Contacts of the helix formed by residues 159 - 175 (chain B) in PDB entry 1NVT
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 159 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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157B ASN* 3.1 5.8 + - - +
158B ARG* 1.3 81.5 + - - +
160B VAL* 1.3 55.4 + - - +
161B GLU* 3.4 12.8 - - + +
162B LYS* 2.7 54.5 + - + +
163B ALA 3.2 2.6 + - - -
289B NAP 2.6 24.5 + - - -
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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
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157B ASN 3.6 14.8 + - - +
158B ARG 3.3 7.4 + - - +
159B THR* 1.3 69.7 - - - +
161B GLU* 1.3 58.1 + - - +
163B ALA* 2.6 30.5 + - - +
164B GLU* 2.7 10.4 + - - +
184B PHE* 4.1 26.0 - - + -
185B SER* 4.5 7.4 - - - +
186B GLY* 4.1 17.0 - - - +
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Residues in contact with GLU 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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159B THR* 4.4 12.8 - - + +
160B VAL* 1.3 78.6 - - - +
162B LYS* 1.3 55.7 + - - +
164B GLU* 3.4 20.6 - - - +
165B ALA* 2.7 34.8 + - - +
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Residues in contact with LYS 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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136B ALA* 4.2 23.2 + - + +
137B GLY* 5.6 1.0 - - - -
157B ASN* 3.8 9.0 - - - +
159B THR* 2.7 32.7 + - + +
161B GLU* 1.3 77.7 - - - +
163B ALA* 1.3 59.5 + - - +
165B ALA* 3.5 7.5 - - - +
166B LEU* 3.3 20.6 + - - +
289B NAP 2.6 39.6 + - - +
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Residues in contact with ALA 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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136B ALA* 4.8 1.8 - - - -
155B ILE* 3.5 35.7 - - + +
157B ASN* 3.7 28.0 - - + +
159B THR 3.2 3.0 + - - -
160B VAL 2.6 17.7 + - - +
162B LYS* 1.3 71.6 - - - +
164B GLU* 1.3 62.8 + - - +
166B LEU* 3.4 3.8 + - - +
167B ALA* 3.0 23.4 + - - +
184B PHE* 3.7 6.1 - - + +
185B SER 4.2 4.7 - - - +
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Residues in contact with GLU 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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160B VAL* 2.7 9.7 + - - +
161B GLU* 3.4 21.1 - - - +
163B ALA* 1.3 74.6 - - - +
165B ALA* 1.3 67.2 + - - +
167B ALA* 3.2 2.8 + - - +
168B LYS* 3.1 54.8 + - + +
178B PHE* 4.2 2.3 - - - -
184B PHE* 3.7 50.2 - - + +
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Residues in contact with ALA 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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161B GLU 2.7 18.8 + - - +
162B LYS* 3.5 10.5 - - - +
164B GLU* 1.3 76.2 - - - +
166B LEU* 1.3 62.5 + - - +
168B LYS* 3.4 8.1 + - - +
169B GLU* 3.1 24.7 + - - +
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Residues in contact with LEU 166 (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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136B ALA* 4.1 29.4 - - + +
140B ALA* 4.7 3.8 - - + +
141B ARG* 3.4 54.1 - - + +
145B PHE* 4.1 9.2 - - + -
155B ILE* 3.4 26.0 - - + -
162B LYS 3.3 10.3 + - - +
163B ALA* 3.8 5.4 - - - +
164B GLU 3.3 0.8 - - - -
165B ALA* 1.3 79.6 - - - +
167B ALA* 1.3 63.5 + - - +
169B GLU* 3.3 7.9 + - - +
170B ILE* 3.0 42.2 + - + +
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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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155B ILE* 3.7 5.5 - - + +
163B ALA 3.0 14.5 + - - +
164B GLU 3.5 8.5 - - - +
166B LEU* 1.3 76.7 - - - +
168B LYS* 1.3 61.7 + - - +
170B ILE 3.3 1.2 + - - -
