Contacts of the helix formed by residues 132 - 140 (chain X) in PDB entry 2W6C
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 132 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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100X TRP* 3.5 31.6 - - - -
130X TYR 3.2 4.8 + - - -
131X ASN* 1.3 74.7 + - - +
133X LYS* 1.3 59.4 + - - +
134X TYR 3.3 0.6 + - - -
135X LEU* 3.3 4.3 + - - +
136X ALA* 2.8 31.0 + - - +
143X LEU* 3.6 18.8 - - - +
448X PHE* 4.5 3.8 - - - -
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Residues in contact with LYS 133 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20X VAL* 4.3 11.2 - - + +
21X PRO* 2.9 34.2 + - - +
22X VAL* 3.4 18.6 - - + +
27X ILE* 3.8 17.5 - - + +
100X TRP* 3.7 14.8 - - + +
131X ASN* 3.2 32.7 + - - +
132X GLY* 1.3 76.8 - - - +
134X TYR* 1.3 92.9 + - + +
137X TYR* 2.9 33.8 + - - +
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Residues in contact with TYR 134 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22X VAL* 4.2 13.2 - - + -
23X LEU* 4.4 21.5 - - + -
131X ASN* 4.0 23.7 + - + -
132X GLY 3.3 0.8 - - - -
133X LYS* 1.3 107.1 + - + +
135X LEU* 1.3 59.3 + - - +
137X TYR* 4.6 1.1 - - - -
138X THR* 2.9 37.3 + - - +
448X PHE 3.3 22.9 - - - +
449X GLY* 4.1 14.6 - - - +
450X LEU* 4.2 21.4 - - + +
452X LEU* 5.4 2.9 - - + -
453X VAL* 3.1 36.8 - - + +
470X MET* 4.4 2.9 - - - +
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Residues in contact with LEU 135 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112X MET* 4.6 11.7 - - + -
132X GLY* 3.3 9.4 + - - +
134X TYR* 1.3 76.4 - - - +
136X ALA* 1.3 70.8 + - - +
139X GLU* 3.0 34.4 + - + +
140X GLU 3.9 0.2 + - - -
141X VAL* 4.1 9.2 - - + +
143X LEU* 3.8 26.2 - - + -
197X PHE* 4.4 16.6 - - + -
447X VAL* 3.8 16.6 - - + +
448X PHE* 4.2 12.5 + - + +
470X MET* 3.3 44.4 - - + +
473X TRP* 5.8 2.0 - - + -
474X ALA* 5.2 2.5 - - + -
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Residues in contact with ALA 136 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27X ILE* 4.1 7.9 - - + -
100X TRP* 3.8 26.7 - - + +
102X PRO* 4.1 6.9 - - + +
132X GLY 2.8 23.3 + - - +
133X LYS 3.9 2.5 - - - +
135X LEU* 1.3 71.8 - - - +
137X TYR* 1.3 55.1 + - - +
140X GLU* 2.6 38.1 + - - -
141X VAL* 3.2 26.8 + - - +
143X LEU* 4.3 4.2 - - + +
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Residues in contact with TYR 137 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22X VAL* 4.0 15.5 - - + -
23X LEU* 4.4 30.0 + - + -
25X SER* 3.7 33.6 - - - -
26X HIS 4.9 0.9 - - - -
27X ILE* 4.0 26.4 - - + +
102X PRO* 5.7 2.7 - - - -
133X LYS 2.9 18.8 + - - +
134X TYR* 4.0 1.3 - - - +
136X ALA* 1.3 79.4 - - - +
138X THR* 1.3 73.6 - - - +
140X GLU* 3.7 9.4 + - - +
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Residues in contact with THR 138 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23X LEU* 4.5 2.8 - - - +
134X TYR 2.9 20.7 + - - -
135X LEU 4.3 0.2 - - - -
137X TYR* 1.3 89.3 - - - +
139X GLU* 1.3 77.4 + - - +
140X GLU* 5.0 2.1 - - - +
452X LEU* 4.0 17.5 - - - +
467X ARG* 4.0 23.9 + - + +
470X MET* 4.3 16.8 - - + +
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Residues in contact with GLU 139 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135X LEU* 3.0 22.7 + - + +
138X THR* 1.3 94.1 - - + +
140X GLU* 1.3 74.2 + - - +
141X VAL* 3.4 9.9 + - + +
467X ARG* 4.6 1.6 - - - +
470X MET* 3.2 23.8 - - + +
471X HIS* 2.6 54.9 + - - +
474X ALA* 3.3 20.6 - - + +
475X THR* 4.8 0.2 + - - -
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Residues in contact with GLU 140 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102X PRO* 4.0 19.0 - - + +
106X PRO* 5.4 2.2 - - + +
109X THR* 3.0 24.0 + - - +
136X ALA 2.6 21.1 + - - -
137X TYR 3.7 7.0 + - - +
138X THR 3.4 4.4 - - - +
139X GLU* 1.3 78.9 - - - +
141X VAL* 1.3 57.2 + - - +
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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