Contacts of the helix formed by residues 45 - 58 (chain Q) in PDB entry 6Y5D
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 45 (chain Q).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43Q ARG 3.3 0.2 + - - -
44Q PRO* 1.3 71.9 - - - +
46Q THR* 1.3 58.8 + - - +
47Q VAL 3.4 1.3 - - - -
48Q ALA* 3.7 11.8 - - - +
49Q LEU* 2.9 37.5 + - - +
45R LYS* 3.4 26.2 - - - -
46R ARG* 5.6 4.3 - - - +
85U C 4.2 3.0 + - - -
86U G 3.3 9.5 + - - -
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Residues in contact with THR 46 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42Q TYR* 3.9 6.3 - - + -
43Q ARG* 3.0 17.8 + - - +
44Q PRO 3.3 0.9 + - - -
45Q GLY* 1.3 79.2 - - - +
47Q VAL* 1.3 62.3 + - - +
49Q LEU* 3.6 7.3 + - - +
50Q ARG* 3.1 40.2 + - - +
53Q ARG* 4.9 1.9 + - - -
146V T 3.7 20.4 - - - +
147V C 2.8 32.4 + - - +
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Residues in contact with VAL 47 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42Q TYR* 3.8 26.7 - - + -
46Q THR* 1.3 72.8 - - - +
48Q ALA* 1.3 61.7 + - - +
50Q ARG* 2.9 34.5 + - - +
51Q GLU* 2.7 50.4 + - + +
86U G 3.3 27.4 + - + +
87U C 4.3 11.2 - - - +
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Residues in contact with ALA 48 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45Q GLY* 3.5 13.9 + - - +
46Q THR 3.4 0.2 - - - -
47Q VAL* 1.3 78.4 - - - +
49Q LEU* 1.3 56.8 + - - +
51Q GLU* 3.2 2.3 + - - -
52Q ILE* 2.9 33.9 + - - +
40R ARG* 3.4 27.5 - - - +
45R LYS* 3.2 35.2 - - + +
46R ARG* 5.7 0.2 - - + -
85U C 5.5 1.6 - - - +
86U G 3.5 8.4 + - - +
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Residues in contact with LEU 49 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112O ILE* 4.1 11.9 - - + +
116O LEU* 3.4 42.4 - - + +
117O LEU* 4.1 16.4 - - + -
118O PRO* 3.8 24.7 - - + -
45Q GLY 2.9 27.1 + - - +
46Q THR* 3.9 5.4 - - - +
48Q ALA* 1.3 75.2 - - - +
50Q ARG* 1.3 62.9 + - - +
52Q ILE* 3.2 13.3 + - + +
53Q ARG* 3.0 44.7 + - - +
45R LYS* 4.1 12.8 - - + +
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Residues in contact with ARG 50 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42Q TYR* 3.4 44.8 + - - -
46Q THR* 3.1 23.1 + - - +
47Q VAL* 2.9 38.2 + - - +
49Q LEU* 1.3 77.4 - - - +
51Q GLU* 1.3 61.9 + - + +
53Q ARG* 3.3 20.6 + - + +
54Q ARG* 3.0 31.0 + - + +
11U A 4.6 16.8 + - - -
12U T 3.8 25.2 - - - +
146V T 4.8 6.7 - - - -
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Residues in contact with GLU 51 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47Q VAL* 2.7 39.3 + - + +
48Q ALA* 3.6 4.7 - - - +
50Q ARG* 1.3 70.4 - - + +
52Q ILE* 1.3 61.0 + - - +
54Q ARG* 3.1 27.9 + - - +
55Q TYR* 2.8 53.7 + - + -
36R ARG* 5.1 8.2 + - - +
40R ARG* 3.0 32.9 + - - +
86U G 5.4 2.1 + - - -
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Residues in contact with ILE 52 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112O ILE* 3.7 14.6 - - + -
