Contacts of the helix formed by residues 157 - 169 (chain B) in PDB entry 6W6Y
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 ASP 157 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20B ASN* 3.7 0.9 - - - -
155B VAL* 3.4 5.1 - - - +
156B PHE* 1.3 81.8 - - + +
158B LYS* 1.3 60.0 + - - +
159B ASN* 2.9 30.2 + - - +
160B LEU* 3.2 28.0 + - + +
161B TYR* 2.9 26.3 + - - +
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Residues in contact with LYS 158 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20B ASN* 3.4 36.5 - - - +
156B PHE 3.5 1.8 + - - +
157B ASP* 1.3 74.2 + - - +
159B ASN* 1.3 60.7 + - - +
161B TYR* 3.3 17.2 + - + -
162B ASP* 2.9 58.8 + - - +
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Residues in contact with ASN 159 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157B ASP* 2.9 22.6 + - - +
158B LYS* 1.3 80.0 - - - +
160B LEU* 1.3 62.1 + - - +
162B ASP* 3.4 7.0 + - - +
163B LYS* 3.1 24.2 + - - +
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Residues in contact with LEU 160 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126B LEU* 4.9 4.5 - - + -
129B ALA* 5.6 5.4 - - + +
136B PRO* 3.7 40.6 - - + -
137B ILE* 5.4 0.4 - - + -
155B VAL* 4.1 13.5 - - + -
157B ASP* 3.2 25.9 + - + +
159B ASN* 1.3 74.2 - - - +
161B TYR* 1.3 68.0 + - - +
163B LYS* 3.1 27.6 + - + +
164B LEU* 2.9 39.0 + - + +
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Residues in contact with TYR 161 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A LEU* 4.2 9.5 - - - +
10B LEU* 3.5 28.8 - - + +
18B ILE* 3.8 24.5 + - + -
19B LYS* 3.7 10.6 - - - -
20B ASN* 3.5 37.9 - - + -
155B VAL* 3.8 12.9 - - + +
157B ASP 2.9 12.9 + - - +
158B LYS* 3.5 26.7 - - + +
160B LEU* 1.3 78.9 - - - +
162B ASP* 1.3 74.3 + - - +
164B LEU* 3.2 6.1 + - - +
165B VAL* 2.9 55.4 + - + +
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Residues in contact with ASP 162 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158B LYS* 2.9 54.8 + - - +
159B ASN* 3.8 6.0 - - - +
160B LEU 3.2 0.2 - - - -
161B TYR* 1.3 85.3 - - - +
163B LYS* 1.3 56.8 + - - +
165B VAL* 3.5 4.5 + - - +
166B SER* 2.9 31.8 + - - -
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Residues in contact with LYS 163 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135B ASP* 5.6 1.0 + - - -
136B PRO* 4.9 8.9 - - - +
137B ILE* 3.7 27.0 - - + +
159B ASN 3.1 15.9 + - - +
160B LEU* 3.1 27.2 + - + +
162B ASP* 1.3 74.7 - - - +
164B LEU* 1.3 58.4 + - - +
166B SER* 3.6 5.5 - - - -
167B SER* 2.9 34.4 + - - +
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Residues in contact with LEU 164 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18B ILE* 3.9 20.6 - - + -
126B LEU* 3.7 22.0 - - + -
136B PRO* 3.7 15.9 - - + +
137B ILE* 3.6 35.8 - - + +
140B LEU* 4.0 23.8 - - + +
155B VAL* 4.0 9.2 - - + -
160B LEU* 2.9 34.1 + - + +
161B TYR* 3.5 6.3 - - - +
163B LYS* 1.3 75.2 - - - +
165B VAL* 1.3 63.4 + - - +
167B SER* 3.3 7.7 + - - -
168B PHE* 3.1 24.9 + - - +
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Residues in contact with VAL 165 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10B LEU* 3.8 22.0 - - + -
12B LEU* 5.1 2.2 - - + -
18B ILE* 4.3 12.3 - - + -
161B TYR* 2.9 53.1 + - + +
162B ASP* 4.0 6.1 - - - +
164B LEU* 1.3 78.6 - - + +
166B SER* 1.3 60.4 + - - +
168B PHE* 3.3 5.4 + - - +
169B LEU* 3.0 55.9 + - + +
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Residues in contact with SER 166 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162B ASP 2.9 20.7 + - - -
163B LYS* 3.6 6.3 - - - -
165B VAL* 1.3 73.5 - - - +
167B SER* 1.3 65.3 - - - +
169B LEU* 3.1 25.5 + - - +
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Residues in contact with SER 167 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137B ILE* 3.1 44.6 - - - +
141B ARG* 3.2 16.6 + - - -
163B LYS* 2.9 16.4 + - - +
164B LEU 3.3 5.4 + - - -
166B SER* 1.3 76.8 - - - +
168B PHE* 1.3 60.2 + - - +
169B LEU 4.7 1.4 - - - +
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Residues in contact with PHE 168 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12B LEU* 3.7 47.8 - - + -
13B THR* 4.4 3.6 - - + -
137B ILE* 5.9 1.6 - - + -
140B LEU* 3.9 24.9 - - + -
141B ARG* 3.3 41.2 + - + +
144B VAL* 3.7 39.3 - - + -
164B LEU 3.1 13.6 + - - +
165B VAL 3.6 5.2 - - - +
166B SER 3.1 0.2 - - - -
167B SER* 1.3 80.1 - - - +
169B LEU* 1.3 65.1 + - + +
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Residues in contact with LEU 169 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7A SER* 4.2 15.9 - - - +
8A GLY* 3.8 36.6 - - - +
19A LYS* 5.6 4.9 - - - +
10B LEU* 4.8 1.6 - - + -
11B LYS 6.0 0.2 - - - +
12B LEU* 5.1 8.7 - - + +
165B VAL* 3.0 45.2 + - + +
166B SER* 3.1 15.2 + - - +
167B SER 4.7 1.2 - - - +
168B PHE* 1.3 90.8 - - + +
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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