Contacts of the helix formed by residues 154 - 174 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75B LEU* 3.4 14.9 - - - +
150B GLN 5.1 2.9 - - - +
151B SER 4.5 12.8 - - - +
152B LEU 3.6 4.6 + - - +
153B MET* 1.3 79.2 - - - +
155B ARG* 1.3 62.8 + - - +
156B ALA* 3.6 14.3 + - - +
157B ARG* 3.7 24.4 + - - +
158B ALA* 3.5 13.3 + - - +
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Residues in contact with ARG 155 (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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70B GLN* 5.0 4.9 + - - +
73B GLN* 3.4 46.2 + - - +
74B THR* 5.0 4.9 + - - +
75B LEU* 3.5 23.1 - - + +
78B LEU* 3.8 18.0 - - + +
154B THR* 1.3 73.0 - - - +
156B ALA* 1.3 66.9 + - - +
157B ARG 3.1 2.9 + - - -
158B ALA* 3.4 2.4 + - - +
159B LYS* 3.2 32.5 + - - +
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Residues in contact with ALA 156 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154B THR* 3.4 8.5 + - - +
155B ARG* 1.3 79.0 - - - +
157B ARG* 1.3 58.6 + - + +
159B LYS* 3.7 16.0 + - - +
160B VAL* 3.2 29.1 + - - +
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Residues in contact with ARG 157 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205A ARG* 4.1 20.5 - - - +
151B SER 4.0 4.9 + - - -
152B LEU* 2.4 54.3 + - - +
153B MET* 4.7 8.1 - - - -
154B THR* 3.7 26.2 + - - +
155B ARG 3.1 0.8 - - - -
156B ALA* 1.3 77.8 - - + +
158B ALA* 1.3 55.0 + - - +
159B LYS 3.1 1.6 - - - -
160B VAL* 2.9 7.5 + - - +
161B ILE* 2.6 43.3 + - + +
404B SOG 3.6 44.4 - - + +
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Residues in contact with ALA 158 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75B LEU* 3.9 24.5 - - + -
78B LEU* 4.2 11.9 - - + -
79B PHE* 3.5 32.0 - - + -
153B MET* 4.6 3.7 - - - -
154B THR 3.5 3.8 + - - +
155B ARG 3.4 7.5 + - - +
157B ARG* 1.3 76.3 - - - +
159B LYS* 1.3 57.7 + - - +
161B ILE* 3.1 7.3 + - - +
162B ILE* 2.7 35.5 + - - +
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Residues in contact with LYS 159 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78B LEU* 4.8 18.4 - - + -
155B ARG* 3.2 19.0 + - - +
156B ALA* 3.7 15.8 - - - +
157B ARG 3.1 0.6 - - - -
158B ALA* 1.3 78.1 - - - +
160B VAL* 1.3 58.2 + - + +
162B ILE* 3.2 12.1 + - + +
163B CYS* 2.9 37.4 + - - +
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Residues in contact with VAL 160 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206A ALA* 4.1 16.6 - - + -
402A SOG 5.1 5.6 - - - -
156B ALA 3.2 14.7 + - - +
157B ARG* 2.9 11.5 + - - +
159B LYS* 1.3 76.5 - - + +
161B ILE* 1.3 59.3 + - - +
163B CYS* 3.7 7.1 + - + +
164B THR* 2.8 28.6 + - - -
404B SOG 3.8 42.0 - - + -
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Residues in contact with ILE 161 (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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79B PHE* 4.3 8.1 - - + -
134B VAL* 3.9 34.8 - - + -
153B MET* 4.0 32.8 - - + -
157B ARG* 2.6 23.8 + - + +
158B ALA* 3.4 10.5 - - - +
160B VAL* 1.3 71.7 - - - +
162B ILE* 1.3 68.1 + - - +
164B THR* 3.0 8.1 + - - +
165B VAL* 2.9 23.7 + - + +
