Contacts of the helix formed by residues 141 - 149 (chain D) in PDB entry 2QW4
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 ARG 141 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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60D VAL 5.6 0.8 + - - -
62D PRO* 6.1 0.6 - - - +
129D GLY* 2.8 27.3 + - - +
131D LEU* 3.7 12.3 - - - +
139D LEU 3.7 0.4 + - - -
140D HIS* 1.3 82.0 + - + +
142D LEU* 1.3 94.4 + - + +
144D CYS* 3.5 5.0 - - - +
145D ALA* 3.4 16.8 + - - +
152D ILE* 4.0 6.7 - - + +
153D ASP* 2.8 37.7 + - - +
156D LEU* 3.5 25.3 - - + +
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Residues in contact with LEU 142 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59D LEU* 3.7 33.9 - - + +
60D VAL 3.6 24.0 - - - +
61D LEU 3.6 17.5 - - - +
62D PRO* 3.8 27.8 - - + -
63D HIS* 4.0 12.5 + - - -
140D HIS* 3.1 14.3 - - + +
141D ARG* 1.3 112.9 - - - +
143D GLN* 1.3 62.0 + - - +
144D CYS 3.2 1.8 - - - -
145D ALA* 3.9 19.0 - - + +
146D ARG* 4.6 2.3 + - - +
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Residues in contact with GLN 143 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55D LYS 2.9 26.8 + - - -
56D PHE* 4.0 1.6 - - - -
57D GLN* 2.7 47.6 + - + +
59D LEU* 3.9 15.5 - - + -
63D HIS* 4.8 10.5 - - + -
71D ASP* 5.5 0.2 - - - +
74D GLN* 5.1 5.9 - - - +
139D LEU* 4.0 13.6 - - + +
140D HIS* 2.9 30.5 + - + +
142D LEU* 1.3 79.2 - - - +
144D CYS* 1.3 61.6 + - - +
145D ALA 3.5 0.2 - - - -
146D ARG* 3.9 17.9 + - - +
147D GLY 4.6 0.9 + - - -
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Residues in contact with CYS 144 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131D LEU* 3.8 15.3 - - - -
133D PHE* 4.0 13.5 - - - -
139D LEU* 3.6 33.0 - - - -
140D HIS 3.3 14.6 - - - -
141D ARG 3.5 9.6 - - - +
143D GLN* 1.3 75.8 - - - +
145D ALA* 1.3 57.7 + - - +
146D ARG 3.2 1.8 - - - -
147D GLY 3.0 4.0 + - - +
148D PHE* 2.8 42.1 + - + +
152D ILE* 3.9 21.1 - - + -
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Residues in contact with ALA 145 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62D PRO* 5.7 5.8 - - + -
63D HIS 6.2 0.7 - - - +
141D ARG 3.4 10.2 + - - +
142D LEU* 3.9 22.4 - - + +
144D CYS* 1.3 76.0 - - - +
146D ARG* 1.3 64.8 + - + +
149D GLY* 2.9 31.6 + - - +
152D ILE* 4.0 9.5 - - + +
241D ARG* 4.4 0.5 + - - -
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Residues in contact with ARG 146 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63D HIS* 3.6 41.8 - - + +
64D PHE* 3.0 27.7 + - - -
65D GLY 4.5 1.2 + - - -
66D LYS 3.3 22.6 + - - -
67D GLU* 3.1 31.2 - - + +
68D ASP* 4.5 6.1 + - - +
71D ASP* 3.0 44.6 + - + +
142D LEU 4.9 2.0 - - - +
143D GLN 3.9 14.4 + - - +
144D CYS 3.2 1.0 - - - -
145D ALA* 1.3 77.7 - - + +
147D GLY* 1.3 55.8 + - - +
241D ARG* 3.3 4.7 + - - -
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Residues in contact with GLY 147 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67D GLU* 5.3 0.7 - - - -
71D ASP* 4.3 20.8 - - - +
72D VAL* 5.6 0.7 - - - -
75D PHE* 3.8 18.4 - - - -
143D GLN 4.6 0.6 + - - -
144D CYS* 3.0 6.5 + - - -
146D ARG* 1.3 81.0 - - - +
148D PHE* 1.3 66.5 + - - +
149D GLY 3.5 0.4 - - - -
241D ARG* 3.0 20.8 + - - +
245D LEU* 4.3 5.2 - - - +
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Residues in contact with PHE 148 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75D PHE* 3.7 32.5 - + - -
78D LEU* 4.0 19.7 - - + -
79D LEU* 5.6 0.2 - - + -
116D PHE* 4.0 26.2 - + - -
120D LEU* 5.5 0.2 - - + -
133D PHE* 3.5 29.2 - + - -
139D LEU* 5.7 0.9 - - + -
144D CYS* 2.8 30.8 + - + +
147D GLY* 1.3 77.6 - - - -
149D GLY* 1.3 68.9 + - - +
151D TRP* 3.6 26.5 + + + +
152D ILE* 3.7 31.9 - - + +
155D ILE* 4.9 2.0 - - + -
241D ARG* 3.0 31.2 - - - +
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Residues in contact with GLY 149 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145D ALA* 2.9 26.2 + - - -
147D GLY 3.5 0.8 - - - -
148D PHE* 1.3 75.3 - - - +
150D ASP* 1.3 55.0 + - - -
151D TRP 2.8 17.3 + - - -
152D ILE* 3.1 22.5 + - - +
241D ARG* 3.7 15.8 - - - -
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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