Contacts of the helix formed by residues 59 - 69 (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 HIS 59 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22D ALA 3.3 24.0 - - - -
23D ARG 2.9 19.5 + - - -
24D ALA 3.8 5.1 - - - -
25D GLY* 3.3 21.4 + - - -
54D ALA* 2.9 12.5 + - + +
57D SER* 3.4 31.2 - - - -
58D GLY* 1.3 75.8 + - - +
60D LEU* 1.3 63.3 + - - +
61D GLU 3.5 2.2 - - - -
62D ILE* 3.2 29.2 + - + +
63D VAL* 3.2 17.6 + - - +
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Residues in contact with LEU 60 (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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58D GLY 3.2 7.5 + - - +
59D HIS* 1.3 72.9 - - - +
61D GLU* 1.3 64.2 + - - +
62D ILE 3.1 0.7 + - - -
63D VAL* 3.2 12.2 + - - +
64D GLU* 3.2 13.9 + - + +
94D GLU* 3.7 43.5 - - + -
95D ILE* 3.8 17.5 - - + +
98D VAL* 3.7 29.6 - - + -
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Residues in contact with GLU 61 (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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27D ASP* 3.5 27.3 - - + +
31D ARG* 3.3 32.2 + - - +
59D HIS 3.5 0.8 - - - -
60D LEU* 1.3 79.4 - - - +
62D ILE* 1.4 60.4 + - + +
64D GLU* 3.7 7.1 + - - +
65D VAL* 3.1 29.3 + - + +
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Residues in contact with ILE 62 (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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21D ALA 4.1 0.2 - - - +
22D ALA* 4.1 15.0 - - + +
25D GLY* 3.5 41.3 - - - +
26D GLN 3.8 3.1 - - - +
27D ASP* 4.2 19.7 - - + +
30D VAL* 4.1 22.0 - - + -
54D ALA* 3.5 20.2 - - + -
59D HIS* 3.2 17.9 + - + +
60D LEU 3.1 1.0 - - - -
61D GLU* 1.4 77.2 - - + +
63D VAL* 1.3 61.3 + - - +
64D GLU 3.2 0.2 - - - -
65D VAL* 3.3 5.9 + - - +
66D LEU* 2.8 43.3 + - + +
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Residues in contact with VAL 63 (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* 3.7 16.8 - - + +
54D ALA* 3.8 16.2 - - + -
55D ALA* 3.9 19.7 - - + +
59D HIS 3.2 15.6 + - - +
60D LEU* 3.4 8.5 - - - +
62D ILE* 1.3 77.2 - - - +
64D GLU* 1.3 57.5 + - - +
66D LEU* 3.2 3.8 + - - +
67D LEU* 2.9 37.7 + - + +
95D ILE* 4.1 18.8 - - + -
98D VAL* 3.5 23.8 - - + -
99D LEU* 4.0 11.2 - - + -
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Residues in contact with GLU 64 (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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60D LEU* 3.2 11.2 + - + +
61D GLU* 3.7 11.2 - - - +
63D VAL* 1.3 76.6 - - - +
65D VAL* 1.3 59.6 + - + +
67D LEU* 3.4 3.7 + - - +
68D LYS* 2.9 51.1 + - + +
98D VAL* 3.3 30.6 - - + +
101D LYS* 4.6 7.2 + - - -
102D TYR* 3.1 32.5 + - - -
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Residues in contact with VAL 65 (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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27D ASP 6.0 0.4 - - - +
30D VAL* 3.8 16.6 - - + -
31D ARG* 4.0 41.7 - - + +
34D ILE* 3.6 24.5 - - + -
61D GLU* 3.1 23.5 + - + +
62D ILE* 3.6 5.8 - - - +
64D GLU* 1.3 78.7 - - + +
66D LEU* 1.3 64.0 + - - +
68D LYS* 3.5 4.6 + - + +
69D HIS* 2.7 42.1 + - + +
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Residues in contact with LEU 66 (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* 4.5 8.7 - - + -
30D VAL* 4.8 0.9 - - + -
34D ILE* 4.0 22.2 - - + -
40D VAL* 4.2 19.8 - - + +
50D PRO* 3.7 26.0 - - + +
51D LEU* 3.6 33.9 - - + +
54D ALA* 4.4 0.9 - - + -
62D ILE* 2.8 43.9 + - + +
63D VAL 3.6 3.4 - - - +
65D VAL* 1.3 73.6 - - + +
67D LEU* 1.3 63.2 + - - +
69D HIS* 3.0 14.8 + - - +
70D GLY 3.2 0.7 + - - -
71D ALA* 3.1 28.3 + - + +
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Residues in contact with LEU 67 (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* 3.8 19.3 - - + -
63D VAL* 2.9 22.8 + - + +
64D GLU 3.9 3.1 - - - +
66D LEU* 1.3 76.1 - - - +
68D LYS* 1.3 57.2 + - - +
70D GLY* 2.9 20.8 + - - -
71D ALA 3.9 11.1 + - - +
73D VAL* 3.7 32.8 - - + -
98D VAL* 3.5 32.8 - - + +
99D LEU* 4.0 9.0 - - + -
102D TYR* 3.7 42.3 - - + -
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Residues in contact with LYS 68 (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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64D GLU* 2.9 40.2 + - + +
65D VAL* 3.8 6.3 - - + +
67D LEU* 1.3 72.0 - - - +
69D HIS* 1.3 66.3 + - + +
70D GLY 3.2 1.8 + - - -
102D TYR* 3.6 26.7 - - + +
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Residues in contact with HIS 69 (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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31D ARG* 5.9 4.7 - - + -
34D ILE* 3.6 33.5 - - + +
40D VAL* 3.7 20.3 - - + +
65D VAL* 2.7 43.7 + - + +
66D LEU 3.0 8.6 + - - +
68D LYS* 1.3 82.4 - - + +
70D GLY* 1.3 59.3 + - - +
71D ALA 3.5 0.2 - - - -
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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