Contacts of the helix formed by residues 144 - 155 (chain B) in PDB entry 3VI4
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 SER 144 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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141B ASN 4.0 8.9 + - - -
142B VAL 3.1 0.6 - - - -
143B LYS* 1.3 76.5 - - - +
145B LEU* 1.3 63.0 + - - +
146B GLY 3.3 0.5 + - - -
147B THR* 3.3 12.5 + - - -
148B ASP* 3.1 28.7 + - - +
213B ASN* 3.1 12.6 - - - +
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Residues in contact with LEU 145 (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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127B TYR* 3.9 33.0 - - + -
141B ASN 4.9 0.2 + - - -
142B VAL* 3.0 31.6 + - + +
144B SER* 1.3 79.4 + - - +
146B GLY* 1.3 62.8 + - - +
148B ASP* 4.8 4.0 - - - +
149B LEU* 3.0 44.4 + - + +
162B ILE* 5.3 0.4 - - + -
212B PHE* 3.8 23.6 - - + -
213B ASN* 3.3 0.2 + - - -
347B VAL* 4.2 24.7 - - + -
348B ILE* 4.1 26.9 - - + -
351B ILE* 5.5 0.7 - - + -
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Residues in contact with GLY 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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145B LEU* 1.3 78.3 - - - +
147B THR* 1.3 56.8 + - - +
150B MET* 3.2 29.1 + - - +
162B ILE* 4.4 7.1 - - - +
209B GLY* 3.7 13.2 - - - -
212B PHE* 3.3 34.5 - - - -
213B ASN* 3.0 9.9 + - - -
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Residues in contact with THR 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* 3.3 7.6 + - - -
145B LEU 3.2 0.4 - - - -
146B GLY* 1.3 74.4 - - - +
148B ASP* 1.3 72.7 + - - +
149B LEU 3.2 1.1 - - - -
150B MET* 3.6 4.5 - - + +
151B ASN* 2.9 26.0 + - - +
209B GLY* 3.7 20.4 - - - -
210B GLU* 3.9 12.3 - - + +
213B ASN* 3.0 22.7 + - - +
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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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144B SER* 3.1 35.4 + - - +
145B LEU* 4.3 2.2 - - - +
147B THR* 1.3 80.0 + - - +
149B LEU* 1.3 57.9 + - - +
151B ASN* 3.4 6.4 + - - +
152B GLU* 3.0 27.7 + - - +
348B ILE* 3.6 25.3 - - + +
65E ASP* 5.5 2.6 - - - +
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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
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125B LEU* 4.3 23.1 - - + -
127B TYR* 5.4 0.7 - - + -
145B LEU* 3.0 30.9 + - + +
148B ASP* 1.3 77.4 - - - +
150B MET* 1.3 54.3 + - - +
152B GLU* 4.4 3.8 - - + -
153B MET* 2.7 53.0 + - + +
160B PHE* 4.4 3.1 - - + -
162B ILE* 3.9 24.2 - - + -
348B ILE* 3.7 34.2 - - + +
351B ILE* 4.2 29.4 - - + -
352B ILE* 5.8 0.4 - - + -
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Residues in contact with MET 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 GLY 3.2 22.4 + - - +
147B THR* 3.3 8.1 + - + +
149B LEU* 1.3 77.4 - - - +
151B ASN* 1.3 63.8 + - - +
153B MET* 3.8 0.7 - - - +
154B ARG* 2.9 66.9 + - - +
160B PHE* 3.5 52.9 - - + +
161B ARG* 5.4 0.2 - - - -
162B ILE* 4.8 6.1 - - + -
206B THR 5.4 0.4 - - - +
207B ASN* 3.3 30.1 - - - +
209B GLY* 3.6 19.5 - - - -
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Residues in contact with ASN 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 THR 2.9 17.0 + - - +
148B ASP* 3.5 7.0 - - - +
150B MET* 1.3 77.2 - - - +
152B GLU* 1.3 63.3 + - - +
154B ARG* 3.5 13.1 + - - +
155B ARG* 3.6 14.4 + - - -
54E PHE* 3.9 10.2 - - - -
58E ASN* 3.9 10.3 + - - +
59E LEU* 3.2 55.5 + - - +
60E ALA 5.3 0.5 - - - +
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Residues in contact with GLU 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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148B ASP 3.0 18.1 + - - +
149B LEU* 3.8 4.3 - - + +
151B ASN* 1.3 78.1 - - - +
153B MET* 1.3 57.9 + - - +
155B ARG* 2.6 74.4 + - - +
156B ILE* 4.0 6.6 + - - +
348B ILE* 3.9 16.0 - - + +
352B ILE* 3.1 40.2 - - + +
61E SER* 4.9 1.0 - - - -
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Residues in contact with MET 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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123B ILE* 3.7 40.6 - - + -
125B LEU* 5.1 1.6 - - + -
149B LEU* 2.7 35.1 + - + +
152B GLU* 1.3 72.0 - - - +
154B ARG* 1.3 58.1 + - - +
156B ILE* 3.0 29.0 + - + +
157B THR* 2.9 26.1 + - - +
160B PHE* 3.7 37.7 - - + -
253B LEU* 4.8 10.1 - - + -
351B ILE* 4.2 20.9 - - + -
352B ILE* 5.0 5.6 - - - -
355B TYR* 5.0 7.6 - - + -
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Residues in contact with ARG 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 MET* 2.9 56.5 + - - +
151B ASN* 3.8 5.8 - - - +
152B GLU 3.2 0.2 - - - -
153B MET* 1.3 72.2 - - - +
155B ARG* 1.3 61.4 + - - +
156B ILE 2.9 6.3 + - - -
157B THR* 3.1 19.4 + - - +
158B SER 5.3 5.8 + - - +
160B PHE* 4.4 13.4 - - + +
207B ASN* 4.2 13.9 + - - +
54E PHE* 3.8 6.1 - - + -
55E ARG* 2.4 34.8 + - - +
57E SER* 4.8 4.0 + - - -
58E ASN* 2.9 34.0 + - - +
102F LEU* 3.5 3.5 - - - +
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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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151B ASN* 3.6 14.9 + - - +
152B GLU* 2.6 59.1 + - - +
154B ARG* 1.3 76.1 - - - +
156B ILE* 1.3 61.9 + - + +
54E PHE* 3.7 14.3 - - - -
59E LEU 2.7 29.9 + - - -
60E ALA* 3.4 1.8 - - - +
61E SER* 3.1 41.5 - - - +
100F LEU* 5.7 1.4 - - - +
102F LEU* 3.8 12.5 - - - +
103F TYR* 3.2 46.2 + - + +
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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
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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