Contacts of the helix formed by residues 45 - 60 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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17B GLU* 3.5 12.3 + - - +
18B GLN* 4.9 5.7 - - - +
43B PHE* 4.1 1.6 - - - +
44B TYR* 1.3 88.9 - - + +
46B ALA* 1.3 66.7 + - - +
47B ALA* 4.4 7.4 - - + +
48B HIS* 3.1 27.8 + - + +
49B GLN* 3.0 20.8 + - - +
88B TYR* 4.0 22.2 + - - -
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Residues in contact with ALA 46 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44B TYR 3.6 4.0 + - - -
45B ARG* 1.3 70.8 - - - +
47B ALA* 1.3 57.9 + - - +
49B GLN* 2.6 39.8 + - - +
50B LYS* 2.9 34.9 + - - +
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Residues in contact with ALA 47 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45B ARG* 4.9 7.8 - - + +
46B ALA* 1.3 77.7 - - - +
48B HIS* 1.3 67.2 + - + +
50B LYS* 3.5 11.7 + - - +
51B ILE* 3.1 30.7 + - - +
82B GLU 4.8 4.0 - - - +
83B ILE* 3.5 36.6 - - + +
88B TYR* 5.1 2.7 - - + -
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Residues in contact with HIS 48 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17B GLU* 2.9 37.1 + - + +
18B GLN* 3.9 16.6 - - + -
21B LEU* 3.6 22.1 - - + +
43B PHE* 3.6 19.2 - - + -
45B ARG* 3.1 31.1 + - + +
46B ALA 2.8 1.8 + - - -
47B ALA* 1.3 77.7 - - + +
49B GLN* 1.3 68.3 + - - +
51B ILE* 3.6 1.0 - - + +
52B PHE* 2.9 27.5 + - - +
88B TYR* 2.6 42.0 + + - -
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Residues in contact with GLN 49 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40B PRO* 3.0 37.7 - - + +
41B GLU* 4.0 23.1 - - - +
43B PHE* 3.3 20.5 - - - +
44B TYR 4.3 2.9 - - - +
45B ARG 3.0 6.9 + - - +
46B ALA* 2.6 32.4 + - - +
48B HIS* 1.3 71.7 - - - +
50B LYS* 1.3 51.9 + - + +
52B PHE* 3.2 1.9 + - - +
53B HIS* 2.8 36.0 + - - +
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Residues in contact with LYS 50 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46B ALA* 2.9 49.6 + - - +
47B ALA* 3.6 10.5 - - - +
49B GLN* 1.3 74.7 - - + +
51B ILE* 1.3 56.0 + - - +
53B HIS* 3.5 6.2 + - - +
54B ALA* 2.9 30.3 + - - +
74B LEU* 3.7 6.9 - - + +
79B GLN* 3.3 37.8 - - + +
82B GLU* 2.8 40.3 + - - +
83B ILE* 4.7 4.5 - - + -
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Residues in contact with ILE 51 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21B LEU* 3.7 36.6 - - + -
25B PHE* 4.9 4.5 - - + -
47B ALA 3.1 12.6 + - - +
48B HIS* 3.3 6.7 + - - +
50B LYS* 1.3 74.9 - - - +
52B PHE* 1.3 53.7 + - - +
54B ALA* 2.8 7.0 + - - +
55B MET* 2.6 46.1 + - - +
70B VAL* 4.8 3.9 - - + +
74B LEU* 4.2 8.1 - - + -
83B ILE* 3.5 40.2 - - + -
88B TYR* 4.4 3.1 - - + -
89B LEU* 3.7 28.3 - - + -
92B LEU* 4.1 8.3 - - + -
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Residues in contact with PHE 52 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20B VAL* 4.2 4.0 - - + -
21B LEU* 3.9 2.5 - - + -
31B LEU* 4.2 7.2 - - + -
34B ALA* 3.8 41.1 - - + -
35B SER* 3.9 4.9 - - - -
38B LEU* 3.5 22.7 - - + -
40B PRO* 4.1 13.7 - - + -
43B PHE* 3.3 36.6 - + + -
48B HIS 2.9 19.4 + - - +
49B GLN 3.8 2.5 - - - +
51B ILE* 1.3 74.3 - - - +
53B HIS* 1.3 61.6 + - - +
55B MET* 3.3 35.4 - - + +
56B LEU* 3.1 44.6 + - + +
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Residues in contact with HIS 53 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40B PRO* 3.7 26.9 - - + +