116O LEU* 4.7 3.6 - - + -
48Q ALA 2.9 20.4 + - - +
49Q LEU* 3.2 21.5 + - + +
51Q GLU* 1.3 74.3 - - - +
53Q ARG* 1.3 65.4 + - - +
56Q GLN* 3.0 53.6 + - - +
40R ARG* 3.4 27.9 - - - +
43R GLY* 3.6 20.2 - - - +
44R VAL 3.4 26.5 - - - +
45R LYS* 3.9 12.1 - - + -
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Residues in contact with ARG 53 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110O PRO* 5.3 4.7 - - - +
112O ILE* 3.6 18.3 - - + +
117O LEU* 4.4 20.2 - - - +
118O PRO* 5.9 1.2 - - - +
46Q THR 4.9 1.6 + - - -
49Q LEU* 3.0 42.3 + - - +
50Q ARG* 3.4 17.5 - - - +
51Q GLU 3.2 0.2 - - - -
52Q ILE* 1.3 77.6 - - - +
54Q ARG* 1.3 62.4 + - - +
56Q GLN* 3.8 9.6 - - - +
57Q LYS* 3.1 31.8 + - - +
146V T 5.6 4.6 + - - -
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Residues in contact with ARG 54 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50Q ARG* 3.0 20.2 + - + +
51Q GLU* 3.1 27.2 + - - +
53Q ARG* 1.3 79.8 - - - +
55Q TYR* 1.3 103.8 + - + +
57Q LYS* 3.3 15.2 + - + +
58Q SER* 2.9 33.3 + - - +
60Q GLU* 6.1 0.2 - - - +
12U T 4.8 13.7 + - - -
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Residues in contact with TYR 55 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51Q GLU* 2.8 45.6 + - + +
54Q ARG* 1.3 109.6 + - + +
56Q GLN* 1.3 64.1 + - - +
58Q SER* 3.4 10.6 - - - +
60Q GLU* 4.8 4.9 - - - -
62Q LEU* 3.5 30.3 - - + -
37R ARG* 3.4 37.4 - - + +
40R ARG* 3.7 14.8 - - + -
41R ARG* 2.5 55.6 + - + +
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Residues in contact with GLN 56 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82O ARG* 3.4 2.7 + - - -
108O VAL* 3.2 43.1 + - + +
109O LEU 3.9 3.2 + - - -
110O PRO* 3.2 28.9 - - + +
111O ASN* 2.8 32.1 + - - +
112O ILE* 3.7 5.9 - - - +
52Q ILE* 3.0 44.3 + - + +
53Q ARG* 3.8 4.8 - - - +
55Q TYR* 1.3 77.7 - - - +
57Q LYS* 1.3 62.2 + - - +
58Q SER 3.7 2.1 - - - +
106Q GLU* 5.9 0.6 + - - -
41R ARG* 3.1 27.1 + - - +
42R GLY 4.5 1.0 - - - -
43R GLY* 4.0 6.5 - - - +
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Residues in contact with LYS 57 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82O ARG* 3.6 26.8 + - - +
110O PRO* 5.5 4.6 - - + +
53Q ARG* 3.1 23.6 + - - +
54Q ARG* 3.3 14.5 - - + +
55Q TYR 3.2 0.2 - - - -
56Q GLN* 1.3 79.8 - - - +
58Q SER* 1.3 62.3 + - - +
59Q THR* 4.4 2.3 - - - +
13U C 3.9 23.8 + - - -
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Residues in contact with SER 58 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107O GLY* 4.0 5.2 - - - -
54Q ARG* 2.9 22.9 + - - +
55Q TYR* 3.4 10.0 + - - +
56Q GLN 3.5 4.0 - - - +
57Q LYS* 1.3 83.9 - - - +
59Q THR* 1.3 63.1 + - - +
60Q GLU* 2.7 31.5 + - - -
41R ARG* 3.0 24.4 + - - -
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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