Contacts of the helix formed by residues 162 - 168 (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 MET 162 (chain C).
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Specific contacts
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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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Residues in contact with LYS 163 (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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158C VAL 3.0 15.0 + - - +
159C ALA* 3.8 18.5 + - + +
162C MET* 1.3 76.3 - - - +
164C ASP* 1.3 71.8 + - - +
166C ILE* 3.3 1.4 + - - +
167C SER* 2.9 28.2 + - - -
175C VAL* 3.8 41.5 + - + +
177C LEU* 4.3 26.0 - - + +
289C LEU* 4.2 17.0 - - + -
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Residues in contact with ASP 164 (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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66A GLU 4.2 3.1 - - - +
67A GLN* 3.7 30.1 - - - +
70A ASN* 5.9 1.1 + - - -
821A GLY* 6.2 0.3 - - - -
159C ALA 4.6 4.4 + - - +
160C ALA 6.0 1.7 - - - +
161C ASN 5.5 0.2 - - - -
162C MET 3.4 0.8 - - - +
163C LYS* 1.3 86.8 + - - +
165C ALA* 1.3 63.0 + - - +
167C SER* 2.9 22.5 + - - -
168C ARG* 3.1 36.4 + - - +
767C ARG* 3.5 36.6 + - - +
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Residues in contact with ALA 165 (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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820A ASN 5.8 1.8 - - - +
161C ASN 4.9 3.8 - - - +
162C MET* 3.3 5.1 + - - +
163C LYS 3.2 0.4 - - - -
164C ASP* 1.3 79.5 - - - +
166C ILE* 1.3 59.5 + - - +
168C ARG* 3.4 14.8 + - - +
169C THR* 2.8 23.2 + - - -
309C GLU* 3.6 25.2 - - - +
313C MET* 3.6 15.0 - - + -
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Residues in contact with ILE 166 (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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162C MET* 2.9 22.1 + - + +
163C LYS 4.0 2.5 - - - +
165C ALA* 1.3 74.7 - - - +
167C SER* 1.3 62.8 + - - +
169C THR* 3.0 20.7 + - - +
172C VAL* 3.5 12.9 - - + +
175C VAL* 4.5 7.2 - - + -
289C LEU* 3.9 20.6 - - + -
291C ILE* 3.4 33.4 - - + -
306C ILE* 4.4 9.0 - - + +
309C GLU* 3.7 18.6 - - + -
310C LEU* 4.2 22.7 - - + -
313C MET* 3.6 19.7 - - + -
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Residues in contact with SER 167 (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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69A MET 4.7 0.3 + - - -
70A ASN* 3.1 28.3 + - - +
71A GLY 3.3 19.8 + - - -
163C LYS* 2.9 17.9 + - - -
164C ASP* 2.9 20.1 + - - -
166C ILE* 1.3 76.6 - - - +
168C ARG* 1.3 59.5 + - - +
169C THR 3.2 0.2 - - - -
172C VAL* 3.9 15.7 - - - +
173C GLY 5.9 0.2 - - - -
174C ASP* 5.8 0.7 - - - -
175C VAL* 3.9 26.4 - - - +
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Residues in contact with ARG 168 (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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66A GLU 3.2 25.5 + - - -
67A GLN 5.6 0.2 - - - -
69A MET 3.0 32.9 + - - +
70A ASN* 4.3 1.8 - - - -
71A GLY 5.0 1.3 - - - +
72A ILE 5.5 2.2 - - - +
75A LEU* 4.1 41.6 - - + +
78A MET* 3.8 21.5 - - - +
820A ASN* 2.8 44.8 + - - +
821A GLY* 4.1 4.8 - - - -
164C ASP* 3.1 47.1 + - - +
165C ALA* 3.4 10.3 + - - +
166C ILE 3.2 0.4 - - - -
167C SER* 1.3 76.0 + - - +
169C THR* 1.3 63.5 + - - +
170C SER* 3.6 1.6 + - - -
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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