Contacts of the helix formed by residues 150 - 162 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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149C MET* 1.3 76.6 - - - +
151C GLN* 1.3 65.9 + - - +
152C GLU* 3.6 13.6 + - - +
153C ASP* 3.2 27.2 + - - +
154C ILE* 3.1 23.2 + - - +
182C TYR* 4.4 1.2 + - - -
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Residues in contact with GLN 151 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150C THR* 1.3 75.2 - - - +
152C GLU* 1.4 73.9 + - - +
154C ILE* 3.2 13.1 + - - +
155C SER* 3.0 31.6 + - - +
178C PHE 5.3 0.8 + - - -
278C ILE* 3.4 21.3 - - - +
279C ALA 2.6 45.1 + - - +
280C GLU* 5.7 0.9 - - - +
285C PRO* 3.6 27.6 - - + +
286C ALA 2.9 18.8 + - - +
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Residues in contact with GLU 152 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150C THR* 3.1 9.7 + - - +
151C GLN* 1.4 93.2 + - - +
153C ASP* 1.3 64.6 + - - +
155C SER* 3.5 6.6 + - - -
156C ASP* 3.0 21.8 + - - +
180C SER 4.7 1.6 - - - +
182C TYR* 3.5 28.4 + - + +
271C GLY* 6.1 2.5 - - - -
275C TYR* 5.3 17.4 - - + +
277C ILE 5.7 0.5 - - - +
278C ILE* 5.6 5.2 - - - +
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Residues in contact with ASP 153 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148C THR 4.5 3.3 - - - +
149C MET* 3.6 24.9 - - + +
150C THR* 3.2 34.5 + - - +
152C GLU* 1.3 75.3 - - - +
154C ILE* 1.3 63.4 + - - +
156C ASP* 3.2 2.6 + - - +
157C TYR* 2.9 23.9 + - - +
182C TYR* 2.8 31.5 + - - -
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Residues in contact with ILE 154 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142C VAL* 3.6 43.1 - - + +
143C ILE* 4.0 5.6 - - - -
144C ASN* 3.7 33.0 - - + +
149C MET* 4.1 10.8 - - + +
150C THR 3.1 18.2 + - - +
151C GLN* 3.2 13.7 + - - +
153C ASP* 1.3 75.9 - - - +
155C SER* 1.3 65.7 + - - +
157C TYR* 3.1 2.6 + - - +
158C VAL* 2.9 23.4 + - + +
285C PRO* 4.3 12.1 - - + +
286C ALA* 4.9 0.4 - - - -
287C SER* 3.9 7.4 - - - -
321C LEU* 3.9 15.7 - - + -
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Residues in contact with SER 155 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151C GLN* 3.0 20.6 + - - +
152C GLU* 3.7 6.7 - - - -
153C ASP 3.3 0.2 - - - -
154C ILE* 1.3 77.6 - - - +
156C ASP* 1.3 61.8 + - - +
158C VAL* 3.6 1.7 + - - +
159C ALA* 3.0 25.5 + - - +
177C LEU* 4.4 3.1 - - - +
178C PHE 3.9 1.0 + - - -
179C GLY* 3.5 11.5 - - - -
180C SER 3.6 27.4 - - - +
286C ALA 4.5 1.9 + - - -
287C SER* 3.2 26.4 + - - -
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Residues in contact with ASP 156 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152C GLU 3.0 12.1 + - - +
153C ASP* 3.7 6.3 - - - +
154C ILE 3.1 0.2 - - - -
155C SER* 1.3 77.7 - - - +
157C TYR* 1.4 65.3 + - - +
159C ALA* 3.2 3.3 + - - +
160C ALA* 2.9 24.3 + - - +
161C ASN* 5.5 0.9 + - - -
180C SER 3.8 6.4 + - - +
181C GLN* 3.7 1.2 - - - +
182C TYR* 2.8 58.2 + - + +
765C ARG* 3.7 16.1 + - - -
769C LYS* 3.5 26.4 + - - -
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Residues in contact with TYR 157 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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687A GLN 5.2 3.8 + - - -
149C MET* 4.2 12.6 - - + -
153C ASP 2.9 15.9 + - - +
154C ILE* 3.8 4.0 - - - +
156C ASP* 1.4 76.3 + - - +
158C VAL* 1.3 59.9 + - + +
161C ASN* 2.9 72.2 + - + +
162C MET* 3.9 13.7 - - + -
313C MET* 4.6 1.7 + - - +
316C PHE* 3.5 18.3 + - - +
317C PHE* 3.4 39.7 - + - -
318C PRO* 3.5 24.2 - - + -
321C LEU* 3.9 16.6 - - + -
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Residues in contact with VAL 158 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142C VAL* 3.5 31.2 - - + -
154C ILE 2.9 19.1 + - - +
155C SER 3.9 3.1 - - - +
157C TYR* 1.3 75.8 - - + +
159C ALA* 1.3 64.3 + - - +
162C MET* 2.9 46.1 + - + -
163C LYS* 3.0 10.5 + - + +
177C LEU* 3.7 22.9 - - + -
287C SER* 4.5 5.8 - - - +
288C GLY 4.6 1.8 - - - +
289C LEU* 3.8 27.8 - - + -
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Residues in contact with ALA 159 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155C SER 3.0 19.6 + - - +
156C ASP 3.7 0.7 - - - +
158C VAL* 1.3 81.5 - - - +
160C ALA* 1.3 59.1 + - - +
163C LYS* 3.8 23.6 + - + +
164C ASP* 4.6 2.9 + - - +
177C LEU* 3.6 23.3 - - + -
181C GLN* 3.6 29.6 - - + -
767C ARG* 3.9 13.9 + - - -
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Residues in contact with ALA 160 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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822A LEU* 5.1 7.8 - - - +
156C ASP* 2.9 17.7 + - - +
159C ALA* 1.3 76.7 - - - +
161C ASN* 1.3 73.9 + - - +
162C MET 3.9 0.2 - - - -
164C ASP* 6.0 2.0 - - - +
181C GLN* 4.1 0.4 - - - -
767C ARG* 3.6 44.1 + - + +
769C LYS* 3.8 22.7 - - - +
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Residues in contact with ASN 161 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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687A GLN 4.4 13.9 - - - +
688A ALA* 5.5 3.1 - - - -
822A LEU* 5.5 8.9 - - - +
156C ASP* 5.5 0.6 + - - -
157C TYR* 2.9 66.4 + - + +
160C ALA* 1.3 90.2 - - - +
162C MET* 1.3 62.0 + - - +
164C ASP 5.5 0.2 - - - -
165C ALA* 4.9 4.2 - - - +
313C MET* 4.2 11.6 - - - +
765C ARG* 6.2 0.2 - - - +
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Residues in contact with MET 162 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140C VAL* 5.6 1.3 - - + -
142C VAL* 4.6 7.6 - - + -
157C TYR* 3.9 23.1 - - + -
158C VAL* 2.9 41.6 + - + +
160C ALA 3.9 0.2 - - - -
161C ASN* 1.3 82.8 - - - +
163C LYS* 1.3 68.6 + - - +
164C ASP 3.4 1.8 - - - -
165C ALA* 3.3 5.3 + - - +
166C ILE* 2.9 27.6 + - + +
289C LEU* 4.7 10.1 - - + -
310C LEU* 3.8 27.1 - - + -
313C MET* 3.7 17.7 - - - +
317C PHE* 3.8 23.8 - - + -
323C ILE* 3.8 10.5 - - + -
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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