Contacts of the helix formed by residues 45 - 60 (chain D) in PDB entry 2R6C
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 45 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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17D GLU* 3.6 5.6 + - - +
18D GLN* 4.7 6.5 - - - +
43D PHE* 4.0 1.7 - - - +
44D TYR* 1.3 90.2 - - + +
46D ALA* 1.3 65.0 + - - +
47D ALA* 4.2 9.0 - - + +
48D HIS* 3.2 35.8 + - + +
49D GLN* 3.1 19.6 + - - +
88D TYR* 3.9 21.2 + - - -
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Residues in contact with ALA 46 (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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44D TYR 3.6 3.8 + - - -
45D ARG* 1.3 71.0 - - - +
47D ALA* 1.3 65.8 + - - +
49D GLN* 2.7 28.6 + - + +
50D LYS* 2.8 35.1 + - - +
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Residues in contact with ALA 47 (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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45D ARG* 4.2 8.5 - - + +
46D ALA* 1.3 77.9 - - - +
48D HIS* 1.3 69.3 + - + +
50D LYS* 3.3 11.6 + - - +
51D ILE* 3.0 29.6 + - - +
82D GLU 5.0 3.8 - - - +
83D ILE* 3.7 33.3 - - + +
88D TYR* 5.2 2.2 - - + -
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Residues in contact with HIS 48 (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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17D GLU* 2.8 37.2 + - + +
18D GLN* 3.9 14.6 - - + -
21D LEU* 3.5 27.1 - - + +
43D PHE* 3.6 16.4 - - + -
45D ARG* 3.2 27.9 + - + +
46D ALA 3.1 0.6 - - - -
47D ALA* 1.3 79.0 - - + +
49D GLN* 1.3 58.4 + - - +
51D ILE* 3.1 2.3 + - + +
52D PHE* 2.7 37.6 + - - +
88D TYR* 2.6 40.0 + + - -
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Residues in contact with GLN 49 (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 PRO* 3.0 39.8 - - + +
41D GLU* 3.9 22.6 + - - +
43D PHE* 3.3 20.3 - - - +
44D TYR 4.3 2.4 - - - +
45D ARG 3.1 6.1 + - - +
46D ALA* 2.7 33.3 + - - +
48D HIS* 1.3 70.6 - - - +
50D LYS* 1.3 53.2 + - + +
52D PHE* 3.7 1.4 - - - +
53D HIS* 2.8 37.3 + - - +
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Residues in contact with LYS 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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46D ALA* 2.8 47.5 + - + +
47D ALA* 3.4 10.3 - - - +
49D GLN* 1.3 75.2 - - + +
51D ILE* 1.3 62.4 + - - +
53D HIS* 3.3 5.3 + - - +
54D ALA* 2.9 24.1 + - - +
74D LEU* 3.9 6.3 - - + +
79D GLN* 3.3 38.3 + - + +
82D GLU* 2.6 39.0 + - + +
83D ILE* 4.7 5.2 - - + -
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Residues in contact with ILE 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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21D LEU* 3.8 25.4 - - + -
25D PHE* 4.9 5.8 - - + -
47D ALA 3.0 15.6 + - - +
48D HIS* 3.1 6.9 + - - +
50D LYS* 1.3 73.7 - - - +
52D PHE* 1.3 54.5 + - - +
54D ALA* 2.8 6.0 + - - +
55D MET* 2.7 45.1 + - - +
70D VAL* 4.7 4.4 - - + +
74D LEU* 4.1 8.3 - - + -
83D ILE* 3.4 42.0 - - + -
88D TYR* 4.4 3.4 - - + -
89D LEU* 3.5 28.9 - - + -
92D LEU* 4.1 15.9 - - + -
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Residues in contact with PHE 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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20D VAL* 4.2 3.6 - - + -
21D LEU* 4.0 3.6 - - + -
31D LEU* 4.2 6.5 - - + -
34D ALA* 4.0 39.9 - - + -
35D SER* 4.1 4.9 - - - -
38D LEU* 3.9 23.1 - - + -
39D ILE 4.5 0.2 - - - -
40D PRO* 4.1 12.6 - - + -
43D PHE* 3.3 38.6 - + + -
48D HIS 2.7 21.1 + - - +
49D GLN 3.8 2.2 - - - +
51D ILE* 1.3 73.8 - - - +
53D HIS* 1.3 60.4 + - - +
55D MET* 3.2 36.6 - - + +
56D LEU* 3.0 44.2 + - + +