404B SOG 3.7 40.6 - - + -
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Residues in contact with ILE 162 (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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78B LEU* 3.4 34.1 - - + +
79B PHE* 3.5 25.4 - - + -
82B SER* 3.5 30.1 - - - +
131B THR* 5.9 2.0 - - + +
158B ALA 2.7 23.9 + - - +
159B LYS* 3.6 11.4 - - + +
161B ILE* 1.3 72.2 - - - +
163B CYS* 1.3 67.2 + - - +
165B VAL* 3.2 8.6 + - - +
166B TRP* 3.0 32.0 + - + +
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Residues in contact with CYS 163 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
402A SOG 5.3 6.7 - - + +
159B LYS* 2.9 21.1 + - - +
160B VAL* 3.7 8.5 - - - +
162B ILE* 1.3 82.8 - - - +
164B THR* 1.3 56.8 + - - +
166B TRP* 3.4 6.8 + - - +
167B ALA* 3.0 26.9 + - - +
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Residues in contact with THR 164 (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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206A ALA* 3.4 23.1 - - + +
210A ALA* 3.8 29.4 - - + -
402A SOG 3.6 20.8 - - + +
160B VAL* 2.8 17.9 + - - +
161B ILE* 3.0 7.1 + - - -
163B CYS* 1.3 72.5 - - - +
165B VAL* 1.3 60.6 + - - +
167B ALA* 3.2 4.7 + - - +
168B ILE* 2.8 41.3 + - + +
404B SOG 4.2 17.4 - - + +
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Residues in contact with VAL 165 (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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406A D10 5.3 6.7 - - + -
127B ALA* 4.0 7.0 - - + +
130B GLU* 3.1 38.4 - - + +
131B THR* 3.7 19.7 - - - +
134B VAL* 3.8 29.4 - - + -
161B ILE* 2.9 17.3 + - + +
162B ILE* 3.6 9.9 - - - +
164B THR* 1.3 77.1 - - - +
166B TRP* 1.3 59.3 + - + +
168B ILE* 4.5 5.2 - - + -
169B SER* 2.8 36.7 + - - +
404B SOG 6.2 2.7 - - + -
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Residues in contact with TRP 166 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82B SER* 3.1 25.2 + - - +
85B CYS* 4.8 6.2 - - + +
86B ALA* 3.5 43.7 - - + -
89B VAL* 5.3 6.1 - - + -
123B LEU* 4.0 36.0 - - + +
124B CYS* 4.8 9.2 - - - -
127B ALA* 3.9 26.4 - - + +
131B THR* 5.1 1.2 + - - -
162B ILE* 3.0 39.2 + - + +
163B CYS* 3.4 6.7 + - - +
164B THR 3.3 0.2 - - - -
165B VAL* 1.3 78.5 - - + +
167B ALA* 1.3 56.9 + - - +
169B SER* 3.8 3.3 - - - -
170B ALA* 2.8 28.6 + - - +
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Residues in contact with ALA 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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181A TRP* 3.6 29.2 - - + -
402A SOG 3.7 20.9 - - + -
163B CYS 3.0 17.4 + - - +
164B THR 3.2 4.2 + - - +
166B TRP* 1.3 73.5 - - - +
168B ILE* 1.3 62.4 + - - +
170B ALA* 3.2 5.3 + - - +
171B LEU* 2.8 30.5 + - - +
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Residues in contact with ILE 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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181A TRP* 5.4 0.2 - - - -
210A ALA* 3.8 19.3 - - + -
214A ILE* 3.6 35.4 - - + -
402A SOG 4.2 16.6 - - + -
406A D10 4.6 18.4 - - + -
130B GLU* 3.3 25.8 - - - +
164B THR* 2.8 28.3 + - + +