171B ALA* 3.0 21.7 + - - +
178B PHE* 4.0 16.2 - - + -
182B VAL* 3.5 22.3 - - + +
183B LYS 3.7 24.0 - - - +
184B PHE* 4.0 5.4 - - + -
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Residues in contact with LYS 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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164B GLU* 3.1 44.0 + - + +
165B ALA* 3.7 9.9 - - - +
166B LEU 3.4 0.2 - - - -
167B ALA* 1.3 76.0 - - - +
169B GLU* 1.3 57.9 + - - +
171B ALA* 3.3 3.5 + - - +
172B GLU* 2.9 32.5 + - - +
178B PHE* 3.3 39.7 - - + -
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Residues in contact with GLU 169 (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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93B GLY* 5.5 0.3 - - - -
141B ARG* 2.8 41.3 + - - -
145B PHE* 4.1 7.4 - - + -
165B ALA 3.1 10.1 + - - +
166B LEU* 3.6 12.5 - - - +
167B ALA 3.3 0.2 - - - -
168B LYS* 1.3 80.8 - - - +
170B ILE* 1.3 61.7 + - - +
172B GLU* 3.3 14.9 - - - +
173B LYS* 3.1 56.4 + - - +
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Residues in contact with ILE 170 (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 ALA* 3.5 35.7 - - + -
145B PHE* 3.6 29.2 - - + +
148B ALA* 3.6 26.5 - - + -
153B ILE* 4.0 5.8 - - + -
155B ILE* 3.6 20.6 - - + -
166B LEU* 3.0 21.4 + - + +
167B ALA 3.7 3.8 - - - +
169B GLU* 1.3 74.1 - - - +
171B ALA* 1.3 66.7 + - - +
173B LYS* 3.5 0.5 + - - +
174B LEU* 3.0 35.9 + - + +
182B VAL* 4.1 11.9 - - + -
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Residues in contact with ALA 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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167B ALA 3.0 16.4 + - - +
168B LYS 3.6 4.0 - - - +
170B ILE* 1.3 76.5 - - - +
172B GLU* 1.3 63.4 + - - +
175B ASN* 3.0 4.5 + - - -
176B LYS* 2.8 55.2 + - + +
177B LYS 4.4 0.4 - - - -
178B PHE* 3.7 28.3 - - + +
182B VAL* 4.4 4.2 - - + +
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Residues in contact with GLU 172 (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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168B LYS 2.9 17.1 + - - +
169B GLU* 3.3 14.9 - - - +
170B ILE 3.2 0.2 - - - -
171B ALA* 1.3 81.4 - - - +
173B LYS* 1.3 79.5 + - - +
175B ASN* 3.5 8.0 + - - -
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Residues in contact with LYS 173 (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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90B GLN 3.6 12.9 + - - -
91B LEU* 3.0 54.1 + - + +
93B GLY* 5.2 2.0 - - - +
145B PHE* 3.9 18.6 - - + -
169B GLU* 3.1 39.0 + - - +
172B GLU* 1.3 92.8 - - - +
174B LEU* 1.3 61.6 + - + +
175B ASN* 3.4 0.9 + - - +
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Residues in contact with LEU 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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91B LEU* 5.1 12.6 - - + -
145B PHE* 3.4 34.5 - - + +
148B ALA* 3.7 30.5 - - + +
149B LYS* 3.9 24.5 - - + +
170B ILE* 3.0 24.0 + - + +
173B LYS* 1.3 79.3 - - + +
175B ASN* 1.3 73.4 + - - +
176B LYS* 3.2 21.9 + - + +
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Residues in contact with ASN 175 (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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171B ALA 3.0 6.5 + - - -
172B GLU 3.5 5.6 + - - -
173B LYS 3.4 4.2 - - - +
174B LEU* 1.3 81.0 - - - +
176B LYS* 1.3 62.8 + - - +
177B LYS* 4.4 17.8 - - - +
181B GLU* 4.8 0.3 - - - +
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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
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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