Contacts of the helix formed by residues 154 - 174 (chain C) in PDB entry 2VT4
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 THR 154 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75C LEU* 3.4 15.3 - - - +
150C GLN 5.1 2.7 - - - +
151C SER 4.5 13.0 - - - +
152C LEU 3.6 4.6 + - - +
153C MET* 1.3 79.2 - - - +
155C ARG* 1.3 62.2 + - - +
156C ALA* 3.6 14.4 + - - +
157C ARG* 3.7 25.0 + - - +
158C ALA* 3.5 12.8 + - - +
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Residues in contact with ARG 155 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70C GLN* 5.0 5.3 + - - +
73C GLN* 3.4 46.4 + - - +
74C THR* 5.0 4.7 + - - +
75C LEU* 3.5 23.7 - - + +
78C LEU* 3.8 17.7 - - + +
154C THR* 1.3 73.0 - - - +
156C ALA* 1.3 66.7 + - - +
157C ARG 3.1 2.0 - - - -
158C ALA* 3.4 2.1 + - - +
159C LYS* 3.2 32.8 + - - +
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Residues in contact with ALA 156 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154C THR* 3.4 8.8 + - - +
155C ARG* 1.3 79.2 - - - +
157C ARG* 1.3 58.0 + - - +
159C LYS* 3.6 14.8 + - - +
160C VAL* 3.1 28.9 + - - +
404C SOG 5.1 10.3 - - - +
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Residues in contact with ARG 157 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151C SER 4.0 4.9 + - - -
152C LEU* 2.4 54.3 + - - +
153C MET* 4.7 7.6 - - - +
154C THR* 3.7 27.0 + - - +
155C ARG 3.1 0.8 - - - -
156C ALA* 1.3 76.5 - - + +
158C ALA* 1.3 55.1 + - - +
159C LYS 3.1 1.3 - - - -
160C VAL* 2.9 6.9 + - - +
161C ILE* 2.6 43.5 + - + +
404C SOG 3.3 55.0 + - + +
205D ARG* 4.2 19.1 - - - +
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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
----------------------------------------------------------
75C LEU* 3.8 24.2 - - + -
78C LEU* 4.2 11.4 - - + -
79C PHE* 3.5 31.5 - - + -
153C MET* 4.6 3.9 - - - -
154C THR 3.5 3.8 + - - +
155C ARG 3.4 8.0 + - - +
157C ARG* 1.3 76.5 - - - +
159C LYS* 1.3 57.7 + - - +
161C ILE* 3.1 6.7 + - - +
162C ILE* 2.7 34.7 + - - +
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Residues in contact with LYS 159 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78C LEU* 4.8 19.1 - - + -
155C ARG* 3.2 23.8 + - - +
156C ALA* 3.7 15.6 - - - +
157C ARG 3.1 0.4 - - - -
158C ALA* 1.3 75.1 - - - +
160C VAL* 1.3 65.2 + - + +
162C ILE* 3.2 12.2 + - + +
163C CYS* 2.9 31.8 + - - +
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Residues in contact with VAL 160 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156C ALA 3.1 15.1 + - - +
157C ARG* 2.9 11.1 + - - +
159C LYS* 1.3 77.7 - - + +
161C ILE* 1.3 58.9 + - - +
163C CYS* 3.6 6.9 + - - +
164C THR* 2.8 28.6 + - - -
404C SOG 3.7 41.3 - - + +
206D ALA* 4.2 15.9 - - + -
402D SOG 5.6 5.1 - - - +
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Residues in contact with ILE 161 (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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79C PHE* 4.3 8.5 - - + -
134C VAL* 3.9 34.8 - - + -
153C MET* 4.1 32.8 - - + -
157C ARG* 2.6 23.5 + - + +
158C ALA* 3.5 10.3 - - - +
160C VAL* 1.3 71.9 - - - +
