Contacts of the helix formed by residues 82 - 91 (chain D) in PDB entry 2V5Q
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 THR 82 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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52D HIS* 3.7 2.0 - - - -
73D VAL 4.5 3.8 - - - -
74D ASP* 3.6 32.7 + - + +
75D ALA 3.3 3.6 - - - +
76D ALA* 4.7 3.8 - - + -
80D GLY 3.5 3.3 + - - +
81D PHE* 1.3 78.5 - - - +
83D PRO* 1.4 76.4 - - - +
84D LEU* 3.4 11.2 + - - +
85D HIS* 2.9 41.7 + - + +
86D LEU* 3.2 11.3 + - - +
105D ASP 5.3 0.2 + - - -
108D ALA* 4.0 25.0 - - + +
109D PHE 6.2 0.2 - - - +
116D PRO* 4.7 0.3 - - - +
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Residues in contact with PRO 83 (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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49D THR* 4.6 0.7 - - - +
51D LEU* 3.8 42.4 - - + +
52D HIS* 3.7 31.6 - - + +
55D ALA* 3.6 12.0 - - + +
72D ASP 4.7 1.1 - - - +
73D VAL 3.3 19.5 - - - +
75D ALA 3.3 13.5 - - - +
82D THR* 1.4 82.2 - - - +
84D LEU* 1.3 55.0 + - - +
86D LEU* 3.2 3.5 + - + +
87D ALA* 3.0 25.3 + - - +
99D LEU* 3.6 15.0 - - + -
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Residues in contact with LEU 84 (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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73D VAL 5.2 0.8 + - - +
74D ASP* 5.9 0.7 - - - +
82D THR* 3.1 10.6 + - - +
83D PRO* 1.3 75.6 - - - +
85D HIS* 1.3 64.6 + - - +
88D ALA* 3.0 27.4 + - + +
96D VAL* 3.8 47.1 - - + +
99D LEU* 3.5 15.1 - - + +
100D LEU* 3.9 22.4 - - + -
104D ALA* 4.1 16.4 - - + -
105D ASP 3.6 22.9 - - - +
106D VAL* 4.0 4.7 - - - -
116D PRO* 3.7 17.9 - - + -
132D LEU* 4.1 7.6 - - + -
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Residues in contact with HIS 85 (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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80D GLY 3.7 9.0 - - - -
81D PHE* 3.6 21.0 - + + -
82D THR* 2.9 39.2 + - + +
84D LEU* 1.3 77.5 - - - +
86D LEU* 1.3 58.2 + - - +
88D ALA* 3.4 1.6 + - - +
89D MET* 3.0 33.2 + - - +
108D ALA* 3.0 29.0 + - + -
109D PHE 4.0 0.4 - - - -
110D ASP* 3.6 16.5 + - + -
114D SER 2.9 22.0 + - - -
116D PRO* 3.5 22.7 - - + +
119D LEU* 3.4 25.2 - - + +
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Residues in contact with LEU 86 (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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320A THR* 4.0 16.4 - - + +
48D LEU* 4.0 13.0 - - + -
52D HIS* 3.7 43.5 - - + +
56D VAL* 3.8 27.3 - - + +
81D PHE* 3.7 32.5 - - + -
82D THR 3.8 8.7 - - - +
83D PRO* 3.2 7.9 + - + +
85D HIS* 1.3 79.7 - - - +
87D ALA* 1.3 61.1 + - - +
89D MET* 3.5 16.6 - - + +
90D THR* 2.8 32.2 + - - +
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Residues in contact with ALA 87 (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 ALA* 4.2 10.5 - - + +
83D PRO 3.0 15.2 + - - +
84D LEU 4.0 1.8 - - - +
86D LEU* 1.3 74.5 - - - +
88D ALA* 1.3 61.0 + - - +
90D THR* 3.3 5.6 + - - -
91D GLY* 3.0 23.0 + - - -
92D HIS* 3.0 14.8 + - + +
95D ILE* 3.6 33.2 - - + -
96D VAL* 3.8 16.3 - - + +
99D LEU* 4.2 3.1 - - + -
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Residues in contact with ALA 88 (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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84D LEU* 3.0 19.6 + - + +
85D HIS 3.8 3.4 - - - +
87D ALA* 1.3 78.0 - - - +
89D MET* 1.3 61.2 + - - +
91D GLY* 3.4 9.4 + - - -
96D VAL* 3.8 10.9 - - + +
116D PRO* 3.6 31.2 - - + +
120D ALA* 3.5 12.0 - - + +
125D HIS* 3.4 11.3 - - - +
128D ILE* 3.8 19.9 - - + +
132D LEU* 4.4 0.9 - - + -
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Residues in contact with MET 89 (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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316A ILE* 3.9 11.9 - - + +
317A THR* 3.5 44.3 - - + +
320A THR* 5.5 0.9 - - - -
56D VAL* 5.8 0.9 - - - -
81D PHE* 3.5 22.2 - - + -
85D HIS 3.0 19.6 + - - +
86D LEU* 3.5 31.2 - - + +
88D ALA* 1.3 76.5 - - - +
90D THR* 1.3 61.5 + - + +
91D GLY 3.4 0.2 - - - -
119D LEU* 3.5 36.6 - - + -
120D ALA* 4.8 0.2 - - - +
123D GLU* 3.4 22.6 - - + +
125D HIS* 2.9 20.4 + - - -
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Residues in contact with THR 90 (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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317A THR* 3.8 20.2 - - + -
321A ILE* 4.0 13.2 - - + -
55D ALA 4.3 0.2 + - - -
56D VAL* 3.7 27.7 + - + +
86D LEU 2.8 23.1 + - - +
87D ALA* 3.3 4.7 + - - -
89D MET* 1.3 76.3 - - + +
91D GLY* 1.3 60.6 + - - +
92D HIS* 2.9 40.1 + - - -
125D HIS* 3.5 10.7 + - - -
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Residues in contact with GLY 91 (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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87D ALA 3.0 6.4 + - - -
88D ALA 3.4 6.2 + - - -
89D MET 3.4 0.8 - - - -
90D THR* 1.3 78.5 - - - +
92D HIS* 1.3 60.1 + - - +
93D LEU* 3.1 9.9 + - - +
125D HIS* 3.5 26.0 - - - -
128D ILE* 4.1 12.2 - - - +
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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