Contacts of the helix formed by residues 145 - 155 (chain B) in PDB entry 3V4V
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 MET 145 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139B MET* 4.0 14.0 - - + +
140B ASP* 3.1 50.7 - - - +
141B LEU* 4.6 1.3 - - - -
142B SER* 2.8 11.0 + - - +
144B SER* 1.3 81.7 - - - +
146B LYS* 1.3 63.6 + - - +
147B ASP 3.5 1.6 - - - -
148B ASP* 3.2 35.9 + - + +
149B LEU* 3.2 18.7 + - - +
232B VAL* 3.8 8.5 - - - +
268B THR* 4.2 25.4 - - - +
269B SER* 4.3 4.5 - - - -
270B ASP* 3.8 31.2 - - - +
330B THR* 6.0 0.2 - - - -
352B LEU* 5.6 0.9 - - + -
356B SER* 4.4 4.5 - - - +
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Residues in contact with LYS 146 (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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143B TYR* 2.8 58.4 + - + +
144B SER 3.3 2.0 - - - -
145B MET* 1.3 80.4 - - - +
147B ASP* 1.3 67.4 + - - +
149B LEU* 3.3 12.5 + - - +
150B GLU* 3.7 21.7 + - - +
202B GLU* 3.8 29.7 + - + +
232B VAL* 3.5 24.9 - - + +
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Residues in contact with ASP 147 (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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144B SER 4.1 6.0 - - - +
146B LYS* 1.3 80.9 + - + +
148B ASP* 1.3 86.0 + - - +
150B GLU* 3.6 27.1 + - - +
151B ARG* 3.6 11.6 + - - +
354B GLU 3.4 11.6 - - - +
355B ASP* 3.8 12.8 - - + +
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Residues in contact with ASP 148 (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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139B MET* 3.6 13.7 - - + -
144B SER 4.1 1.9 - - - +
145B MET* 3.2 38.0 - - + +
146B LYS 3.2 0.4 - - - -
147B ASP* 1.3 101.8 - - - +
149B LEU* 1.3 59.0 + - - +
151B ARG* 3.2 4.3 + - - +
152B VAL* 3.0 31.4 + - - +
270B ASP* 5.5 0.2 - - - +
330B THR* 5.5 3.3 - - - +
352B LEU* 5.1 1.0 - - - +
353B SER 4.6 1.4 - - - +
354B GLU* 2.8 19.7 - - - +
355B ASP 3.4 10.0 - - - +
356B SER* 2.9 26.8 + - - +
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Residues in contact with LEU 149 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139B MET* 3.7 26.9 - - + +
141B LEU* 4.0 15.0 - - + -
145B MET 3.2 8.5 + - - +
146B LYS 3.3 10.0 + - - +
148B ASP* 1.3 79.5 - - - +
150B GLU* 1.3 57.2 + - + +
152B VAL* 4.4 2.2 - - + -
153B ARG* 3.0 35.8 + - + +
174B PHE* 4.8 4.3 - - + -
227B VAL* 4.3 26.0 - - + +
230B GLN* 3.9 13.2 - - + +
231B SER* 3.8 37.2 - - - +
232B VAL* 4.0 6.5 - - + +
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Residues in contact with GLU 150 (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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146B LYS* 3.7 22.1 - - + +
147B ASP* 3.7 23.5 - - - +
148B ASP 3.2 0.4 - - - -
149B LEU* 1.3 80.4 - - + +
151B ARG* 1.3 64.6 + - - +
153B ARG* 3.5 28.2 + - - +
154B GLN* 3.8 26.5 + - - +
202B GLU* 5.2 4.9 - - - +
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Residues in contact with ARG 151 (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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147B ASP 3.6 6.1 + - - +
148B ASP 3.2 1.4 + - - +
150B GLU* 1.3 85.0 - - + +
152B VAL* 1.3 62.1 + - - +
153B ARG 3.5 0.2 - - - -
154B GLN* 3.7 17.9 + - - +
155B LEU* 3.3 40.5 + - - +
355B ASP* 3.3 36.8 - - + +
356B SER 3.9 5.4 - - - +
357B SER* 3.5 27.5 + - - +
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Residues in contact with VAL 152 (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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137B TYR* 3.7 39.0 - - + +
139B MET* 4.2 12.1 - - + -
148B ASP 3.0 21.4 + - - +
149B LEU* 4.0 6.7 - - + +
150B GLU 3.4 0.2 - - - -
151B ARG* 1.3 73.6 - - - +
153B ARG* 1.3 68.1 + - - +
154B GLN 3.1 2.2 - - - -
155B LEU* 3.0 24.3 + - + +
156B GLY 3.9 0.7 + - - -
174B PHE* 4.9 3.6 - - + -
223B PHE* 4.3 11.1 - - + -
227B VAL* 4.7 10.5 - - + -
356B SER* 3.9 22.4 - - - +
359B VAL* 5.0 5.4 - - + -
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Residues in contact with ARG 153 (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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149B LEU* 3.0 18.4 + - + +
150B GLU* 3.5 37.4 + - - +
151B ARG 3.5 0.2 - - - -
152B VAL* 1.3 77.7 - - - +
154B GLN* 1.3 84.1 + - - +
156B GLY* 4.0 1.2 + - - -
223B PHE* 4.9 0.5 - - - -
224B GLU* 3.7 29.4 - - + +
227B VAL* 3.6 19.2 + - + +
228B GLY* 3.6 33.3 + - - +
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Residues in contact with GLN 154 (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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150B GLU* 3.8 20.0 + - - +
151B ARG* 3.7 18.7 + - - +
152B VAL 3.1 0.8 - - - -
153B ARG* 1.3 96.7 - - + +
155B LEU* 1.3 60.5 + - + +
156B GLY 2.9 11.4 + - - -
157B HIS 4.4 0.5 + - - -
158B ALA* 4.8 3.5 + - - +
224B GLU* 3.4 15.7 - - - +
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Residues in contact with LEU 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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151B ARG* 3.3 33.2 + - - +
152B VAL* 3.0 14.2 + - + +
154B GLN* 1.3 76.1 - - + +
156B GLY* 1.3 62.2 + - - +
157B HIS 3.8 0.4 - - - -
158B ALA* 4.0 18.8 - - + +
159B LEU* 3.9 16.1 + - - +
223B PHE* 4.8 1.5 - - - -
356B SER 4.1 18.6 - - - +
357B SER 4.1 9.2 - - - +
359B VAL* 4.2 7.6 - - + -
360B VAL* 3.7 33.6 - - + +
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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