Contacts of the helix formed by residues 171 - 180 (chain A) in PDB entry 1YI2
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 171 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8190 A 4.6 4.2 - - - -
8200 G 2.4 77.4 + - + +
8560 G 6.3 0.4 - - - -
8570 A 4.8 8.2 + - - -
18470 A 4.1 6.2 - - - +
169A PHE* 2.6 14.4 + - - +
170A VAL* 1.3 78.4 - - + +
172A ALA* 1.3 65.2 + - - +
174A ASN* 2.9 52.2 + - - +
175A LYS 3.5 3.1 + - - -
13Z ARG* 5.8 0.8 - - - +
14Z PHE* 4.9 6.9 - - + -
18Z TYR* 3.8 24.0 - - + +
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Residues in contact with ALA 172 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8200 G 2.9 14.5 + - - +
8570 A 3.4 38.8 - - + +
18460 U 3.1 35.5 + - - +
171A LYS* 1.3 68.6 - - - +
173A GLY* 1.3 62.7 + - - +
175A LYS* 3.0 7.2 + - - +
176A HIS* 2.8 23.1 + - - +
186A TRP* 3.5 5.3 - - + -
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Residues in contact with GLY 173 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8200 G 2.8 22.1 + - - -
8570 A 3.2 40.6 + - - -
171A LYS* 4.9 0.2 - - - -
172A ALA* 1.3 73.2 - - - +
174A ASN* 1.3 61.7 + - - +
176A HIS* 3.1 11.7 - - - +
177A HIS* 2.9 22.0 + - - -
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Residues in contact with ASN 174 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8570 A 5.1 0.7 + - - -
16520 C 5.0 1.4 + - - -
16530 A 5.2 9.4 + - - +
169A PHE* 2.6 41.2 + - + +
170A VAL* 4.6 2.8 - - - +
171A LYS* 2.9 38.0 + - - +
173A GLY* 1.3 73.2 - - - +
175A LYS* 1.3 69.5 + - - +
177A HIS* 3.2 14.4 + - - +
178A LYS* 3.2 19.1 + - - +
14Z PHE* 6.0 1.8 - - - -
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Residues in contact with LYS 175 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18470 A 2.9 47.2 + - - +
18480 G 4.7 5.9 + - - -
169A PHE* 3.8 25.4 - - + -
171A LYS 3.5 2.0 + - - -
172A ALA 3.0 8.6 + - - +
174A ASN* 1.3 76.7 - - - +
176A HIS* 1.3 55.5 + - - +
178A LYS* 2.9 4.6 + - + +
179A MET* 2.7 58.3 + - - +
186A TRP* 3.7 21.5 - - + +
188A ASN* 6.1 0.4 - - - +
8809A CL 3.8 24.0 - - - -
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Residues in contact with HIS 176 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7820 G 6.0 2.0 - - - -
8570 A 3.5 51.2 + - - +
8580 U 4.3 8.1 + - - -
8740 A 6.3 0.4 - - - -
172A ALA 2.8 11.9 + - - +
173A GLY 3.1 9.9 - - - +
175A LYS* 1.3 76.2 - - - +
177A HIS* 1.3 74.1 + + - +
179A MET* 3.3 2.3 + - - +
180A LYS* 3.0 52.3 + - + +
186A TRP* 3.7 26.2 - - + -
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Residues in contact with HIS 177 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8570 A 2.9 29.9 + - - -
8580 U 5.5 1.3 - - - -
16530 A 3.3 84.2 + + + +
173A GLY 2.9 24.3 + - - -
174A ASN* 3.2 9.4 + - - +
176A HIS* 1.3 94.1 + + - +
178A LYS* 1.3 63.1 + - - +
180A LYS* 3.5 15.7 + - - +
181A ALA* 3.9 3.6 + - - +
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Residues in contact with LYS 178 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16520 C 2.9 44.2 + - - +
16530 A 3.9 14.7 + - - -
18770 G 3.9 15.6 + - - -
18780 G 4.3 6.2 + - - -
52A SER* 4.2 6.5 - - - +
164A ARG* 4.9 2.6 - - - +
169A PHE* 3.6 22.2 - - + -
174A ASN 3.2 8.0 + - - +
175A LYS 2.9 7.2 + - - +
177A HIS* 1.3 74.6 - - - +
179A MET* 1.3 66.0 + - - +
181A ALA* 2.8 26.0 + - - +
182A ARG* 3.8 36.8 - - + +
8809A CL 3.1 27.5 - - + +
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Residues in contact with MET 179 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18790 U 5.7 1.6 - - - +
175A LYS* 2.7 43.6 + - + +
176A HIS* 3.6 6.3 - - - +
178A LYS* 1.3 75.8 - - + +
180A LYS* 1.3 61.3 + - - +
181A ALA 3.1 1.6 + - - -
182A ARG* 3.1 36.4 + - + +
184A THR* 3.7 42.0 - - + +
186A TRP* 3.2 45.1 - - + -
8809A CL 4.6 6.1 - - - -
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Residues in contact with LYS 180 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7830 C 3.1 37.2 + - - +
7840 A 5.7 3.6 - - - -
8580 U 5.8 1.4 + - - -
19A PRO* 4.0 4.9 - - - +
22A ARG* 3.6 26.8 + - - +
176A HIS* 3.0 39.6 + - + +
177A HIS* 3.6 12.6 - - - +
178A LYS 3.1 0.4 - - - -
179A MET* 1.3 75.9 - - - +
181A ALA* 1.3 57.2 + - - +
182A ARG 3.3 3.5 + - - +
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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