Contacts of the helix formed by residues 155 - 175 (chain C) in PDB entry 3V81
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 155 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87C PHE* 3.2 33.2 - - - -
153C TRP* 3.4 17.2 - - - -
154C LYS* 1.3 77.7 - - - +
156C SER* 1.3 59.4 + - - +
157C PRO 3.6 0.7 - - - -
158C ALA* 4.2 3.5 - - - +
159C ILE* 2.6 36.5 + - - +
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Residues in contact with SER 156 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115C TYR* 3.8 24.4 - - - -
149C LEU* 3.7 16.5 - - - +
150C PRO 3.4 17.8 + - - -
152C GLY 5.6 1.8 - - - -
153C TRP* 3.4 32.3 + - - +
154C LYS 3.3 0.2 + - - -
155C GLY* 1.3 74.8 - - - +
157C PRO* 1.3 69.4 - - - +
159C ILE 3.3 0.5 + - - -
160C PHE* 2.9 31.7 + - - +
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Residues in contact with PRO 157 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90C VAL* 4.3 10.3 - - + -
115C TYR* 3.2 26.2 - - + +
153C TRP 4.2 4.5 - - - +
154C LYS 3.6 13.9 - - - +
156C SER* 1.3 95.6 - - - +
158C ALA* 1.3 60.5 + - - +
160C PHE* 3.6 0.9 + - - +
161C GLN* 3.1 30.6 + - + +
184C MET* 5.8 6.3 - - - -
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Residues in contact with ALA 158 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87C PHE* 4.2 20.6 - - + -
88C TRP 4.3 4.5 - - - +
89C GLU* 5.6 0.7 - - - -
90C VAL* 3.5 31.2 - - + +
154C LYS 5.1 2.2 + - - +
155C GLY* 4.2 7.2 - - - +
156C SER 3.3 0.4 - - - -
157C PRO* 1.3 82.3 - - - +
159C ILE* 1.3 58.8 + - - +
162C SER* 3.0 25.6 + - - -
52D PRO* 3.9 17.3 - - + +
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Residues in contact with ILE 159 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8C VAL* 3.9 37.5 - - + +
10C VAL* 4.5 6.7 - - + -
87C PHE* 4.0 22.9 - - + -
118C VAL* 5.0 4.7 - - + -
119C PRO 5.8 1.8 - - - +
120C LEU* 5.6 1.1 - - + -
149C LEU* 4.1 19.1 - - + -
153C TRP* 3.8 25.8 - - + -
155C GLY* 2.6 27.6 + - - +
156C SER 4.1 1.6 - - - +
158C ALA* 1.3 73.3 - - - +
160C PHE* 1.3 55.1 + - - +
162C SER* 2.5 15.7 + - - +
163C SER* 2.3 32.1 + - - +
52D PRO* 4.3 3.4 - - + -
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Residues in contact with PHE 160 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111C VAL* 4.6 8.7 - - + -
114C ALA* 3.4 38.1 - - + -
115C TYR* 3.2 33.7 - + + -
118C VAL* 4.9 12.6 - - + -
149C LEU* 4.0 8.5 - - + +
156C SER 2.9 17.7 + - - +
157C PRO 3.8 2.9 - - - +
159C ILE* 1.3 76.2 - - - +
161C GLN* 1.3 68.0 + - + +
163C SER* 2.9 17.6 + - - -
164C MET* 2.9 46.3 + - + -
184C MET* 4.4 15.0 - - - -
185C ASP* 4.3 13.7 - - - -
214C LEU* 5.5 4.3 - - + -
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Residues in contact with GLN 161 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90C VAL* 2.9 38.9 - - + +
91C GLN* 2.4 28.8 + - - +
157C PRO* 3.1 17.7 + - + +
159C ILE 3.5 0.2 - - - -
160C PHE* 1.3 86.1 - - + +
162C SER* 1.3 51.1 + - - +
164C MET* 4.2 3.6 - - - -
165C THR* 2.6 39.2 + - - +
182C GLN* 3.6 29.4 + - + +
184C MET* 4.2 20.9 - - - +
140D PRO* 4.7 14.7 - - + +
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Residues in contact with SER 162 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8C VAL* 5.0 2.8 - - - +
90C VAL* 5.3 1.7 - - - +
158C ALA 3.0 14.4 + - - -
159C ILE* 2.5 29.6 + - - +
161C GLN* 1.3 73.4 - - - +
163C SER* 1.3 65.2 + - - +
165C THR* 3.4 6.8 + - - -
166C LYS* 3.0 33.7 + - - +
51D GLY* 5.5 0.2 - - - -
52D PRO* 3.4 28.1 - - - +
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Residues in contact with SER 163 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5C ILE* 5.0 7.0 - - - -
6C GLU 5.3 5.4 - - - -
8C VAL* 5.8 0.5 - - - +
118C VAL* 4.5 18.6 - - - +
159C ILE* 2.3 35.7 + - - +
160C PHE* 2.9 5.7 + - - -
162C SER* 1.3 73.0 + - - +
164C MET* 1.3 67.3 + - - +
166C LYS* 2.9 23.7 + - - +
167C ILE* 2.8 35.3 + - - +
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Residues in contact with MET 164 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111C VAL* 4.5 4.5 - - + -
160C PHE* 2.9 47.6 + - + +
161C GLN* 3.7 6.1 - - - +
163C SER* 1.3 77.1 - - - +
165C THR* 1.3 61.8 + - - +
167C ILE* 3.4 9.4 + - + +
168C LEU* 3.0 63.0 + - + +
182C GLN* 3.9 19.7 - - + +
184C MET 5.9 1.3 - - - +
187C LEU* 3.4 28.5 - - + -
209C LEU* 3.5 18.4 - - + -
214C LEU* 4.2 16.6 - - + -
