Contacts of the helix formed by residues 152 - 160 (chain C) in PDB entry 1CN4
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 LYS 152 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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43C ASP* 2.6 36.0 + - - +
44C THR* 4.5 4.7 + - - +
45C LYS 4.2 16.9 + - - -
46C VAL* 3.7 19.4 - - + +
51C TRP* 3.7 27.1 - - + -
62C GLU* 2.6 36.5 + - + +
63C VAL* 4.5 4.6 - - + +
147C ASN 4.0 1.8 + - - -
148C PHE* 3.3 34.6 + - + +
151C GLY* 1.3 67.8 - - - -
153C LEU* 1.3 69.2 + - - +
155C LEU* 3.3 3.8 + - - +
156C TYR* 3.0 22.2 + - - +
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Residues in contact with LEU 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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6C ILE* 4.5 6.1 - - + -
12C LEU* 4.2 16.2 - - + -
63C VAL* 3.9 22.8 - - + +
67C LEU* 4.7 12.3 - - + -
105C LEU* 4.1 17.3 - - + -
109C LEU* 4.5 14.6 - - + -
148C PHE* 2.9 16.1 + - + +
149C LEU* 2.8 46.9 - - + +
152C LYS* 1.3 75.1 - - - +
154C LYS* 1.3 52.7 + - - +
156C TYR* 2.7 25.4 + - + +
157C THR* 2.8 35.5 + - + +
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Residues in contact with LYS 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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153B HIS* 3.5 32.7 + - + -
203B PRO* 6.0 1.8 - - - -
204B SER* 3.3 24.2 - - - +
9C SER* 4.8 22.4 + - - +
12C LEU* 4.6 16.7 - - + +
16C LEU* 4.4 11.9 - - + -
149C LEU 2.8 11.5 + - - +
150C ARG* 3.0 26.7 - - - +
153C LEU* 1.3 75.5 - - - +
155C LEU* 1.3 59.7 + - + +
156C TYR 3.5 0.3 + - - -
157C THR* 3.7 19.7 + - - +
158C GLY* 3.8 5.9 + - - -
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Residues in contact with LEU 155 (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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93B PHE* 3.5 29.6 - - + -
150B MET* 4.3 27.7 - - + +
153B HIS* 4.9 4.9 - - + +
204B SER* 5.9 0.7 - - - -
205B PHE* 4.3 14.6 - - + -
46C VAL* 4.0 17.0 - - + -
48C PHE* 3.9 28.5 - - + -
51C TRP* 3.8 25.5 + - + +
59C GLN* 4.4 2.6 - - - +
150C ARG 4.6 1.3 - - - +
151C GLY 3.1 22.9 + - - +
152C LYS 3.7 4.9 - - - +
153C LEU 3.0 1.2 - - - -
154C LYS* 1.3 77.4 - - + +
156C TYR* 1.3 62.4 + - - +
158C GLY* 4.3 1.5 - - - -
159C GLU* 4.3 11.3 + - - +
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Residues in contact with TYR 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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51C TRP* 4.7 1.8 - - + -
56C VAL* 3.3 35.8 - - + +
59C GLN* 3.8 19.5 - - + +
60C ALA* 3.0 36.3 - - + +
63C VAL* 4.0 21.5 - - + -
109C LEU* 5.4 6.3 - - + -
112C LEU* 4.6 17.1 - - + +
113C GLY 4.8 0.9 + - - -
114C ALA* 4.5 17.6 + - + -
117C GLU* 3.1 15.2 + - - -
152C LYS 3.0 15.2 + - - +
153C LEU* 2.7 6.4 + - + +
155C LEU* 1.3 76.5 - - - +
157C THR* 1.3 74.2 + - + +
158C GLY 2.8 3.1 + - - -
159C GLU* 3.1 4.5 + - - +
160C ALA* 3.0 36.1 + - + +
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Residues in contact with THR 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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6C ILE* 3.7 32.5 + - + +
7C CYS* 5.6 0.2 - - - -
12C LEU* 4.1 6.4 - - + +
109C LEU* 5.2 2.2 - - + -
112C LEU* 4.6 4.0 - - - -
153C LEU* 2.8 44.4 - - + +
154C LYS* 3.7 14.4 + - - +
156C TYR* 1.3 81.9 - - + +
158C GLY* 1.3 56.9 + - - +
160C ALA* 4.5 2.7 - - - -
161C CYS* 2.5 46.3 + - - +
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Residues in contact with GLY 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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150B MET* 6.3 3.1 - - - -
153B HIS* 6.2 1.8 - - - -
154C LYS* 3.8 10.4 + - - -
155C LEU 4.7 2.2 - - - -
156C TYR 2.8 2.8 + - - -
157C THR* 1.3 88.0 + - - +
159C GLU* 1.3 64.5 + - - +
161C CYS* 2.9 15.6 + - - +
162C ARG 3.5 8.7 - - - +
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Residues in contact with GLU 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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150B MET* 6.0 4.8 - - - +
56C VAL* 4.5 20.4 - - + +
59C GLN* 4.9 7.9 - - - +
155C LEU 4.3 10.0 + - - +
156C TYR 3.1 6.0 + - - +
158C GLY* 1.3 73.5 - - - +
160C ALA* 1.3 56.7 + - - +
162C ARG* 3.1 39.5 + - - +
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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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4C ARG* 5.0 1.9 + - - -
56C VAL* 3.5 25.7 - - + +
112C LEU* 4.9 14.6 - - + +
156C TYR* 3.0 35.6 + - + +
157C THR* 3.7 3.4 - - - +
159C GLU* 1.3 72.5 - - - +
161C CYS* 1.3 54.1 + - - +
162C ARG* 2.6 29.5 + - - +
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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