Contacts of the helix formed by residues 154 - 163 (chain B) in PDB entry 3NTV
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 GLN 154 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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103B ARG* 5.2 0.5 + - - -
130B ASN* 4.9 2.1 + - - +
132B LEU* 3.6 38.4 - - + +
153B ALA* 1.3 92.5 - - - +
155B SER* 1.3 51.4 + - - +
156B LYS 3.4 2.7 - - - -
157B LYS* 3.1 20.4 + - + +
158B PHE* 2.8 45.3 + - + -
200B LYS* 5.4 1.6 - - - -
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Residues in contact with SER 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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148B ILE* 4.4 6.5 - - - +
149B ASP 3.6 16.8 - - - -
150B ALA* 2.8 33.7 + - - -
152B LYS 4.0 5.6 - - - -
153B ALA 3.0 7.7 + - - -
154B GLN* 1.3 71.2 - - - +
156B LYS* 1.4 63.1 + - - +
158B PHE* 3.3 10.1 + - - +
159B PHE* 3.0 18.9 + - - +
200B LYS* 4.3 8.9 - - - +
204B TYR* 3.5 26.6 - - - +
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Residues in contact with LYS 156 (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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154B GLN 3.4 0.4 - - - -
155B SER* 1.4 79.4 + - - +
157B LYS* 1.4 58.3 + - - +
159B PHE* 3.2 6.2 + - - +
160B GLU* 3.0 40.3 + - - +
203B ASP* 4.4 17.8 + - - +
204B TYR* 3.6 20.4 - - + +
207B TRP* 3.6 63.1 - - + +
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Residues in contact with LYS 157 (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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132B LEU* 3.7 14.3 - - + +
154B GLN* 3.1 24.4 + - + +
156B LYS* 1.4 78.5 - - - +
158B PHE* 1.3 56.3 + - - +
160B GLU* 3.2 21.8 + - + +
161B ILE* 2.8 62.2 + - + +
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Residues in contact with PHE 158 (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 ILE* 3.6 28.3 - - + -
103B ARG* 4.2 7.6 - - - -
131B ALA* 3.6 40.6 - - + -
132B LEU* 3.8 20.0 - - + -
148B ILE* 4.4 15.3 - - + +
149B ASP 5.7 0.2 - - - -
152B LYS* 3.5 26.7 - - + -
153B ALA* 3.9 8.1 - - + -
154B GLN* 2.8 41.5 + - - -
155B SER* 3.7 7.6 - - - +
156B LYS 3.3 0.2 - - - -
157B LYS* 1.3 70.5 - - - +
159B PHE* 1.3 66.8 + - - +
161B ILE* 4.6 1.3 - - + -
162B TYR* 3.0 41.4 + + + +
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Residues in contact with PHE 159 (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 ILE* 3.9 10.9 - - + +
155B SER 3.0 12.5 + - - +
156B LYS* 3.4 9.2 - - - +
158B PHE* 1.3 76.0 - - - +
160B GLU* 1.4 57.4 + - - +
163B THR* 2.8 51.5 + - + +
172B VAL* 3.8 31.0 - - + -
204B TYR* 3.6 18.8 - - + -
207B TRP* 3.4 29.4 - + + -
208B LEU* 3.5 29.4 - - + -
211B GLN* 4.6 6.7 - - + -
214B TYR* 3.7 40.2 - + - -
228B SER* 4.9 0.2 - - - -
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Residues in contact with GLU 160 (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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156B LYS* 3.0 25.1 + - - +
157B LYS* 3.2 33.1 + - + +
159B PHE* 1.4 76.8 - - + +
161B ILE* 1.3 61.4 + - + +
163B THR* 4.2 3.4 + - - -
164B PRO* 3.4 17.5 - - - +
207B TRP* 3.7 31.3 + - + -
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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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131B ALA 4.5 2.7 - - - +
132B LEU* 3.7 37.2 - - + +
135B PHE* 3.2 42.0 - - + +
157B LYS* 2.8 57.6 + - + +
158B PHE* 4.0 5.2 - - + +
160B GLU* 1.3 73.1 - - - +
162B TYR* 1.4 80.6 + - + +
164B PRO* 3.3 8.1 - - - +
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Residues in contact with TYR 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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76B LEU* 3.7 29.6 - - + +
78B ILE* 3.7 20.2 - - + -
101B ILE* 3.6 11.0 - - + +
131B ALA* 2.5 30.9 + - + -
134B GLN* 3.3 24.9 + - - +
135B PHE* 3.6 18.3 + + - -
138B VAL* 3.6 25.4 - - + -
146B ILE* 3.5 15.3 - - + +
158B PHE* 3.0 35.6 + + - +
159B PHE* 5.6 0.2 - - - -
161B ILE* 1.4 92.3 - - + +
163B THR* 1.3 58.7 + - - +
164B PRO* 3.2 3.6 - - - -
165B LEU* 3.0 30.4 + - + +
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Residues in contact with THR 163 (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 ILE* 3.8 14.1 - - + -
159B PHE* 2.8 44.4 + - + +
160B GLU* 4.2 2.9 + - - -
162B TYR* 1.3 74.2 - - - +
164B PRO* 1.4 62.7 - - - +
165B LEU 3.0 0.2 - - - -
166B LEU* 2.8 20.6 + - + +
172B VAL* 3.7 31.0 - - + -
214B TYR* 3.2 21.0 + - - +
230B LYS* 2.8 16.1 + - - -
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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
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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