Contacts of the helix formed by residues 49 - 72 (chain B) in PDB entry 1QRV
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 LYS 49 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43B TRP* 3.0 70.6 + - + +
44B ARG* 4.3 8.3 + - - +
46B MET* 2.8 45.4 + - - +
47B LYS* 3.5 5.5 + - - +
48B ASP* 1.3 72.7 - - - +
50B SER* 1.3 58.7 + - - +
51B GLU 3.3 2.9 - - - -
52B TRP* 3.2 7.2 + - - -
53B GLU* 2.9 51.4 + - + +
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Residues in contact with SER 50 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48B ASP* 2.9 29.3 + - - -
49B LYS* 1.3 76.5 - - - +
51B GLU* 1.3 61.0 + - - +
53B GLU* 3.5 12.4 + - - +
54B ALA* 2.8 33.6 + - - +
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Residues in contact with GLU 51 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48B ASP 5.1 0.8 + - - -
49B LYS 3.3 1.0 - - - -
50B SER* 1.3 81.7 + - - +
52B TRP* 1.3 90.1 + - + +
54B ALA* 3.6 6.2 - - - +
55B LYS* 3.1 58.2 + - + +
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Residues in contact with TRP 52 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B ALA* 3.3 28.0 - - - +
14B LEU* 3.8 15.3 - - + +
15B TRP* 3.5 43.6 - + + -
18B SER* 3.0 34.5 - - - -
43B TRP* 4.1 9.2 - + + -
46B MET* 3.8 26.4 - - - -
48B ASP 5.2 0.4 - - - -
49B LYS* 3.2 10.6 + - - +
51B GLU* 1.3 104.3 + - + +
53B GLU* 1.3 61.4 + - - +
55B LYS* 3.4 29.4 + - + +
56B ALA* 2.9 24.3 + - - +
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Residues in contact with GLU 53 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B ALA* 3.9 15.3 - - + -
43B TRP* 5.7 0.7 - - + -
49B LYS* 2.9 49.4 + - + +
50B SER* 3.5 9.7 + - - +
52B TRP* 1.3 74.2 - - - +
54B ALA* 1.3 65.8 + - - +
56B ALA* 3.9 1.7 - - - +
57B ALA* 3.0 23.6 + - - +
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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
----------------------------------------------------------
50B SER 2.8 17.8 + - - +
51B GLU* 3.6 7.0 - - - +
53B GLU* 1.3 77.5 - - - +
55B LYS* 1.3 62.9 + - + +
57B ALA* 3.2 20.2 - - - +
58B LYS* 3.2 29.1 + - - +
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Residues in contact with LYS 55 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B LEU* 3.6 18.4 - - + -
51B GLU* 3.1 45.1 + - - +
52B TRP* 3.6 27.7 - - + +
54B ALA* 1.3 75.4 - - + +
56B ALA* 1.3 65.9 + - - +
58B LYS* 3.2 13.8 + - + +
59B ALA* 2.9 23.4 + - - +
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Residues in contact with ALA 56 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B PRO* 5.4 0.7 - - - +
9B LEU 4.0 4.1 - - - +
10B SER* 4.0 3.4 - - - -
11B ALA* 3.4 32.5 - - + +
14B LEU* 3.2 10.0 - - + +
52B TRP 2.9 18.3 + - - +
53B GLU* 4.0 3.8 - - - +
55B LYS* 1.3 76.4 - - - +
57B ALA* 1.3 58.2 + - - +
59B ALA* 3.4 5.8 + - - +
60B LYS* 2.9 29.5 + - - +
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Residues in contact with ALA 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 GLU 3.0 15.0 + - - +
54B ALA* 3.2 14.6 - - - +
56B ALA* 1.3 77.4 - - - +
58B LYS* 1.3 62.5 + - + +
60B LYS* 3.2 9.3 + - - +
61B ASP* 3.1 27.7 + - - +
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Residues in contact with LYS 58 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54B ALA* 3.2 28.6 + - - +
55B LYS* 3.2 12.0 + - + +
57B ALA* 1.3 72.7 - - + +
59B ALA* 1.3 61.7 + - - +
60B LYS 3.0 1.8 - - - -
61B ASP* 2.9 16.5 + - - +
62B ASP* 2.8 38.3 + - - +
65B ARG* 6.3 0.2 - - - +
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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
----------------------------------------------------------
8B PRO* 3.6 10.0 - - + +
9B LEU* 4.3 17.3 - - + +
14B LEU* 4.8 6.5 - - + -
55B LYS 2.9 17.2 + - - +
56B ALA* 3.6 10.1 - - - +
58B LYS* 1.3 76.6 - - - +
60B LYS* 1.3 56.4 + - - +
62B ASP* 3.5 12.7 + - - +
63B TYR* 3.0 27.9 + - - +
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Residues in contact with LYS 60 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B PRO* 4.3 14.5 - - + +
56B ALA 2.9 14.1 + - - +
57B ALA* 3.2 13.0 - - - +
58B LYS 3.0 0.2 - - - -
59B ALA* 1.3 75.3 - - - +
61B ASP* 1.3 63.2 + - - +
63B TYR* 3.1 18.8 + - - +
64B ASP* 2.8 64.3 + - - +
