Contacts of the helix formed by residues 167 - 186 (chain D) in PDB entry 2VCK
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 TYR 167 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132A ASP* 2.5 51.3 + - - -
133A GLY* 4.0 2.0 - - - -
27D TYR* 3.4 11.8 + - + +
116D ILE* 3.9 20.0 - - + -
118D PHE* 4.5 3.2 - - + -
155D PHE* 3.7 29.4 - + + -
157D ARG* 3.6 31.2 - - + +
158D TYR 5.0 4.7 + - - -
159D CYS* 4.5 15.6 - - + +
163D GLU 4.7 0.2 - - - -
164D VAL 3.2 4.6 + - - -
165D ASP 3.0 0.8 - - - -
166D GLN* 1.4 111.8 + - + +
168D LEU* 1.3 57.0 + - - +
169D ASP 3.3 2.5 - - - -
170D THR* 3.4 7.8 + - - -
171D PHE* 3.0 27.4 + - - +
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Residues in contact with LEU 168 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26D ASN* 3.7 48.0 - - + +
27D TYR* 3.5 28.3 + - + +
30D ALA* 4.3 0.4 - - + -
165D ASP* 3.2 27.7 + - + +
167D TYR* 1.3 75.1 - - - +
169D ASP* 1.3 64.1 + - - +
171D PHE* 3.2 10.3 + - + +
172D LYS* 2.8 56.2 + - - +
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Residues in contact with ASP 169 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173A LEU* 3.4 27.3 - - + +
176A THR* 3.8 15.7 - - + +
177A LYS* 3.1 26.9 + - - +
180A GLU* 2.5 30.4 - - - +
165D ASP 4.7 1.0 + - - -
166D GLN 4.9 0.8 + - - -
167D TYR 3.3 0.6 - - - -
168D LEU* 1.3 81.9 - - - +
170D THR* 1.3 56.5 + - - +
172D LYS* 3.2 19.7 + - - +
173D LEU* 3.0 22.9 + - - +
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Residues in contact with THR 170 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133A GLY* 2.7 40.1 + - - +
134A LEU* 4.5 2.3 - - - +
173A LEU* 4.0 11.0 - - + +
177A LYS* 5.6 2.5 - - - +
118D PHE* 4.3 2.0 - - + -
135D PRO* 4.2 3.6 - - + -
155D PHE* 3.7 20.4 - - + -
166D GLN 5.2 1.1 + - - -
167D TYR* 3.4 13.1 + - - -
168D LEU 3.3 0.6 - - - -
169D ASP* 1.3 75.4 - - - +
171D PHE* 1.3 65.5 + - - +
173D LEU* 2.9 16.8 + - + +
174D TYR* 3.0 41.9 + - + -
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Residues in contact with PHE 171 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27D TYR* 3.4 55.0 - + + -
30D ALA* 4.3 8.1 - - + -
31D LEU* 4.4 3.4 - - + -
102D PHE* 3.7 26.0 - + - -
104D MSE 3.9 27.4 - - + -
106D LEU* 5.5 0.9 - - + -
118D PHE* 3.6 40.1 - + + -
167D TYR 3.0 14.8 + - - +
168D LEU* 3.3 10.1 - - + +
170D THR* 1.3 75.3 - - - +
172D LYS* 1.3 60.0 + - - +
174D TYR* 3.2 4.7 + - - +
175D LEU* 2.9 53.5 + - + +
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Residues in contact with LYS 172 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26D ASN 5.3 0.2 - - - -
30D ALA* 4.0 28.7 - - + -
33D GLU* 5.2 7.0 + - - -
34D THR* 5.8 1.1 - - - +
168D LEU* 2.8 45.7 + - + +
169D ASP* 3.6 17.7 + - - +
170D THR 3.2 0.2 - - - -
171D PHE* 1.3 75.4 - - - +
173D LEU* 1.3 59.4 + - - +
175D LEU* 3.3 9.4 + - + +
176D THR* 2.9 34.5 + - - +
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Residues in contact with LEU 173 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135A PRO* 5.9 0.4 - - + -
