Contacts of the helix formed by residues 49 - 58 (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 49 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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19D LEU* 3.6 4.5 - - - -
40D VAL 4.7 3.8 - - - -
41D ASN* 4.5 9.0 - - + +
42D ALA 3.3 11.4 - - - +
43D VAL* 3.7 17.9 - - + -
47D GLY 4.3 0.7 - - - +
48D LEU* 1.3 74.2 - - - +
50D PRO* 1.4 76.5 - - - +
51D LEU* 3.5 10.4 + - - +
52D HIS* 2.8 44.4 + - + +
53D LEU* 3.1 13.0 + - - +
72D ASP 5.1 1.3 + - - +
75D ALA* 4.0 21.5 - - + +
83D PRO* 4.6 0.9 - - - +
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Residues in contact with PRO 50 (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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18D LEU* 3.8 23.6 - - + -
19D LEU* 3.5 18.6 - - + +
22D ALA* 3.6 20.4 - - + +
39D ASP 4.5 1.8 - - - +
40D VAL 3.3 22.2 - - - +
42D ALA* 3.3 16.4 - - + +
49D THR* 1.4 82.6 - - - +
51D LEU* 1.3 55.0 + - - +
53D LEU* 3.1 3.9 + - + -
54D ALA* 2.8 31.7 + - - +
66D LEU* 3.7 25.4 - - + -
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Residues in contact with LEU 51 (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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40D VAL 5.1 0.6 + - - -
49D THR* 3.1 9.6 + - - +
50D PRO* 1.3 76.6 - - - +
52D HIS* 1.3 55.9 + - - +
54D ALA* 4.0 1.1 - - - +
55D ALA* 2.8 36.4 + - - +
63D VAL* 3.7 42.7 - - + +
66D LEU* 3.6 19.8 - - + +
67D LEU* 3.8 16.2 - - + -
71D ALA* 4.2 10.5 - - + -
72D ASP 3.4 25.8 - - - +
73D VAL* 3.8 15.5 - - - -
83D PRO* 3.8 17.3 - - + -
99D LEU* 4.2 5.8 - - + -
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Residues in contact with HIS 52 (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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47D GLY 3.9 15.0 - - - -
48D LEU* 3.6 24.7 - - + -
49D THR* 2.8 37.7 + - + +
51D LEU* 1.3 76.2 - - - +
53D LEU* 1.3 54.2 + - - +
55D ALA* 3.2 2.4 + - - +
56D VAL* 2.8 37.5 + - - +
75D ALA* 3.0 32.0 + - + -
76D ALA 4.2 0.2 - - - -
77D ASP* 3.8 3.8 + - + -
81D PHE 2.7 28.9 + - - -
83D PRO* 3.7 22.1 - - + +
86D LEU* 3.7 23.0 - - + +
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Residues in contact with LEU 53 (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* 5.4 1.3 - - + -
19D LEU* 3.4 50.5 - - + +
22D ALA 4.2 3.6 - - - +
23D ARG* 3.4 58.1 - - + +
44D ASP* 5.1 2.5 - - + +
48D LEU* 3.9 28.5 - - + -
49D THR 3.1 8.2 + - - +
50D PRO* 3.1 5.8 + - + +
52D HIS* 1.3 77.2 - - - +
54D ALA* 1.3 61.7 + - - +
56D VAL* 3.7 10.0 - - + +
57D SER* 2.5 33.6 + - - -
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Residues in contact with ALA 54 (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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22D ALA 3.8 10.7 + - - +
50D PRO 2.8 16.3 + - - +
51D LEU 4.0 1.3 - - - +
53D LEU* 1.3 75.9 - - - +
55D ALA* 1.3 64.4 + - - +
57D SER 3.3 0.9 + - - -
58D GLY 3.1 4.3 + - - -
59D HIS* 2.9 32.0 + - + +
62D ILE* 3.5 31.4 - - + -
63D VAL* 3.8 16.8 - - + +
66D LEU* 4.4 2.7 - - + -
95D ILE* 4.0 0.2 - - - +
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Residues in contact with ALA 55 (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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51D LEU 2.8 19.8 + - - +
52D HIS 3.6 2.9 - - - +
54D ALA* 1.3 76.5 - - - +
56D VAL* 1.3 63.2 + - - +
58D GLY 3.0 12.0 + - - -
63D VAL* 3.9 4.2 - - + +
83D PRO* 3.6 31.0 - - + +
86D LEU* 4.9 0.4 - - + -
87D ALA* 4.2 6.4 - - + +
92D HIS* 3.5 12.1 - - - -
95D ILE* 3.6 30.3 - - + +
99D LEU* 4.4 1.3 - - + -
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Residues in contact with VAL 56 (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* 5.7 0.7 - - - +
320A THR* 4.0 28.9 - - + -
321A ILE* 4.0 30.5 - - + +
23D ARG* 6.0 1.1 - - - +
52D HIS 2.8 18.7 + - - +
53D LEU* 3.7 13.7 - - + +
55D ALA* 1.3 73.1 - - - +
57D SER* 1.3 73.4 + - - +
58D GLY 3.4 0.2 - - - -
86D LEU* 3.8 30.7 - - + +
89D MET* 5.5 1.6 - - + -
90D THR* 3.7 30.3 - - + +
92D HIS* 3.9 5.5 + - - -
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Residues in contact with SER 57 (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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321A ILE* 5.0 5.8 - - - +
23D ARG* 3.9 14.6 + - - +
53D LEU* 2.5 23.6 + - - -
54D ALA 3.3 0.8 + - - -
55D ALA 3.0 1.0 - - - -
56D VAL* 1.3 86.8 - - - +
58D GLY* 1.3 61.0 + - - +
59D HIS* 3.4 34.1 + - - -
92D HIS* 3.9 6.7 + - - -
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Residues in contact with GLY 58 (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 3.0 6.9 + - - -
56D VAL 3.4 0.8 - - - -
57D SER* 1.3 79.9 - - - +
59D HIS* 1.3 61.1 + - - +
60D LEU* 3.2 8.9 + - - +
92D HIS* 3.5 24.6 + - - -
95D ILE* 3.4 18.8 - - - +
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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