165B VAL* 4.7 4.3 - - + +
167B ALA* 1.3 75.2 - - - +
169B SER* 1.3 62.1 + - - +
171B LEU* 3.2 8.2 + - + +
172B VAL* 3.0 34.6 + - + +
404B SOG 5.6 3.8 - - + -
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Residues in contact with SER 169 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123B LEU* 3.3 20.3 - - - +
126B THR* 3.2 19.3 - - - +
127B ALA* 3.2 28.2 - - - -
130B GLU* 2.9 20.0 + - - -
165B VAL 2.8 18.0 + - - -
166B TRP 3.8 2.9 - - - -
168B ILE* 1.3 73.3 - - - +
170B ALA* 1.3 61.6 + - - +
172B VAL* 3.5 0.4 + - - -
173B SER* 2.8 28.6 + - - -
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Residues in contact with ALA 170 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181A TRP* 4.9 6.7 - - + -
123B LEU* 3.3 16.7 - - + +
166B TRP 2.8 20.2 + - - +
167B ALA* 3.2 7.8 + - - +
169B SER* 1.3 75.9 - - - +
171B LEU* 1.3 60.9 + - - +
174B PHE* 3.0 28.7 + - + +
175B LEU* 3.1 14.9 + - + +
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Residues in contact with LEU 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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171A LEU* 3.6 32.0 - - + +
172A VAL* 4.2 18.2 - - + -
175A LEU* 4.2 7.6 - - + -
176A PRO* 3.9 24.0 - - + -
179A MET* 5.9 0.9 - - - -
181A TRP* 4.1 16.1 - - + -
214A ILE* 6.2 1.1 - - + -
402A SOG 4.5 15.5 - - + -
167B ALA 2.8 20.9 + - - +
168B ILE* 3.2 9.4 + - + +
170B ALA* 1.3 73.5 - - - +
172B VAL* 1.3 63.5 + - + +
175B LEU* 3.8 27.2 - - + +
176B PRO* 3.3 21.5 - - - +
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Residues in contact with VAL 172 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171A LEU* 4.4 11.2 - - + -
172A VAL* 5.1 9.0 - - + -
214A ILE* 5.9 2.0 - - + -
406A D10 5.3 7.2 - - + -
126B THR* 4.0 14.8 - - + -
130B GLU* 4.4 4.3 - - - +
168B ILE* 3.0 30.6 + - + +
169B SER 3.8 1.1 - - - +
171B LEU* 1.3 86.1 - - + +
173B SER* 1.3 71.1 + - - +
176B PRO* 3.6 12.8 - - - +
207B TYR* 6.0 0.2 - - - -
211B SER* 5.4 1.6 - - - -
214B ILE* 4.0 26.9 - - + +
215B SER* 4.2 11.3 + - - +
402B SOG 3.8 15.2 - - + +
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Residues in contact with SER 173 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119B SER 4.6 1.8 - - - +
122B VAL* 3.1 34.2 + - - +
123B LEU* 4.4 2.1 - - - -
126B THR* 2.9 26.2 + - - +
169B SER 2.8 15.3 + - - -
171B LEU 3.4 0.4 - - - -
172B VAL* 1.3 81.7 - - - +
174B PHE* 1.3 66.7 + - - +
176B PRO* 3.8 4.7 - - - -
177B ILE* 3.5 26.2 + - - +
207B TYR* 5.7 2.0 - - - -
211B SER* 6.5 0.2 - - - -
215B SER* 4.0 5.4 - - - -
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Residues in contact with PHE 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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116B LEU* 4.0 20.4 - - + -
119B SER* 3.3 41.0 + - - -
120B LEU* 4.2 15.0 - - + -
123B LEU* 4.2 17.8 - - + +
169B SER 3.9 1.8 + - - -
170B ALA* 3.0 26.6 + - + +
173B SER* 1.3 76.6 - - - +
175B LEU* 1.3 76.1 + - + +
177B ILE* 3.2 6.6 + - - +
178B MET* 3.1 38.1 + - + +
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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