169A ASP* 3.5 42.4 - - + +
170A THR* 4.0 14.4 - - + +
173A LEU* 3.5 30.5 - - + -
133D GLY 4.5 3.1 - - - +
134D LEU* 3.7 33.7 - - + -
135D PRO* 5.0 5.4 - - + -
169D ASP 3.0 11.9 + - - +
170D THR* 2.9 10.3 + - - +
172D LYS* 1.3 75.1 - - - +
174D TYR* 1.3 67.9 + - + +
176D THR* 3.2 8.2 + - - -
177D LYS* 3.0 24.4 + - + +
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Residues in contact with TYR 174 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102D PHE* 3.8 20.9 - + + -
118D PHE* 3.8 28.0 - + + -
119D ASP* 4.9 1.6 - - - -
120D PHE* 3.5 38.8 - + + -
134D LEU* 3.9 17.0 - - + -
135D PRO* 3.4 32.2 + - + +
153D ASN* 2.7 33.3 + - + -
154D ILE 4.7 0.2 + - - -
155D PHE* 3.8 16.7 - - + -
170D THR* 3.0 38.6 + - + -
171D PHE 3.6 6.3 - - - +
173D LEU* 1.3 80.0 - - + +
175D LEU* 1.3 56.6 + - - +
177D LYS* 3.2 0.9 + - - +
178D TYR* 2.9 25.9 + - - +
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Residues in contact with LEU 175 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30D ALA* 3.5 32.5 - - + +
31D LEU* 3.7 22.9 - - + -
34D THR* 3.6 20.8 - - + +
35D PHE* 4.2 12.5 - - + -
102D PHE* 3.6 29.2 - - + -
171D PHE* 2.9 44.1 + - + +
172D LYS* 3.6 12.3 - - + +
173D LEU 3.2 0.2 - - - -
174D TYR* 1.3 75.7 - - - +
176D THR* 1.3 56.8 + - - +
178D TYR* 3.2 5.3 + - - +
179D LYS* 2.8 31.0 + - - +
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Residues in contact with THR 176 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169A ASP* 3.7 33.9 - - + +
34D THR* 4.7 3.7 + - - +
172D LYS* 2.9 21.6 + - - +
173D LEU* 3.2 9.7 + - - -
175D LEU* 1.3 76.5 - - - +
177D LYS* 1.3 62.1 + - - +
179D LYS* 3.4 8.3 + - + +
180D GLU* 3.1 27.6 + - + +
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Residues in contact with LYS 177 (chain D).
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 5.4 0.8 + - - -
166A GLN* 3.4 27.0 + - - +
169A ASP* 3.5 28.0 + - + +
170A THR* 5.4 3.4 - - - -
120D PHE* 4.2 12.1 - - + -
131D VAL* 4.1 22.0 - - + -
132D ASP 5.2 3.4 - - - -
134D LEU* 3.8 25.6 - - + -
173D LEU* 3.0 17.6 + - + +
174D TYR 3.6 7.4 - - - +
176D THR* 1.3 72.5 - - - +
178D TYR* 1.3 65.8 + - - +
180D GLU* 3.2 27.5 + - - +
181D MSE 3.2 29.4 + - + +
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Residues in contact with TYR 178 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35D PHE* 3.6 23.6 - + + -
71D PHE* 3.9 20.6 - + - -
91D LEU* 3.7 6.4 + - + -
93D PRO* 3.4 22.9 - - - +
99D LEU* 5.3 0.9 - - + -
100D PRO* 2.7 38.8 + - + -
101D CYS 4.3 0.4 - - - -
102D PHE* 3.5 37.8 + + + -
120D PHE* 3.8 22.2 - + + -
174D TYR 2.9 16.5 + - - +
175D LEU* 3.2 8.5 + - - +
177D LYS* 1.3 73.6 - - - +
179D LYS* 1.3 64.7 - - - +
181D MSE 3.1 17.8 - - + +
182D ILE* 3.0 38.8 + - + +
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Residues in contact with LYS 179 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34D THR* 3.8 34.5 + - + +
