Contacts of the helix formed by residues 159 - 172 (chain A) in PDB entry 1YOB
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 159 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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131A ASP 5.6 0.4 + - - -
132A GLY* 4.8 12.1 + - - -
156A GLN* 3.1 15.8 + - + +
158A GLY* 1.3 80.3 - - - +
160A THR* 1.3 59.0 + - - +
161A ASP 3.5 1.8 - - - -
162A GLU* 3.4 35.2 + - - +
163A ARG* 2.8 74.3 + - + +
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Residues in contact with THR 160 (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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17A VAL* 4.6 12.1 - - + -
151A LEU* 4.5 8.8 - - + +
152A ASP 5.3 0.3 + - - -
153A LEU* 3.1 37.1 - - + +
156A GLN 3.8 3.3 + - - -
157A SER* 3.4 20.7 + - - -
158A GLY 3.6 0.2 - - - -
159A LYS* 1.3 76.7 - - - +
161A ASP* 1.3 63.5 + - - +
163A ARG* 3.1 6.2 + - - +
164A VAL* 2.7 53.8 + - + +
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Residues in contact with ASP 161 (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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20A SER* 5.0 7.8 + - - -
24A ARG* 5.2 4.6 + - - +
157A SER 4.9 0.6 + - - -
158A GLY 5.3 1.7 + - - +
159A LYS 3.5 0.2 - - - -
160A THR* 1.3 82.3 - - - +
162A GLU* 1.3 64.8 + - - +
164A VAL* 4.0 4.4 - - - +
165A ALA* 3.0 28.1 + - - +
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Residues in contact with GLU 162 (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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158A GLY 4.9 3.4 + - - +
159A LYS* 3.4 41.9 + - - +
161A ASP* 1.3 80.4 - - - +
163A ARG* 1.3 65.3 + - + +
165A ALA* 4.1 3.5 - - - +
166A ALA* 3.3 23.5 + - + +
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Residues in contact with ARG 163 (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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128A TRP* 3.7 23.8 - - + +
131A ASP 4.8 0.2 + - - -
132A GLY* 3.3 16.6 + - - -
133A TYR* 2.8 43.0 + - - -
149A LEU* 4.2 8.1 - - + -
150A ALA 3.8 5.9 + - - -
151A LEU* 3.9 14.8 - - + -
152A ASP 4.5 8.7 - - - +
156A GLN* 3.0 47.3 + - - +
159A LYS* 2.8 55.1 + - + +
160A THR 3.6 2.9 - - - +
162A GLU* 1.3 78.8 - - + +
164A VAL* 1.3 61.7 + - - +
166A ALA 3.4 0.2 + - - -
167A TRP* 3.0 24.6 + - - +
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Residues in contact with VAL 164 (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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17A VAL* 4.4 9.0 - - + -
20A SER* 5.0 11.9 - - - +
21A ILE* 4.2 19.7 - - + -
24A ARG* 4.6 7.6 - - - +
149A LEU* 4.0 22.7 - - + -
151A LEU* 4.2 9.4 - - + -
160A THR* 2.7 40.5 + - + +
161A ASP* 4.0 4.9 - - - +
163A ARG* 1.3 73.5 - - - +
165A ALA* 1.3 61.7 + - - +
167A TRP* 3.4 2.6 + - + +
168A LEU* 3.0 40.3 + - + +
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Residues in contact with ALA 165 (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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24A ARG* 4.1 20.1 - - - +
161A ASP 3.0 17.9 + - - +
162A GLU* 4.1 4.3 - - - +
164A VAL* 1.3 75.3 - - - +
166A ALA* 1.3 57.8 + - - +
168A LEU* 3.2 6.7 + - - +
169A ALA* 2.9 28.5 + - - +
179A LEU* 5.3 1.0 - - - +
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Residues in contact with ALA 166 (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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128A TRP* 3.8 20.5 - - + -
162A GLU* 3.3 16.3 + - + +
165A ALA* 1.3 76.2 - - - +
167A TRP* 1.3 60.0 + - - +
169A ALA* 3.3 8.1 + - - +
170A GLN* 2.8 28.2 + - - +
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Residues in contact with TRP 167 (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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21A ILE* 4.5 11.0 - - + -
51A ILE* 3.9 22.2 - - + -
92A ALA* 3.7 24.2 - - + -
93A LEU 3.1 37.0 - - - -
94A PHE* 4.0 9.6 - - + -
126A GLY* 3.0 35.3 + - - -
128A TRP* 3.9 21.0 - + + -
149A LEU* 3.5 37.7 - - + +
163A ARG 3.0 18.5 + - - +
164A VAL* 3.7 4.3 - - + +
166A ALA* 1.3 72.9 - - - +
168A LEU* 1.3 78.1 + - + +
170A GLN* 3.0 7.6 + - - +
171A ILE* 2.9 41.8 + - + +
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Residues in contact with LEU 168 (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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21A ILE* 4.0 26.0 - - + -
24A ARG* 3.5 38.6 - - + +
25A PHE* 4.1 15.3 - - + -
51A ILE* 5.1 4.0 - - + -
164A VAL* 3.0 34.2 + - + +
165A ALA* 3.5 7.2 - - - +
167A TRP* 1.3 89.5 - - + +
169A ALA* 1.3 63.9 + - - +
171A ILE* 3.3 15.8 + - + +
172A ALA* 2.9 26.0 + - - +
177A LEU* 5.0 2.4 - - + +
179A LEU* 4.1 15.7 - - + +
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Residues in contact with ALA 169 (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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165A ALA 2.9 13.9 + - - +
166A ALA* 3.4 11.7 - - - +
168A LEU* 1.3 77.1 - - - +
170A GLN* 1.3 63.1 + - - +
172A ALA* 3.7 12.2 + - - +
173A PRO* 3.9 5.0 - - - +
179A LEU* 4.1 18.4 - - + +
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Residues in contact with GLN 170 (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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126A GLY* 3.3 24.6 - - - -
127A SER* 2.9 28.7 + - - +
128A TRP* 3.7 19.5 - - - -
145A LYS* 5.4 1.9 + - - +
166A ALA 2.8 13.5 + - - +
167A TRP* 3.0 10.7 + - - +
169A ALA* 1.3 80.1 - - - +
171A ILE* 1.3 60.0 + - - +
173A PRO* 3.6 10.0 - - - +
174A GLU* 4.1 7.1 - - - +
702A SO4 3.3 18.7 + - - +
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Residues in contact with ILE 171 (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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51A ILE* 4.4 12.6 - - + -
92A ALA* 3.8 13.7 - - + -
125A VAL* 4.1 7.0 - - + +
126A GLY* 3.7 33.7 - - - +
167A TRP* 2.9 39.3 + - + +
168A LEU* 3.6 16.2 - - + +
170A GLN* 1.3 77.7 - - + +
172A ALA* 1.3 67.6 + - - +
173A PRO* 3.3 2.2 - - - -
174A GLU* 3.0 19.0 + - - +
175A PHE* 3.3 40.6 - - + -
177A LEU* 5.5 3.1 - - + -
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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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168A LEU 2.9 17.9 + - - +
169A ALA 3.8 4.9 - - - +
171A ILE* 1.3 74.6 - - - +
173A PRO* 1.3 70.5 - - + +
175A PHE 3.0 9.9 + - - -
177A LEU* 3.1 39.6 + - + +
179A LEU* 3.5 39.9 - - + +
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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