Contacts of the helix formed by residues 158 - 167 (chain A) in PDB entry 2WXL
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 GLY 158 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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156A GLN 3.5 2.2 + - - -
157A LEU* 1.3 74.1 - - - +
159A TRP* 1.3 56.6 + - - -
160A VAL 3.3 2.7 - - - -
161A GLU* 2.8 23.3 + - - -
162A TRP* 2.7 32.7 + - - +
286A ARG* 5.0 1.3 - - - -
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Residues in contact with TRP 159 (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 LEU 3.8 0.6 + - - -
158A GLY* 1.3 71.4 - - - -
160A VAL* 1.3 89.1 + - + +
162A TRP* 3.4 7.5 + - - +
163A LEU* 3.1 36.0 + - + +
237A GLU 3.2 26.5 - - - -
238A GLU* 3.9 6.0 + - - -
239A TYR 3.8 24.5 - - - -
240A ALA* 4.3 0.9 - - + -
251A TYR* 6.4 0.2 - - + -
279A SER* 3.4 29.7 + - - +
282A ILE* 3.5 40.0 - - + +
283A LEU* 3.6 36.1 - - + +
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Residues in contact with VAL 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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158A GLY 3.3 0.4 - - - -
159A TRP* 1.3 116.1 - - + +
161A GLU* 1.3 58.9 + - + +
163A LEU* 3.3 8.8 + - + +
164A GLN* 2.9 45.5 + - + +
251A TYR* 4.8 15.3 - - + -
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Residues in contact with GLU 161 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157A LEU* 3.7 26.5 - - + +
158A GLY* 2.8 31.9 + - - +
160A VAL* 1.3 74.0 - - + +
162A TRP* 1.3 65.8 + - - +
164A GLN* 3.2 20.7 + - - +
165A TYR* 3.0 21.5 + - - +
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Residues in contact with TRP 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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154A ARG* 3.9 24.2 - - + -
155A GLN* 4.3 5.6 - - - -
157A LEU* 4.0 11.3 - - + +
158A GLY 2.7 19.8 + - - +
159A TRP* 3.6 8.7 - - - +
161A GLU* 1.3 73.6 - - - +
163A LEU* 1.3 56.4 + - - +
165A TYR* 3.1 31.6 + + - +
166A SER* 2.8 51.3 + - - -
167A PHE* 4.3 8.3 - + - -
282A ILE* 3.5 27.3 + - + +
285A MET* 4.3 7.0 - - + +
286A ARG* 3.6 48.4 - - + +
289A GLN* 3.0 45.3 - - + -
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Residues in contact with LEU 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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159A TRP* 3.1 29.7 + - + +
160A VAL* 3.4 12.1 - - + +
162A TRP* 1.3 81.6 - - - +
164A GLN* 1.3 56.8 + - - +
167A PHE* 2.6 64.5 + - + +
240A ALA* 3.7 26.7 - - + -
249A TYR* 3.9 26.9 - - + -
251A TYR* 3.5 25.8 - - + -
282A ILE* 4.0 16.8 - - + -
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Residues in contact with GLN 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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160A VAL* 2.9 29.1 + - - +
161A GLU* 3.4 27.0 - - - +
163A LEU* 1.3 79.1 - - - +
165A TYR* 1.3 59.7 + - - +
168A PRO* 3.5 22.7 - - - +
169A LEU* 6.0 0.9 - - + -
251A TYR* 3.4 25.0 - - + +
639A ALA 5.3 0.2 - - - -
640A ASN* 4.7 3.6 + - - +
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Residues in contact with TYR 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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154A ARG* 3.1 43.3 + - - -
157A LEU* 4.3 11.4 - - + -
161A GLU 3.0 11.5 + - - +
162A TRP* 3.1 35.2 + + - +
164A GLN* 1.3 79.1 - - - +
166A SER* 1.3 81.1 + - - +
168A PRO* 4.1 3.3 - - - +
289A GLN* 5.1 1.2 + - - -
637A ALA 4.8 0.7 - - - -
638A LEU* 3.3 17.0 - - - -
639A ALA* 3.5 28.9 - - - +
640A ASN* 3.7 2.0 - - - +
641A ARG* 2.9 65.1 + - + +
671A TYR* 5.0 2.9 + - - -
675A SER* 4.2 12.0 + - - -
678A HIS* 5.2 0.5 - - - +
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Residues in contact with SER 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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162A TRP* 2.8 32.5 + - - -
165A TYR* 1.3 94.1 - - - +
167A PHE* 1.3 91.3 + - - +
168A PRO* 3.5 6.4 - - - +
289A GLN* 5.1 2.4 + - - -
641A ARG* 3.3 34.1 + - - +
642A LYS* 5.3 0.5 + - - +
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Residues in contact with PHE 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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162A TRP* 4.3 8.1 - - - -
163A LEU* 2.6 39.3 + - + +
166A SER* 1.3 103.0 - - - +
168A PRO* 1.3 69.5 - - - +
169A LEU* 4.3 0.5 - - - +
247A HIS* 3.5 58.1 - + + +
248A GLU* 4.8 0.4 - - - -
249A TYR* 3.7 37.0 + + + +
251A TYR* 2.9 19.6 + - - -
282A ILE* 6.0 0.2 - - + -
285A MET* 3.8 33.0 - - + -
289A GLN* 5.9 0.4 - - - -
641A ARG* 4.4 4.0 - - - -
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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