Contacts of the helix formed by residues 38 - 59 (chain Q) in PDB entry 5GJQ
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 ASN 38 (chain Q).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29Q SER 5.5 2.0 - - - +
32Q LYS 4.4 15.0 - - - +
33Q ARG 5.8 0.2 - - - +
35Q ILE* 4.2 9.1 - - - +
36Q GLN* 4.0 3.6 - - - +
37Q GLU* 1.3 74.3 + - - +
39Q ASP* 1.3 60.0 + - - +
41Q GLU* 3.2 30.1 - - + -
42Q ALA* 2.8 38.6 - - + +
79Q SER* 4.0 5.9 - - - -
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Residues in contact with ASP 39 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36Q GLN* 4.0 8.0 - - + +
37Q GLU* 2.6 23.8 - - + +
38Q ASN* 1.3 75.2 - - - +
40Q GLU* 1.3 66.6 + - + +
41Q GLU 4.0 0.6 - - - +
42Q ALA* 3.9 1.0 - - - +
43Q VAL* 3.4 14.7 + - - +
79Q SER* 4.6 10.9 - - - +
84Q LYS* 5.8 0.7 - - - -
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Residues in contact with GLU 40 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36Q GLN* 5.2 3.3 - - + +
39Q ASP* 1.3 76.8 - - + +
41Q GLU* 1.3 66.8 + - - +
43Q VAL* 3.2 11.1 - - - +
44Q GLN* 2.9 22.4 + - - +
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Residues in contact with GLU 41 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2Q ALA* 4.3 25.1 - - + -
3Q ALA 5.6 0.2 - - - +
29Q SER 5.8 1.1 - - - +
32Q LYS 5.4 2.9 - - - +
33Q ARG 5.8 0.2 - - - +
36Q GLN* 4.9 6.5 - - + +
38Q ASN* 3.2 22.9 - - + -
39Q ASP 3.2 0.6 - - - +
40Q GLU* 1.3 77.7 - - - +
42Q ALA* 1.3 49.5 - - - +
44Q GLN* 2.7 12.0 + - - +
45Q VAL* 2.2 38.4 + - + +
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Residues in contact with ALA 42 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38Q ASN* 2.8 29.4 + - + +
39Q ASP 3.9 1.6 - - - +
41Q GLU* 1.3 75.6 - - - +
43Q VAL* 1.3 53.8 + - - +
45Q VAL* 3.3 12.4 - - + +
46Q LYS* 2.3 38.6 + - - +
75Q PRO* 5.7 6.7 - - + +
76Q PHE* 6.3 0.7 - - - -
79Q SER* 5.5 3.4 - - - -
80Q ILE* 6.1 4.9 - - + -
88Q LEU* 5.8 1.1 - - - -
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Residues in contact with VAL 43 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39Q ASP 3.4 6.6 + - - +
40Q GLU* 3.2 16.5 + - - +
42Q ALA* 1.3 77.3 - - - +
44Q GLN* 1.3 57.8 + - - +
46Q LYS* 3.2 10.1 - - - +
47Q GLU* 2.9 21.7 + - - +
84Q LYS* 3.9 31.9 + - - +
87Q ARG* 5.4 3.4 - - - +
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Residues in contact with GLN 44 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6Q VAL* 5.0 17.6 - - + +
29Q SER* 5.4 1.4 - - - -
40Q GLU 2.9 11.4 + - - +
41Q GLU* 2.7 17.1 + - - +
43Q VAL* 1.3 71.9 - - - +
45Q VAL* 1.3 62.6 + - - -
46Q LYS 3.2 0.2 - - - -
47Q GLU* 3.0 25.4 + - + +
48Q GLN* 3.1 7.3 + - - +
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Residues in contact with VAL 45 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26Q ILE 5.4 0.7 - - - +
29Q SER* 3.9 31.6 - - - +
30Q ILE* 3.9 17.7 - - + +
38Q ASN* 6.1 0.7 - - + -
41Q GLU 2.2 26.1 + - - +
42Q ALA* 3.3 15.5 - - - +
44Q GLN* 1.3 65.6 - - - +
46Q LYS* 1.3 52.0 + - - +
48Q GLN* 3.1 7.6 - - - +
49Q SER* 2.6 33.4 + - - -
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Residues in contact with LYS 46 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42Q ALA 2.3 29.4 + - - +
43Q VAL* 3.2 9.6 - - - +
45Q VAL* 1.3 65.6 - - - +
47Q GLU* 1.3 54.9 + - - +
49Q SER* 2.6 14.6 + - - -
50Q ILE* 2.3 38.7 + - - +
88Q LEU* 3.0 37.2 - - + -
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Residues in contact with GLU 47 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43Q VAL 2.9 10.2 + - - +
44Q GLN* 3.0 25.0 + - + +
46Q LYS* 1.3 73.6 - - - +
48Q GLN* 1.3 63.9 + - - +
50Q ILE* 3.5 7.7 - - - +
51Q LEU* 3.5 13.5 + - - +
