Contacts of the helix formed by residues 163 - 171 (chain C) in PDB entry 1R9T
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 ILE 163 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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39C ALA 3.9 0.7 - - - +
40C GLU* 3.4 43.3 - - + +
41C ILE 3.7 3.1 - - - +
42C PRO* 4.0 9.6 - - + -
82C TYR* 4.7 13.9 - - + +
84C ARG* 5.4 3.1 - - - +
162C GLY* 1.3 76.9 - - - +
164C ALA* 1.3 69.5 + - - +
165C LYS* 2.5 6.4 + - + +
166C GLU* 2.4 49.4 + - + +
167C HIS 3.6 0.7 - - - +
170C TRP* 3.4 12.6 - - - +
10K PHE* 4.0 23.3 - - + -
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Residues in contact with ALA 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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995B ARG* 4.4 4.7 - - - +
996B ARG* 6.3 0.2 - - - +
997B GLU* 5.4 1.3 - - - +
38C ILE* 3.5 10.3 - - + +
39C ALA* 3.1 38.8 - - + +
40C GLU 5.1 0.2 - - - +
41C ILE 5.7 0.4 + - - -
163C ILE* 1.3 70.1 - - - +
165C LYS* 1.4 56.0 - - - +
166C GLU 2.2 15.3 + - - -
167C HIS 2.9 22.5 + - - +
168C ALA* 4.2 7.4 - - + +
170C TRP* 3.4 17.4 + - - +
171C GLY* 4.4 7.4 - - - +
172C PRO* 5.7 0.6 - - + +
6K ARG* 3.9 3.5 + - - -
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Residues in contact with LYS 165 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
995B ARG* 3.9 29.7 + - - +
997B GLU* 5.6 0.9 - - - +
39C ALA* 3.4 18.1 + - + +
40C GLU* 4.5 22.9 - - + +
163C ILE* 2.5 8.6 + - + +
164C ALA* 1.4 75.3 - - - +
166C GLU* 1.3 61.4 + - - +
254C LYS* 4.5 5.7 - - - +
6K ARG* 3.0 21.3 + - - +
9K LEU* 3.8 29.9 + - + +
10K PHE* 3.8 40.4 - - + +
37K LYS 4.4 2.4 + - - -
38K GLU* 4.2 12.5 - - - +
39K ASP* 3.1 41.2 + - - +
41K THR* 5.5 0.4 - - - -
69K ALA* 5.8 2.0 - - - +
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Residues in contact with GLU 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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82C TYR* 6.2 0.2 - - - -
84C ARG* 4.7 10.9 + - - -
161C LYS 5.3 1.7 - - - +
162C GLY* 5.1 3.1 - - - -
163C ILE* 2.4 27.5 + - + +
164C ALA 2.2 22.0 + - - -
165C LYS* 1.3 69.1 - - - +
167C HIS* 1.3 66.6 + - - +
170C TRP* 3.5 18.1 - - + -
6K ARG* 3.1 26.8 + - - +
7K PHE* 4.0 23.6 + - - +
10K PHE* 3.5 31.9 - - + -
70L ARG* 3.0 39.9 + - - -
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Residues in contact with HIS 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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847B ASP* 3.0 40.0 + - + +
848B ARG* 5.4 0.2 - - - -
65C HIS* 5.0 3.2 - - - -
69C LEU* 5.1 5.6 - - + +
163C ILE 3.6 0.9 - - - +
164C ALA* 2.9 17.9 + - - +
166C GLU* 1.3 83.3 - - - +
168C ALA* 1.3 84.4 + - - +
169C LYS* 2.8 43.9 + - + +
170C TRP* 3.4 17.4 + - + -
6K ARG* 3.9 8.3 - - - +
69L ALA 3.7 2.2 - - - -
70L ARG* 3.0 49.3 + - + +
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Residues in contact with ALA 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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844B SER* 4.4 18.4 - - - +
847B ASP* 3.7 23.6 - - + +
848B ARG* 4.6 24.9 + - + +
995B ARG* 6.3 1.3 - - + -
996B ARG* 5.9 0.7 - - - +
164C ALA* 4.2 9.9 - - + +
167C HIS* 1.3 93.8 - - - +
169C LYS* 1.3 76.8 - - - +
170C TRP 2.9 1.5 + - - -
171C GLY* 3.4 14.2 + - - +
6J ARG* 4.4 6.4 + - - -
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Residues in contact with LYS 169 (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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43C THR* 5.4 1.0 - - - +
45C ALA* 4.7 8.0 - - + +
46C ILE 3.7 17.7 + - - +
47C ASP* 3.1 19.7 + - - -
68C GLY* 3.4 34.3 - - - +
69C LEU* 3.5 16.8 - - + -
167C HIS* 2.8 20.8 + - + +
168C ALA 1.3 87.6 - - - +
170C TRP* 1.3 101.0 + - + +
171C GLY 3.3 5.4 + - - +
6J ARG* 3.3 24.2 + - - +
69L ALA 2.4 30.2 + - - +
70L ARG* 3.5 0.6 - - - +
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Residues in contact with TRP 170 (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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41C ILE 4.3 2.9 - - - +
43C THR* 3.3 39.0 - - + -
44C LEU 4.2 0.2 - - - -
45C ALA* 3.4 29.2 + - + +
47C ASP* 3.1 37.9 - - + -
160C LYS* 3.7 1.7 + - + -
161C LYS 4.5 6.7 - - - -
162C GLY* 3.3 31.3 - - - +
163C ILE 3.4 2.5 - - - -
164C ALA 3.4 20.1 + - - +
166C GLU* 3.5 27.4 - - + -
167C HIS* 3.4 28.0 + - + +
168C ALA 2.9 1.4 - - - -
169C LYS* 1.3 100.7 - - - +
171C GLY* 1.3 68.2 + - - +
172C PRO* 3.3 6.8 - - - +
70L ARG* 3.2 23.1 - - - -
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Residues in contact with GLY 171 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
848B ARG* 5.9 0.7 - - - -
996B ARG* 5.4 7.6 - - - -
38C ILE 4.4 9.2 - - - -
43C THR* 4.9 1.6 - - - +
164C ALA* 3.9 6.7 - - - +
168C ALA* 3.4 11.1 + - - -
169C LYS 3.3 9.7 + - - +
170C TRP* 1.3 78.8 - - - +
172C PRO* 1.3 67.5 - - - +
173C ALA* 2.7 9.4 - - - -
235C VAL* 5.4 0.9 - - - +
237C SER* 4.2 4.9 + - - -
6J ARG* 4.2 10.9 + - - -
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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