162C ILE* 1.3 67.2 + - - +
164C THR* 3.0 8.1 + - - +
165C VAL* 2.9 23.3 + - + +
404C SOG 3.7 38.6 - - + -
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Residues in contact with ILE 162 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78C LEU* 3.4 33.9 - - + +
79C PHE* 3.5 25.8 - - + -
82C SER* 3.5 29.4 - - - +
131C THR* 5.9 1.8 - - + +
158C ALA 2.7 24.7 + - - +
159C LYS* 3.6 11.4 - - + +
161C ILE* 1.3 72.8 - - - +
163C CYS* 1.3 68.2 + - - +
165C VAL* 3.2 9.6 + - - +
166C TRP* 3.0 31.6 + - + +
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Residues in contact with CYS 163 (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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159C LYS* 2.9 20.9 + - - +
160C VAL* 3.7 8.5 - - + +
162C ILE* 1.3 83.3 - - - +
164C THR* 1.3 56.9 + - - +
166C TRP* 3.4 7.0 + - - +
167C ALA* 3.0 27.5 + - - +
402D SOG 5.4 9.6 - - - -
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Residues in contact with THR 164 (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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160C VAL* 2.8 17.2 + - - +
161C ILE* 3.0 7.1 + - - -
163C CYS* 1.3 73.1 - - - +
165C VAL* 1.3 60.3 + - - +
167C ALA* 3.2 5.1 + - - +
168C ILE* 2.8 52.4 + - + +
404C SOG 4.1 18.1 - - + +
206D ALA* 3.5 21.1 - - - +
210D ALA* 3.9 17.5 - - + -
402D SOG 3.9 22.8 - - + +
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Residues in contact with VAL 165 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127C ALA* 4.0 6.7 - - + +
130C GLU* 3.1 41.0 - - + +
131C THR* 3.7 20.2 - - - +
134C VAL* 3.8 29.6 - - + -
161C ILE* 2.9 17.8 + - + +
162C ILE* 3.6 9.9 - - - +
164C THR* 1.3 76.4 - - - +
166C TRP* 1.3 58.8 + - + +
168C ILE* 4.5 6.3 - - + -
169C SER* 2.8 36.9 + - - +
404C SOG 6.0 3.4 - - + -
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Residues in contact with TRP 166 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82C SER* 3.1 27.9 + - - +
85C CYS* 4.8 6.4 - - + +
86C ALA* 3.5 40.8 - - + -
89C VAL* 5.2 6.1 - - + -
123C LEU* 4.0 35.1 - - + +
124C CYS* 4.8 9.2 - - - -
127C ALA* 3.9 27.1 - - + +
131C THR* 5.1 1.0 + - - -
162C ILE* 3.0 39.4 + - + +
163C CYS* 3.9 6.7 - - - +
164C THR 3.3 0.2 - - - -
165C VAL* 1.3 78.5 - - + +
167C ALA* 1.3 57.9 + - - +
169C SER* 3.8 2.7 - - - -
170C ALA* 2.9 28.4 + - - +
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Residues in contact with ALA 167 (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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163C CYS 3.0 17.4 + - - +
164C THR* 3.2 7.6 + - - +
166C TRP* 1.3 75.3 - - - +
168C ILE* 1.3 61.3 + - - +
170C ALA* 3.2 3.6 + - - +
171C LEU* 2.8 30.5 + - - +
181D TRP* 3.5 34.4 - - + -
402D SOG 4.4 13.7 - - + -
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Residues in contact with ILE 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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130C GLU* 3.3 26.0 - - - +
164C THR* 2.8 28.9 + - + +
165C VAL* 4.7 4.9 - - + +
167C ALA* 1.3 75.4 - - - +
169C SER* 1.3 61.9 + - - +
171C LEU* 3.2 6.1 + - - +
172C VAL* 3.0 35.0 + - + +
