Contacts of the helix formed by residues 159 - 168 (chain A) in PDB entry 1YYH
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 SER 159 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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129A ILE* 4.0 2.7 - - - -
150A VAL 4.7 7.6 - - - -
151A ASN* 5.2 0.9 - - - -
152A ALA 3.4 17.0 - - - -
153A VAL* 3.7 0.2 - - - +
157A GLY 3.7 2.0 + - - -
158A LYS* 1.3 75.7 - - - +
160A ALA* 1.3 65.3 + - - +
161A LEU* 3.4 11.0 + - - +
162A HIS* 2.9 40.0 + - - -
163A TRP* 3.1 13.7 + - - -
181A ALA* 6.5 0.2 - - - -
182A ASN 5.3 1.2 + - - -
185A MET* 3.8 26.2 - - - +
193A PRO* 4.7 1.0 - - - +
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Residues in contact with ALA 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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128A LEU* 3.8 41.3 - - + +
129A ILE* 3.6 20.7 - - + +
132A ALA* 3.6 8.1 - - + +
150A VAL 4.6 4.1 + - - +
152A ALA 4.2 2.8 + - - -
159A SER* 1.3 73.4 - - - +
161A LEU* 1.3 56.4 + - - +
163A TRP* 3.3 2.0 + - - +
164A ALA* 2.8 28.4 + - - +
176A LEU* 3.6 20.2 - - + -
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Residues in contact with LEU 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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150A VAL 5.4 0.8 + - - +
159A SER* 3.1 10.1 + - - +
160A ALA* 1.3 76.1 - - - +
162A HIS* 1.3 64.5 + - - +
164A ALA* 3.3 0.8 + - - -
165A ALA* 2.9 24.1 + - - +
173A ALA* 3.7 41.7 - - + +
176A LEU* 3.6 13.0 - - + +
177A LEU* 3.8 20.0 - - + -
181A ALA* 4.1 16.8 - - + +
182A ASN 3.9 7.9 - - - +
183A LYS* 3.8 29.6 - - - -
193A PRO* 3.9 14.4 - - + -
209A LEU* 4.1 11.4 - - + -
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Residues in contact with HIS 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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157A GLY 4.0 15.3 - - - -
158A LYS* 3.8 10.8 - - + -
159A SER* 2.9 42.0 + - - +
161A LEU* 1.3 75.1 - - - +
163A TRP* 1.3 58.4 + - - +
165A ALA* 3.3 4.3 + - - +
166A ALA* 2.9 27.7 + - - +
185A MET* 3.0 36.3 + - + -
187A ASN* 3.7 9.4 + - - -
191A GLU 2.8 28.6 + - - -
193A PRO* 3.6 24.2 - - + +
196A LEU* 3.7 28.1 - - + +
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Residues in contact with TRP 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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129A ILE* 3.3 25.3 - - + +
132A ALA* 4.7 2.2 - - + -
133A ARG* 3.4 64.8 - - + -
154A ASP* 2.9 25.0 + - - -
156A LEU* 6.5 1.3 - - + -
158A LYS* 3.4 41.6 - - + +
159A SER 3.1 18.1 + - - -
160A ALA* 3.7 7.0 - - - +
162A HIS* 1.3 77.2 - - - +
164A ALA* 1.3 65.6 + - - +
166A ALA* 3.1 19.3 + - + +
167A VAL* 3.0 38.5 + - + +
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Residues in contact with ALA 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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132A ALA* 4.3 5.2 - - + +
160A ALA 2.8 20.0 + - - +
161A LEU 3.3 4.5 + - - +
163A TRP* 1.3 70.4 - - - +
165A ALA* 1.3 58.9 + - - +
167A VAL* 4.2 1.1 - - - -
168A ASN* 2.9 9.7 + - - -
169A ASN* 2.8 51.9 + - - +
172A ALA* 4.1 10.5 - - + -
173A ALA* 3.8 21.5 - - + +
176A LEU* 4.3 4.0 - - + -
205A THR* 4.0 3.6 + - - -
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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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161A LEU* 2.9 17.5 + - + +
162A HIS 3.6 4.7 - - - +
164A ALA* 1.3 76.6 - - - +
166A ALA* 1.3 51.6 + - - +
168A ASN 3.3 1.7 + - - -
193A PRO* 3.1 35.2 - - + +
197A ALA* 3.7 13.6 - - + +
202A SER* 2.8 36.7 + - - -
205A THR* 3.7 11.8 - - + +
209A LEU* 4.1 8.5 - - + -
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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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158A LYS* 6.1 1.8 - - + +
162A HIS 2.9 20.0 + - - +
163A TRP* 3.1 24.8 + - + +
165A ALA* 1.3 71.3 - - - +
167A VAL* 1.3 61.1 + - + +
196A LEU* 4.4 16.9 - - + +
200A GLU* 3.4 39.0 - - + +
202A SER* 3.4 4.0 + - - -
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Residues in contact with VAL 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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132A ALA 3.7 22.0 - - - +
133A ARG* 4.0 19.7 - - + +
135A ALA* 5.9 1.8 - - + -
163A TRP* 3.0 37.7 + - + +
166A ALA* 1.3 77.8 - - + +
168A ASN* 1.3 69.5 + - - +
169A ASN* 3.4 13.6 + - + -
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Residues in contact with ASN 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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164A ALA 2.9 7.2 + - - -
165A ALA 3.3 5.9 + - - -
166A ALA 3.4 0.6 - - - -
167A VAL* 1.3 80.8 - - - +
169A ASN* 1.3 60.0 + - - +
170A VAL* 3.0 12.2 + - - +
201A GLY 5.3 0.6 + - - -
202A SER* 3.5 25.9 - - - +
203A TYR 4.5 0.2 - - - +
204A GLU* 2.8 30.1 + - - +
205A THR* 3.0 35.2 + - - -
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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