Contacts of the helix formed by residues 51 - 62 (chain D) in PDB entry 2IBS
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 51 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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45D GLU* 3.3 15.0 - - - -
48D CYS* 2.8 11.1 + - - -
49D ALA 3.2 2.0 + - - -
50D HIS* 1.3 77.9 - - - +
52D PRO* 1.4 68.1 - - - +
53D PHE 3.3 2.7 - - - -
54D LEU* 3.6 3.9 + - - +
55D ARG* 3.1 29.1 + - - +
79D LEU* 3.7 16.3 - - - +
80D PRO* 5.4 0.7 - - - +
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Residues in contact with PRO 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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23D THR* 5.7 5.4 - - - +
28D VAL* 4.3 12.1 - - + +
45D GLU* 3.4 14.1 - - - +
48D CYS 3.5 6.5 - - - +
50D HIS* 3.8 31.8 - - + +
51D GLY* 1.4 89.7 - - - +
53D PHE* 1.3 70.1 + - + +
54D LEU 3.5 0.2 - - - -
55D ARG* 3.9 7.9 - - - +
56D ALA* 3.1 29.6 + - - +
1002D NEA 6.2 2.0 - - - +
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Residues in contact with PHE 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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23D THR* 3.8 22.4 - - + -
28D VAL* 3.9 32.3 - - + -
31D MET* 3.6 46.9 - - + -
32D VAL* 4.7 2.9 - - + +
45D GLU* 3.2 25.8 + - + +
52D PRO* 1.3 85.9 - - + +
54D LEU* 1.3 59.4 + - - +
56D ALA* 4.1 2.5 - - - +
57D PHE* 3.0 31.2 + - - +
103D LEU* 3.8 32.7 - - + +
104D GLY* 3.7 14.6 - - - -
105D ASN* 3.7 17.3 - - + -
1002D NEA 5.9 0.9 - - - -
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Residues in contact with LEU 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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43D VAL* 4.1 16.8 - - + +
44D LEU 4.3 0.2 - - - -
45D GLU* 3.2 27.4 + - + +
48D CYS* 5.0 0.2 - - + -
51D GLY 3.9 4.0 - - - +
52D PRO 3.5 0.4 - - - -
53D PHE* 1.3 73.3 - - - +
55D ARG* 1.3 64.5 + - + +
57D PHE* 4.6 1.8 - - - -
58D ARG* 3.1 24.9 + - - +
67D PHE* 3.9 25.9 - - + -
68D VAL 3.5 36.3 - - - +
69D GLY* 4.1 3.6 - - - +
79D LEU* 3.9 28.5 - - + -
80D PRO* 5.9 0.9 - - + -
82D TRP* 3.6 14.1 - - + -
83D ALA* 4.4 12.3 - - + -
103D LEU* 4.7 1.6 - - + -
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Residues in contact with ARG 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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50D HIS* 2.9 40.5 + - - +
51D GLY 3.1 13.3 + - - +
52D PRO* 3.9 8.1 - - + +
54D LEU* 1.3 76.5 - - - +
56D ALA* 1.3 57.3 + - - +
58D ARG* 3.2 4.0 + - - +
59D GLU* 3.0 38.6 + - + +
78D ASP* 3.2 17.4 + - - -
80D PRO* 3.5 38.9 - - + +
82D TRP* 4.0 11.2 - - + -
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Residues in contact with ALA 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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28D VAL* 3.8 24.0 - - + -
29D ASP* 5.4 4.9 - - - +
32D VAL* 3.9 12.2 - - + +
52D PRO 3.1 17.1 + - - +
53D PHE 4.1 1.3 - - - +
55D ARG* 1.3 76.1 - - - +
57D PHE* 1.3 64.9 + - - +
59D GLU* 3.4 9.2 + - - +
60D ALA* 3.2 24.4 + - - +
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Residues in contact with PHE 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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32D VAL* 4.0 9.5 - - + +
35D ALA* 3.9 19.7 - - + -
37D ALA* 4.1 16.4 - - + -
43D VAL* 4.0 15.3 - - + -
53D PHE 3.0 19.9 + - - +
54D LEU* 4.0 4.7 - - - +
56D ALA* 1.3 75.8 - - - +
58D ARG* 1.3 56.8 + - - +
61D HIS* 2.8 72.8 + + + +
65D TYR* 3.7 31.6 - + - -
67D PHE* 3.6 20.0 - + + -
101D LEU* 3.5 30.7 - - + -
103D LEU* 4.3 8.5 - - + -
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Residues in contact with ARG 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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54D LEU 3.1 19.4 + - - +
55D ARG 3.2 5.4 + - - +
57D PHE* 1.3 75.6 - - - +
59D GLU* 1.3 60.5 + - + +
62D GLY* 3.0 48.6 + - - +
63D THR* 3.6 35.8 + - + +
67D PHE* 3.6 19.2 - - + -
82D TRP* 3.3 67.1 - - + +
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Residues in contact with GLU 59 (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 ARG* 3.0 34.4 + - + +
56D ALA* 3.7 9.4 - - - +
58D ARG* 1.3 76.8 - - + +
60D ALA* 1.3 59.6 + - - +
62D GLY 5.0 0.3 + - - -
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Residues in contact with ALA 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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32D VAL* 3.9 20.9 - - + -
56D ALA 3.2 13.7 + - - +
59D GLU* 1.3 80.8 - - + +
61D HIS* 1.3 66.5 + - + +
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Residues in contact with HIS 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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32D VAL* 3.2 40.6 + - + +
33D SER* 5.1 3.0 + - - -
35D ALA 3.8 9.8 + - - -
36D GLU* 6.0 1.3 - - - -
57D PHE* 2.8 54.7 + + + +
60D ALA* 1.3 79.9 - - + +
62D GLY* 1.3 56.4 + - - +
65D TYR* 3.7 27.5 + - - +
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Residues in contact with GLY 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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58D ARG* 3.0 34.8 + - - +
59D GLU 4.8 0.4 + - - -
60D ALA 3.8 0.6 - - - -
61D HIS* 1.3 79.6 - - - +
63D THR* 1.3 63.5 + - - -
64D ALA 3.5 2.5 - - - -
65D TYR* 3.4 16.7 - - - -
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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