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Residues in contact with HIS 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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40D PRO* 3.8 27.1 - - + +
49D GLN 2.8 21.4 + - - +
50D LYS* 3.6 5.4 - - - +
52D PHE* 1.3 71.3 - - - +
54D ALA* 1.3 54.3 + - - +
56D LEU* 2.9 10.1 + - + +
57D ARG* 2.7 86.2 + - - +
79D GLN* 6.0 0.4 + - - -
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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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50D LYS 2.9 12.6 + - - +
51D ILE 2.8 8.4 + - - +
53D HIS* 1.3 76.0 + - - +
55D MET* 1.3 55.1 + - - +
57D ARG* 3.1 8.6 + - - +
58D VAL* 2.8 41.2 + - - +
70D VAL* 4.2 7.2 - - + -
73D GLU* 4.0 16.4 - - + -
74D LEU* 3.8 28.3 - - + +
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Residues in contact with MET 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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21D LEU* 3.7 16.6 - - + +
24D VAL* 3.5 51.1 - - + -
25D PHE* 5.2 7.4 - - - -
31D LEU* 3.7 13.2 - - + +
51D ILE* 2.7 32.3 + - - +
52D PHE* 3.2 46.2 - - + +
54D ALA* 1.3 73.3 - - - +
56D LEU* 1.3 60.8 + - - +
58D VAL* 3.5 3.8 + - - +
59D ALA* 3.2 20.1 + - - +
65D VAL* 3.8 17.1 - - + +
70D VAL* 4.4 9.7 - - + +
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Residues in contact with LEU 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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299C SER* 5.3 11.7 - - - +
31D LEU* 4.6 9.4 - - + -
35D SER* 3.9 23.3 - - - +
38D LEU 5.2 1.8 - - - +
39D ILE* 5.4 0.2 - - - -
40D PRO* 4.3 16.2 - - + -
52D PHE* 3.0 46.1 + - + +
53D HIS* 2.9 11.2 + - + +
55D MET* 1.3 70.1 - - - +
57D ARG* 1.3 60.0 + - - +
58D VAL 3.1 2.2 - - - -
59D ALA* 2.8 28.9 + - + +
60D ASP* 3.0 24.8 + - - +
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Residues in contact with ARG 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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53D HIS* 2.7 58.2 + - - +
54D ALA* 3.1 8.9 + - - +
56D LEU* 1.3 73.1 - - - +
58D VAL* 1.3 61.2 + - - +
60D ASP* 3.7 14.8 + - + +
61D ARG* 3.4 26.7 + - - +
73D GLU* 4.2 21.2 + - - +
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Residues in contact with VAL 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 ALA 2.8 20.7 + - - +
55D MET 3.8 4.3 - - - +
57D ARG* 1.3 75.7 - - - +
59D ALA* 1.3 64.2 - - - +
60D ASP 3.1 1.1 + - - -
61D ARG* 3.5 15.3 + - - +
62D GLY 3.3 15.1 - - - -
63D GLU* 3.4 16.6 - - + +
64D PRO 3.3 29.6 - - - +
65D VAL* 4.1 7.4 - - + -
69D THR* 3.5 25.4 - - + +
70D VAL* 4.4 3.4 - - - -
73D GLU* 3.5 29.2 - - + +
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Residues in contact with ALA 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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302C ARG* 4.8 8.5 + - - -
345C SER* 4.2 7.8 + - - -
31D LEU* 3.7 20.6 - - + -
55D MET 3.2 13.0 + - - +
56D LEU* 2.8 17.4 + - + +
58D VAL* 1.3 74.6 - - - +
60D ASP* 1.3 57.8 + - - +
61D ARG 3.0 12.8 + - - -
62D GLY 3.4 15.1 - - - +
65D VAL* 4.0 7.8 - - + +
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Residues in contact with ASP 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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298C VAL* 5.9 2.3 - - - +
299C SER* 5.3 10.6 + - - -
341C GLU* 3.6 36.5 - - + +
345C SER* 4.8 9.6 + - - -
56D LEU* 3.0 26.2 + - - +
57D ARG* 4.0 13.7 - - + +
58D VAL 3.1 1.4 - - - -
59D ALA* 1.3 79.2 - - - +
61D ARG* 1.3 65.9 + - - +
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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