
500B GTP 3.3 46.9 + - - -
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Residues in contact with MET 170 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160B LEU* 3.7 15.5 - - + -
161B PRO* 3.7 25.7 - - + +
162B PHE 5.8 2.0 - - - +
163B VAL* 6.4 1.3 - - - -
166B GLY 3.5 11.5 + - - +
167B LYS* 3.9 5.6 - - - +
168B VAL 3.3 0.4 - - - -
169B ARG* 1.3 75.1 - - - +
171B LYS* 1.3 61.5 + - - +
173B ALA* 3.1 20.1 + - + -
174B MET* 2.8 58.3 + - + +
348B ASP 3.1 28.3 - - - +
349B THR* 4.0 4.5 - - - +
350B GLY* 3.7 24.0 - - - +
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Residues in contact with LYS 171 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167B LYS 2.8 19.3 + - - +
168B VAL* 3.4 12.2 - - + +
170B MET* 1.3 77.9 - - - +
172B ASN* 1.3 71.8 + - - +
174B MET* 3.4 6.3 + - - +
175B GLU* 3.1 22.8 + - + +
348B ASP* 5.1 10.3 + - - +
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Residues in contact with ASN 172 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99B GLY 3.8 14.2 - - - +
101B PRO* 3.9 27.8 - - + +
132B GLY 4.0 15.1 - - - +
137B THR* 3.4 10.8 - - + +
168B VAL* 2.8 38.5 + - - +
169B ARG* 3.7 5.1 - - - +
171B LYS* 1.3 83.5 - - - +
173B ALA* 1.3 57.7 + - - +
175B GLU* 3.2 9.6 + - - +
176B GLY 2.9 23.9 + - - -
179B ARG* 4.8 0.2 + - - -
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Residues in contact with ALA 173 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131B LEU* 3.5 33.2 - - + +
132B GLY* 3.9 4.7 - - - +
137B THR* 4.7 0.4 - - - -
160B LEU* 4.3 3.1 - - + -
161B PRO* 3.5 18.2 - - + -
169B ARG 2.8 16.5 + - - +
170B MET* 3.1 23.1 + - + -
172B ASN* 1.3 77.2 - - - +
174B MET* 1.3 58.3 + - - +
176B GLY* 3.1 1.9 + - - -
177B LEU* 2.9 24.7 + - - +
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Residues in contact with MET 174 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160B LEU* 4.5 4.3 - - - -
170B MET* 2.8 44.2 + - + +
171B LYS* 3.8 6.3 - - - +
173B ALA* 1.3 72.3 - - - +
175B GLU* 1.3 61.9 + - - +
177B LEU* 3.2 18.0 + - + +
178B GLU* 3.0 20.1 + - - +
346B PHE* 3.4 53.3 - - + -
347B THR 3.6 22.2 - - - +
348B ASP* 5.4 1.1 - - - -
350B GLY* 4.3 7.9 - - - +
351B LEU* 4.3 6.3 - - + -
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Residues in contact with GLU 175 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101B PRO* 6.5 0.2 - - + -
171B LYS* 3.1 14.6 + - + +
172B ASN* 3.4 14.8 - - - +
173B ALA 3.2 0.2 - - - -
174B MET* 1.3 76.0 - - - +
176B GLY* 1.3 59.9 + - - +
178B GLU* 2.9 32.6 + - - +
179B ARG* 3.0 41.4 + - - +
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Residues in contact with GLY 176 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131B LEU* 4.6 8.5 - - - -
137B THR* 3.7 24.0 - - - -
141B PRO* 4.2 2.6 - - - +
172B ASN 2.9 10.9 + - - -
173B ALA 3.1 4.0 + - - -
175B GLU* 1.3 77.1 - - - +
177B LEU* 1.3 57.2 + - - +
179B ARG* 3.2 14.1 + - - +
180B LEU* 2.8 32.6 + - - +
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Residues in contact with LEU 177 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131B LEU* 3.5 20.6 - - + +
158B VAL* 3.9 8.1 - - + -
160B LEU* 4.1 19.5 - - + -
173B ALA 2.9 9.7 + - - +
174B MET* 3.4 23.1 - - + +
176B GLY* 1.3 77.3 - - - +
178B GLU* 1.3 60.8 + - - +
180B LEU* 4.2 3.4 - - + -
181B LYS* 3.3 27.9 + - - +
187B LEU* 3.8 19.0 - - + +
189B VAL* 3.7 31.9 - - + -
346B PHE* 4.1 27.4 - - + -
351B LEU* 4.6 2.0 - - + -
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Residues in contact with GLU 178 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174B MET 3.0 10.9 + - - +
175B GLU* 2.9 29.1 + - - +
177B LEU* 1.3 80.2 - - - +
179B ARG* 1.3 59.2 + - + +
180B LEU 3.6 0.2 + - - -
181B LYS* 3.7 28.8 + - - +
182B GLN* 3.1 37.8 + - - +
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Residues in contact with ARG 179 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101B PRO* 3.7 28.5 - - - +
105B GLU* 4.1 22.9 + - - -
137B THR* 3.2 34.3 + - - +
138B GLY* 4.3 4.7 + - - -
141B PRO* 3.4 19.5 - - + +
175B GLU* 3.0 36.0 + - - +
176B GLY* 3.2 12.5 + - - +
178B GLU* 1.3 77.0 - - + +
180B LEU* 1.3 64.4 + - - +
181B LYS 3.5 0.2 - - - -
182B GLN* 3.6 15.1 + - - +
183B HIS* 3.5 24.3 + - + -
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Residues in contact with LEU 180 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127B ILE* 5.3 1.1 - - + -
131B LEU* 4.6 10.3 - - + -
140B ALA* 3.9 14.4 - - + +
141B PRO* 3.8 31.2 - - + +
144B ALA* 4.1 3.4 - - + -
156B ALA* 4.1 7.2 - - + -
158B VAL* 3.9 25.6 - - + -
176B GLY 2.8 17.5 + - - +
177B LEU* 4.0 8.1 - - + +
178B GLU 3.3 0.2 - - - -
179B ARG* 1.3 75.1 - - - +
181B LYS* 1.3 55.5 + - - +
182B GLN 3.0 10.4 + - - -
183B HIS* 3.1 8.1 + - - +
184B THR* 2.9 46.1 + - + +
187B LEU* 3.6 24.5 - - + -
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Residues in contact with LYS 181 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177B LEU 3.3 12.2 + - - +
178B GLU* 3.7 35.1 + - - +
180B LEU* 1.3 77.6 - - - +
182B GLN* 1.3 63.6 + - + +
183B HIS 3.3 0.8 + - - -
184B THR* 3.4 20.3 + - - +
187B LEU* 3.8 16.1 - - + +
247B GLY 6.5 0.7 - - - -
341B GLN* 6.1 3.0 - - - +
346B PHE* 5.4 14.8 - - + -
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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