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Residues in contact with THR 165 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161C GLN 2.6 23.1 + - - -
162C SER* 3.5 8.4 - - - -
164C MET* 1.3 76.8 - - - +
166C LYS* 1.3 59.1 + - + +
168C LEU* 3.3 2.9 + - - +
169C GLU* 2.9 30.2 + - + +
172C LYS* 6.3 0.4 - - - +
182C GLN* 3.1 27.2 + - - +
139D THR* 5.9 3.1 - - + -
140D PRO* 4.2 17.2 - - + +
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Residues in contact with LYS 166 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6C GLU* 4.1 32.4 + - + +
8C VAL* 3.9 24.6 - - - +
162C SER* 3.0 27.0 + - - +
163C SER* 2.9 20.1 + - - +
165C THR* 1.3 75.1 - - - +
167C ILE* 1.3 64.3 + - + +
169C GLU* 3.4 9.0 + - - +
170C PRO* 3.1 17.7 - - - +
52D PRO* 6.3 0.7 - - - -
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Residues in contact with ILE 167 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5C ILE* 4.4 13.9 - - + -
163C SER* 2.8 25.6 + - - +
164C MET* 3.5 9.2 - - - +
166C LYS* 1.3 77.0 - - + +
168C LEU* 1.3 57.9 + - + +
170C PRO* 2.8 25.2 - - - +
208C HIS* 3.4 10.5 + - + -
209C LEU* 4.1 24.0 - - + -
212C TRP* 3.9 55.5 - - + +
214C LEU* 3.6 26.2 - - + -
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Residues in contact with LEU 168 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164C MET* 3.0 51.5 + - + +
165C THR* 3.8 4.0 - - - +
167C ILE* 1.3 76.6 - - + +
169C GLU* 1.3 69.3 + - - +
171C PHE* 3.1 17.9 + - + +
172C LYS* 3.1 24.5 + - - +
180C ILE* 4.1 25.4 - - + -
182C GLN* 4.1 23.3 - - + +
187C LEU* 3.7 25.8 - - + -
205C LEU* 5.3 5.8 - - + -
208C HIS* 5.0 1.8 - - - -
209C LEU* 3.8 14.6 - - + -
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Residues in contact with GLU 169 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165C THR* 2.9 15.6 + - + +
166C LYS* 3.5 12.1 - - - +
168C LEU* 1.3 78.6 - - - +
170C PRO* 1.3 72.1 - - + +
172C LYS* 3.1 19.1 + - - +
173C LYS* 3.1 32.4 + - - +
49D LYS* 5.4 9.5 + - - +
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Residues in contact with PRO 170 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166C LYS 3.1 12.3 - - - +
167C ILE* 2.8 29.6 - - - +
168C LEU 3.3 0.2 - - - -
169C GLU* 1.3 86.2 - - + +
171C PHE* 1.3 65.4 + - - +
173C LYS* 3.5 17.9 + - + +
174C GLN* 3.7 12.6 + - - +
208C HIS* 3.6 16.4 - - + +
212C TRP* 4.9 8.3 - - + -
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Residues in contact with PHE 171 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168C LEU* 3.1 11.6 + - + +
170C PRO* 1.3 80.2 - - - +
172C LYS* 1.3 68.1 + - + +
174C GLN* 2.8 22.6 + - - +
175C ASN* 2.8 52.1 + - + +
178C ILE* 4.7 14.8 - - + -
180C ILE* 4.9 2.2 - - + -
201C LYS* 4.4 13.2 - - + -
204C GLU* 4.4 9.9 - - + -
205C LEU* 3.1 62.1 - - + -
208C HIS* 3.9 30.8 + + + +
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Residues in contact with LYS 172 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165C THR* 6.3 0.8 - - - +
168C LEU* 3.1 25.9 + - - +
169C GLU* 3.1 14.4 + - - +
171C PHE* 1.3 85.4 - - + +
173C LYS* 1.3 63.4 + - - +
175C ASN* 3.0 23.3 + - - +
176C PRO* 3.4 6.1 - - - +
178C ILE 5.8 5.4 - - - +
180C ILE* 3.7 55.5 + - + +
182C GLN* 4.9 9.5 - - - +
138D GLU 5.9 0.2 + - - -
139D THR* 5.0 17.4 + - - +
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Residues in contact with LYS 173 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169C GLU* 3.1 36.9 + - - +
170C PRO* 3.6 13.2 - - + +
171C PHE 3.0 0.8 + - - -
172C LYS* 1.3 79.3 - - - +
174C GLN* 1.3 65.0 + - + +
176C PRO* 3.5 16.2 - - - +
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Residues in contact with GLN 174 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170C PRO 3.9 11.9 - - - +
171C PHE* 2.8 8.6 + - - +
173C LYS* 1.3 83.9 - - + +
175C ASN* 1.3 68.9 + - - +
176C PRO* 3.3 7.4 - - - +
201C LYS* 5.2 0.2 + - - -
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Residues in contact with ASN 175 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171C PHE* 2.8 56.5 + - + +
172C LYS* 3.0 11.3 + - - +
174C GLN* 1.3 88.1 + - - +
176C PRO* 1.3 65.6 - - - +
177C ASP 2.8 5.8 + - - -
178C ILE* 2.8 29.2 + - + +
201C LYS* 2.9 42.2 - - - +
204C GLU* 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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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