35D PHE* 3.6 17.4 - - + -
175D LEU 2.8 16.8 + - - +
176D THR* 3.7 7.2 - - - +
178D TYR* 1.3 78.0 - - - +
180D GLU* 1.3 53.4 + - + +
182D ILE* 3.3 0.6 + - - +
183D ASP* 2.6 72.6 + - - +
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Residues in contact with GLU 180 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169A ASP* 2.4 29.5 - - - +
176D THR* 3.1 23.4 + - + +
177D LYS* 3.2 33.5 + - - +
178D TYR 3.2 0.2 - - - -
179D LYS* 1.3 76.5 - - + +
181D MSE 1.3 57.5 + - - +
183D ASP* 3.8 3.9 - - - +
184D ASN* 2.9 45.3 + - - +
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Residues in contact with MSE 181 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99D LEU* 4.0 16.9 - - + +
100D PRO* 4.0 30.1 - - - -
120D PHE* 3.9 20.2 - - + -
129D PHE* 4.0 9.9 - - + -
131D VAL* 3.9 22.9 - - + -
177D LYS* 3.2 18.6 + - + +
178D TYR* 3.1 31.0 - - + +
180D GLU* 1.3 77.3 - - - +
182D ILE* 1.3 65.4 + - + +
184D ASN* 4.5 3.6 - - - +
185D ASN* 2.7 36.1 + - - +
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Residues in contact with ILE 182 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35D PHE* 4.3 4.9 - - + -
37D GLN* 5.1 0.4 - - - +
70D HIS* 3.4 39.6 - - + +
71D PHE* 3.7 29.6 - - + -
93D PRO* 3.7 30.3 - - + -
99D LEU* 4.0 13.9 - - + -
178D TYR* 3.0 40.1 + - + +
179D LYS* 3.7 5.2 - - - +
181D MSE 1.3 75.2 - - - +
183D ASP* 1.3 62.3 + - - +
186D LYS* 2.8 31.4 + - - -
187D PRO* 3.8 1.2 - - + +
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Residues in contact with ASP 183 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35D PHE* 5.5 1.0 - - - -
37D GLN* 5.6 1.4 + - - -
70D HIS* 4.1 17.9 + - - -
179D LYS* 2.6 62.3 + - - +
180D GLU* 3.9 4.2 - - - +
182D ILE* 1.3 78.4 - - - +
184D ASN* 1.3 64.3 + - - +
186D LYS* 2.7 38.8 + - - +
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Residues in contact with ASN 184 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180D GLU* 2.9 33.1 + - - +
181D MSE 4.0 5.2 - - - +
183D ASP* 1.3 81.2 - - - +
185D ASN* 1.3 66.0 + - - +
186D LYS* 4.7 2.3 + - - +
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Residues in contact with ASN 185 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97D ALA* 3.7 33.7 - - + +
99D LEU* 3.7 16.5 - - + +
181D MSE 2.7 30.5 + - - +
184D ASN* 1.3 85.2 - - - +
186D LYS* 1.3 71.6 + - - +
187D PRO* 4.0 5.4 - - + +
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Residues in contact with LYS 186 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70D HIS* 3.8 31.4 + - + +
182D ILE 2.8 16.8 + - - -
183D ASP* 2.7 36.1 + - - +
184D ASN 4.7 2.0 + - - +
185D ASN* 1.3 76.5 - - - +
187D PRO* 1.3 71.8 - - - +
188D VAL* 3.5 13.4 + - + +
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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
------------------------------------------------------------
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