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Residues in contact with ASP 61 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57B ALA 3.3 15.1 - - - +
58B LYS* 2.9 16.3 + - - +
60B LYS* 1.3 80.9 - - - +
62B ASP* 1.3 62.9 + - - +
64B ASP* 3.1 14.4 + - - +
65B ARG* 2.9 47.4 + - - +
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Residues in contact with ASP 62 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58B LYS* 2.8 28.0 + - - +
59B ALA* 3.5 15.3 - - - +
61B ASP* 1.3 72.4 - - - +
63B TYR* 1.3 63.5 + - - +
65B ARG* 2.8 38.1 + - - +
66B ALA* 2.9 22.1 + - - +
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Residues in contact with TYR 63 (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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4B LYS* 5.2 8.8 - - - +
5B PRO* 3.8 21.1 + - + +
6B LYS 3.1 28.3 - - - -
7B ARG* 3.8 14.8 - - + +
8B PRO* 3.6 30.3 - - + -
59B ALA 3.0 15.0 + - - +
60B LYS* 3.3 15.9 - - - +
62B ASP* 1.3 76.9 - - - +
64B ASP* 1.3 75.7 + - - +
66B ALA* 3.0 7.7 + - - +
67B VAL* 2.9 49.9 + - + +
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Residues in contact with ASP 64 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60B LYS* 2.8 51.7 + - - +
61B ASP* 3.3 14.8 - - - +
63B TYR* 1.3 81.1 - - - +
65B ARG* 1.3 57.4 + - + +
67B VAL* 3.2 9.6 + - - +
68B LYS* 2.9 28.3 + - - +
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Residues in contact with ARG 65 (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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58B LYS* 6.3 0.2 - - - +
61B ASP* 2.9 32.2 + - - +
62B ASP* 2.8 40.6 + - - +
64B ASP* 1.3 76.8 - - + +
66B ALA* 1.3 58.0 + - - +
68B LYS* 3.3 28.0 + - - +
69B GLU* 3.0 28.1 + - - +
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Residues in contact with ALA 66 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5B PRO* 3.4 22.1 - - + +
62B ASP 2.9 12.5 + - - +
63B TYR* 3.0 10.7 + - - +
65B ARG* 1.3 77.6 - - - +
67B VAL* 1.3 58.4 + - - +
69B GLU* 3.6 6.2 + - - +
70B PHE* 3.0 28.2 + - - +
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Residues in contact with VAL 67 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5B PRO* 4.0 11.0 - - + -
63B TYR* 2.9 61.4 + - + +
64B ASP* 3.3 11.7 - - - +
65B ARG 3.1 0.2 - - - -
66B ALA* 1.3 76.2 - - - +
68B LYS* 1.3 65.5 + - - +
70B PHE* 3.2 2.4 + - + +
71B GLU* 2.9 52.2 + - + +
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Residues in contact with LYS 68 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B ASP 2.9 12.7 + - - +
65B ARG* 3.4 36.5 + - - +
67B VAL* 1.3 79.3 - - - +
69B GLU* 1.3 61.7 + - - +
71B GLU* 3.5 5.4 + - - +
72B ALA* 3.3 26.4 + - + +
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Residues in contact with GLU 69 (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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65B ARG 3.0 16.4 + - - +
66B ALA* 3.9 7.4 - - - +
68B LYS* 1.3 77.4 - - - +
70B PHE* 1.3 62.8 + - - +
72B ALA 3.5 3.3 - - - +
73B ASN* 3.0 52.5 + - - +
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Residues in contact with PHE 70 (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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2A SER* 4.6 9.6 - - - -
3B ASP 3.4 39.0 - - - -
4B LYS* 3.7 23.8 - - + -
5B PRO* 3.8 17.5 - - + -
66B ALA 3.0 18.7 + - - +
67B VAL* 3.2 5.3 + - + +
69B GLU* 1.3 77.7 - - - +
71B GLU* 1.3 76.6 + - + +
73B ASN 4.4 7.7 + - - -
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Residues in contact with GLU 71 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67B VAL* 2.9 36.5 + - + +
68B LYS* 4.0 5.5 - - - +
70B PHE* 1.3 90.5 - - + +
72B ALA* 1.3 59.0 + - + +
73B ASN 3.6 2.9 + - - -
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Residues in contact with ALA 72 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68B LYS* 3.3 13.4 + - + +
69B GLU* 3.5 3.9 - - - +
71B GLU* 1.3 78.5 - - + +
73B ASN* 1.3 80.9 + - - +
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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
------------------------------------------------------------
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