49B GLN 2.8 17.8 + - - +
50B LYS* 3.7 7.0 - - - +
52B PHE* 1.3 74.9 - - - +
54B ALA* 1.3 55.4 + - - +
56B LEU* 2.9 9.9 + - + +
57B ARG* 2.8 84.4 + - + +
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Residues in contact with ALA 54 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50B LYS 2.9 14.6 + - - +
51B ILE* 2.8 8.6 + - - +
53B HIS* 1.3 75.7 + - - +
55B MET* 1.3 66.1 + - - +
57B ARG* 2.9 9.6 + - - +
58B VAL* 2.9 28.6 + - - +
70B VAL* 4.4 6.7 - - + -
73B GLU* 4.1 16.4 - - + -
74B LEU* 3.7 27.1 - - + +
77B SER* 6.0 1.3 - - - +
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Residues in contact with MET 55 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21B LEU* 3.5 19.5 - - + +
24B VAL* 3.5 49.4 - - + -
25B PHE* 5.0 8.3 - - - -
31B LEU* 4.1 9.9 - - + -
51B ILE* 2.6 34.5 + - - +
52B PHE* 3.3 38.4 - - + +
54B ALA* 1.3 74.5 - - - +
56B LEU* 1.3 61.4 + - - +
58B VAL* 3.3 4.7 + - - +
59B ALA* 3.1 18.7 + - - +
65B VAL* 3.7 18.1 - - + +
70B VAL* 4.4 14.0 - - + +
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Residues in contact with LEU 56 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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341A GLU* 4.7 20.4 - - - +
344A ARG* 5.2 4.3 - - - +
31B LEU* 4.7 12.1 - - + -
35B SER* 3.8 25.1 - - - +
38B LEU 5.1 1.3 - - - +
39B ILE* 5.5 0.2 - - - -
40B PRO* 4.3 16.2 - - + -
52B PHE* 3.1 43.2 + - + +
53B HIS* 2.9 9.9 + - + +
55B MET* 1.3 75.0 - - - +
57B ARG* 1.3 62.4 + - - +
58B VAL 3.0 2.2 - - - -
59B ALA* 2.8 26.7 + - + +
60B ASP* 2.9 20.3 + - - +
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Residues in contact with ARG 57 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53B HIS* 2.8 63.0 + - + +
54B ALA* 3.5 11.7 - - - +
56B LEU* 1.3 73.1 - - - +
58B VAL* 1.3 61.4 + - - +
60B ASP* 3.6 14.7 + - + +
61B ARG* 3.4 24.2 + - - +
73B GLU* 4.2 20.8 + - - +
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Residues in contact with VAL 58 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54B ALA 2.9 16.2 + - - +
55B MET* 3.6 8.5 - - - +
57B ARG* 1.3 74.8 - - - +
59B ALA* 1.3 61.5 + - - +
60B ASP 3.0 4.7 + - - -
61B ARG* 3.4 13.2 + - - +
62B GLY 3.3 13.3 - - - -
63B GLU* 3.4 17.4 - - + +
64B PRO 3.2 27.8 - - - +
65B VAL* 4.4 2.9 - - + -
69B THR* 3.5 24.9 - - + +
70B VAL* 4.5 4.9 - - + -
73B GLU* 3.5 33.9 - - + +
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Residues in contact with ALA 59 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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344A ARG* 3.2 36.1 + - - +
31B LEU* 4.0 12.3 - - + -
55B MET 3.1 11.8 + - - +
56B LEU* 2.8 13.6 + - + +
58B VAL* 1.3 72.5 - - - +
60B ASP* 1.3 56.6 + - - +
61B ARG 2.9 13.5 + - - -
62B GLY 3.0 16.8 - - - +
65B VAL* 3.9 15.9 - - + +
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Residues in contact with ASP 60 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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340A SER* 4.5 4.4 + - - -
341A GLU* 3.4 25.2 - - - +
344A ARG* 2.7 35.7 + - - +
56B LEU* 2.9 18.4 + - - +
57B ARG* 3.7 17.2 - - + +
58B VAL 3.0 1.6 - - - -
59B ALA* 1.3 75.7 - - - +
61B ARG* 1.3 66.5 + - - +
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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