Contacts of the helix formed by residues 150 - 162 (chain B) in PDB entry 5NC5
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 150 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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149B MET* 1.3 74.7 - - - +
151B GLN* 1.3 64.7 + - - +
152B GLU* 3.3 16.4 + - - +
153B ASP* 2.9 34.3 + - - +
154B ILE* 3.0 27.3 + - - +
285B PRO* 4.2 4.9 - - - -
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Residues in contact with GLN 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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150B THR* 1.3 73.4 - - - +
152B GLU* 1.3 74.9 + - - +
154B ILE* 3.9 11.3 - - - +
155B SER* 2.2 42.0 + - - +
178B PHE 5.7 2.8 + - - -
179B GLY* 5.9 3.8 - - - -
277B ILE* 3.5 23.0 + - - +
278B ILE* 3.6 15.0 - - - +
279B ALA* 3.0 33.9 + - - +
285B PRO* 3.7 10.9 - - + +
286B ALA 3.5 25.7 + - - +
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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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150B THR* 3.0 15.3 - - - +
151B GLN* 1.3 99.8 + - - +
153B ASP* 1.3 63.2 + - - +
155B SER* 3.9 5.1 - - - -
156B ASP* 3.4 16.8 + - - +
180B SER 4.4 4.4 - - - +
182B TYR* 3.6 17.8 - - + -
271B GLY* 4.4 4.0 - - - -
272B GLY* 3.4 32.6 - - - +
274B ASN 3.9 10.7 - - - +
275B TYR* 3.8 27.5 - - + -
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Residues in contact with ASP 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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148B THR 4.3 3.5 - - - +
149B MET* 3.4 29.7 - - + +
150B THR* 2.9 38.2 + - - +
152B GLU* 1.3 76.4 - - - +
154B ILE* 1.3 64.8 + - - +
156B ASP* 3.5 2.6 + - - +
157B TYR* 3.2 17.2 + - - +
182B TYR* 2.6 35.6 + - - +
270B LEU 5.5 0.5 - - - +
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Residues in contact with ILE 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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142B VAL* 3.6 37.9 - - + +
144B ASN* 3.9 20.9 - - + +
149B MET* 3.9 20.4 - - + -
150B THR 3.0 18.6 + - - +
151B GLN* 3.3 7.8 + - - +
153B ASP* 1.3 76.4 - - - +
155B SER* 1.3 58.8 + - - +
157B TYR* 3.1 3.8 + - + +
158B VAL* 2.8 28.8 + - + +
285B PRO* 3.4 33.7 - - + +
286B ALA* 4.0 4.0 - - - +
287B SER* 4.1 9.6 - - - -
321B LEU* 4.1 7.6 - - + -
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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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151B GLN* 2.2 32.6 + - - +
152B GLU* 3.9 3.1 - - - -
154B ILE* 1.3 75.8 - - - +
156B ASP* 1.3 56.4 + - - +
158B VAL* 3.2 4.0 + - - +
159B ALA* 2.7 32.3 + - - +
177B LEU* 4.1 3.1 - - - +
179B GLY* 4.1 5.7 - - - -
180B SER 3.4 34.3 - - - -
287B SER* 3.6 25.0 + - - -
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Residues in contact with ASP 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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152B GLU 3.4 9.1 + - - +
153B ASP 3.9 2.5 - - - +
154B ILE 3.2 0.6 - - - -
155B SER* 1.3 74.7 - - - +
157B TYR* 1.3 63.6 + - - +
159B ALA* 3.8 1.2 - - - +
160B ALA* 2.8 40.3 + - - +
180B SER 4.2 0.6 + - - -
181B GLN* 3.6 10.8 - - - +
182B TYR* 3.1 49.6 + - + +
765B ARG* 3.0 22.2 + - - -
769B LYS* 2.5 27.8 + - - -
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Residues in contact with TYR 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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149B MET* 4.3 10.3 - - + -
153B ASP 3.2 11.5 + - - +
154B ILE* 3.1 9.5 + - - +
156B ASP* 1.3 79.4 + - - +
158B VAL* 1.3 63.5 + - + +
161B ASN* 2.8 72.6 + - + +
162B MET* 4.1 12.1 - - + -
313B MET* 4.9 0.3 + - - +
316B PHE* 3.6 17.4 + - - +
317B PHE* 3.4 22.8 - + - -
318B PRO* 3.4 30.3 - - + -
321B LEU* 3.8 24.7 - - + -
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Residues in contact with VAL 158 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142B VAL* 3.8 37.7 - - + -
154B ILE* 2.8 21.2 + - + +
155B SER* 3.5 3.8 - - - +
157B TYR* 1.3 77.1 - - + +
159B ALA* 1.3 61.3 + - - +
162B MET* 2.9 41.3 + - + -
163B LYS* 3.0 11.3 + - + -
177B LEU* 3.6 24.2 - - + -
287B SER* 4.8 4.5 - - - -
288B GLY 4.4 2.5 - - - +
289B LEU* 3.8 25.8 - - + -
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Residues in contact with ALA 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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155B SER 2.7 20.2 + - - +
156B ASP 3.8 3.1 - - - +
158B VAL* 1.3 79.2 - - - +
160B ALA* 1.3 61.4 + - + +
161B ASN 3.7 0.2 + - - -
163B LYS* 4.1 14.0 + - + +
164B ASP* 3.4 20.4 - - - +
177B LEU* 3.6 21.5 - - + -
181B GLN* 4.2 24.2 - - + +
767B ARG* 3.9 8.0 + - - +
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Residues in contact with ALA 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 ASP* 2.8 31.9 + - - +
159B ALA* 1.3 74.7 - - + +
161B ASN* 1.3 73.8 + - - +
164B ASP* 4.1 5.0 - - - +
181B GLN* 5.9 0.4 - - - +
765B ARG* 5.9 2.0 - - - +
767B ARG* 3.8 38.1 + - - +
769B LYS* 5.0 1.6 - - - +
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Residues in contact with ASN 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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157B TYR* 2.8 67.8 + - + +
160B ALA* 1.3 89.8 - - - +
162B MET* 1.4 59.9 + - - +
164B ASP* 5.5 1.8 - - - -
165B ALA* 5.0 4.2 - - - +
313B MET* 4.0 12.0 - - - +
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Residues in contact with MET 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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140B VAL* 4.9 0.7 - - + -
142B VAL* 3.9 26.7 - - + -
157B TYR* 4.1 22.0 - - + -
158B VAL* 2.9 33.2 + - + +
160B ALA 3.9 0.2 - - - -
161B ASN* 1.4 82.8 - - - +
163B LYS* 1.3 69.2 + - - +
164B ASP 3.2 1.8 - - - +
165B ALA* 3.0 15.4 + - - +
166B ILE* 3.1 16.8 + - + +
289B LEU* 4.3 15.5 - - + -
310B LEU* 3.8 29.2 - - + -
313B MET* 3.8 17.0 - - + -
317B PHE* 4.2 15.5 - - + -
323B ILE* 4.3 2.7 - - + -
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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