404C SOG 5.4 5.2 - - + -
406C D10 4.5 5.6 - - + -
210D ALA* 3.8 19.1 - - + -
214D ILE* 3.8 34.8 - - + -
402D SOG 4.0 18.4 - - + -
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Residues in contact with SER 169 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123C LEU* 3.3 20.1 - - - +
126C THR* 3.2 19.6 - - - +
127C ALA* 3.2 28.5 - - - -
130C GLU* 2.9 20.1 + - - -
165C VAL 2.8 14.6 + - - -
166C TRP 3.8 2.9 - - - -
168C ILE* 1.3 77.3 - - - +
170C ALA* 1.3 61.3 + - - +
172C VAL 3.5 0.2 + - - -
173C SER* 2.8 28.4 + - - -
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Residues in contact with ALA 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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123C LEU* 3.3 17.1 - - + +
166C TRP 2.9 20.1 + - - +
167C ALA* 3.2 7.4 + - - +
169C SER* 1.3 74.5 - - - +
171C LEU* 1.3 63.1 + - - +
174C PHE* 3.0 29.5 + - + +
175C LEU* 3.1 14.5 + - + +
181D TRP* 4.8 7.4 - - + -
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Residues in contact with LEU 171 (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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167C ALA 2.8 21.3 + - - +
168C ILE* 3.2 6.5 + - + +
170C ALA* 1.3 73.7 - - - +
172C VAL* 1.3 63.2 + - + +
175C LEU* 3.8 27.2 - - + +
176C PRO* 3.2 22.0 - - - +
171D LEU* 3.5 34.9 - - + +
172D VAL* 4.3 8.7 - - + -
175D LEU* 4.1 8.1 - - + -
176D PRO* 3.8 17.9 - - + -
179D MET* 5.8 1.1 - - - -
181D TRP* 4.1 12.1 - - + -
402D SOG 3.7 35.2 - - + -
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Residues in contact with VAL 172 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126C THR* 4.0 14.6 - - + -
130C GLU* 4.3 4.9 - - - +
168C ILE* 3.0 30.8 + - + +
169C SER* 3.8 1.1 - - - +
171C LEU* 1.3 86.3 - - + +
173C SER* 1.3 71.3 + - - +
176C PRO* 3.6 12.4 - - - +
207C TYR* 6.0 0.3 - - - -
211C SER* 5.4 1.9 - - - -
214C ILE* 4.0 25.7 - - + +
215C SER* 4.2 12.1 + - - +
402C SOG 3.8 14.3 - - + +
406C D10 5.3 7.4 - - + -
171D LEU* 4.3 11.9 - - + -
172D VAL* 5.1 8.7 - - + -
214D ILE* 6.0 2.7 - - + -
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Residues in contact with SER 173 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119C SER 4.5 2.0 - - - +
122C VAL* 3.1 35.4 + - - +
123C LEU* 4.4 2.1 - - - -
126C THR* 2.9 26.6 + - - +
169C SER 2.8 15.5 + - - -
171C LEU 3.4 0.4 - - - -
172C VAL* 1.3 81.2 - - - +
174C PHE* 1.3 66.0 + - - +
176C PRO* 3.8 4.9 - - - -
177C ILE* 3.5 26.4 + - - +
207C TYR* 5.7 2.0 - - - -
211C SER* 6.5 0.2 - - - -
215C SER* 4.0 5.2 - - - -
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Residues in contact with PHE 174 (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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116C LEU* 4.0 20.9 - - + -
119C SER* 3.3 40.8 - - - -
120C LEU* 4.2 14.8 - - + -
123C LEU* 4.2 17.8 - - + +
169C SER 3.9 1.8 + - - -
170C ALA* 3.0 26.4 + - + +
173C SER* 1.3 76.6 - - - +
175C LEU* 1.3 76.3 - - + +
177C ILE* 3.2 6.6 + - - +
178C MET* 3.1 37.3 + - + +
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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