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Residues in contact with GLN 48 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26Q ILE* 3.6 35.2 - - + -
29Q SER* 5.0 2.5 - - - -
44Q GLN 3.1 9.4 + - - +
45Q VAL* 3.1 12.1 - - - +
47Q GLU* 1.3 70.4 - - - +
49Q SER* 1.3 52.2 + - - +
50Q ILE 2.6 4.5 + - - -
51Q LEU* 2.5 18.4 + - - -
52Q GLU* 2.2 33.9 + - + +
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Residues in contact with SER 49 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45Q VAL 2.6 20.3 + - - -
46Q LYS* 2.6 16.2 + - - -
48Q GLN* 1.3 69.6 - - - +
50Q ILE* 1.3 47.4 + - - -
52Q GLU* 3.4 13.0 - - - +
53Q LEU* 2.4 39.7 + - - +
88Q LEU* 6.1 0.4 - - - -
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Residues in contact with ILE 50 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46Q LYS 2.3 27.9 + - - +
47Q GLU* 3.5 9.9 - - - +
48Q GLN 2.6 1.8 + - - -
49Q SER* 1.3 62.3 - - - +
51Q LEU* 1.3 55.4 + - - +
53Q LEU* 2.9 8.0 + - - +
54Q GLY* 2.8 30.8 + - - -
91Q SER* 5.2 7.6 - - - -
95Q LEU* 4.2 27.1 - - + +
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Residues in contact with LEU 51 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19Q ASP* 4.9 7.9 - - + -
47Q GLU 3.5 8.0 + - - +
48Q GLN* 2.5 9.7 + - - +
50Q ILE* 1.3 74.9 - - - +
52Q GLU* 1.3 50.1 + - - +
54Q GLY* 2.6 8.5 + - - +
55Q SER* 2.3 38.5 + - - -
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Residues in contact with GLU 52 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19Q ASP* 4.8 4.2 - - + +
23Q SER* 5.8 2.5 - - - -
26Q ILE* 3.9 16.4 - - + -
48Q GLN* 2.2 47.9 + - + +
49Q SER* 3.4 8.1 - - - +
51Q LEU* 1.3 67.7 - - - +
53Q LEU* 1.3 48.4 + - - +
55Q SER* 3.0 11.3 - - - -
56Q LEU* 2.1 38.0 + - - +
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Residues in contact with LEU 53 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49Q SER 2.4 38.4 + - - +
50Q ILE* 2.9 10.3 + - - +
51Q LEU 2.8 0.6 + - - -
52Q GLU* 1.3 67.9 - - - +
54Q GLY* 1.3 51.9 + - - +
55Q SER 2.9 1.1 - - - -
56Q LEU* 2.8 11.2 + - + +
57Q LEU* 2.3 37.4 + - - +
62Q GLN* 4.2 4.9 + - + +
65Q GLU* 5.3 4.0 - - + -
91Q SER 5.1 7.6 - - - +
92Q LEU* 4.7 19.7 - - + -
95Q LEU* 5.4 5.4 - - + -
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Residues in contact with GLY 54 (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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50Q ILE 2.8 9.4 + - - -
51Q LEU* 2.6 12.2 + - - -
53Q LEU* 1.3 71.0 - - - +
55Q SER* 1.3 49.1 + - - -
57Q LEU* 3.4 10.2 - - - +
58Q ALA* 2.4 33.3 + - - +
95Q LEU* 5.8 6.7 - - - +
99Q MET* 5.8 3.6 - - - -
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Residues in contact with SER 55 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19Q ASP* 3.2 35.0 - - - -
20Q ARG* 5.0 2.0 - - - -
23Q SER* 5.8 4.0 - - - -
51Q LEU 2.3 28.8 + - - -
52Q GLU* 3.3 10.1 - - - -
54Q GLY* 1.3 65.8 - - - +
56Q LEU* 1.3 54.0 + - - -
57Q LEU 3.1 1.1 - - - -
58Q ALA* 3.1 10.1 - - - +
59Q LYS* 2.3 39.3 + - - +
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Residues in contact with LEU 56 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52Q GLU 2.1 31.8 + - - +
53Q LEU* 2.8 15.0 + - - +
55Q SER* 1.3 65.2 - - - +
57Q LEU* 1.3 47.7 + - - +
59Q LYS* 2.8 3.6 - - - -
60Q THR 2.5 6.8 + - - -
61Q GLY* 1.5 67.5 + - - +
62Q GLN* 2.7 6.3 - - - +
65Q GLU* 4.0 8.7 - - + -
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Residues in contact with LEU 57 (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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53Q LEU 2.3 28.1 + - - +
54Q GLY* 3.4 11.7 - - - +
56Q LEU* 1.3 63.4 - - - +
58Q ALA* 1.3 54.8 + - - +
60Q THR* 2.1 36.7 + - - +
61Q GLY 3.7 1.8 - - - +
62Q GLN* 3.1 17.1 - - + +
95Q LEU 5.6 2.2 - - - +
96Q PHE* 6.1 1.1 - - + -
99Q MET* 4.3 26.0 - - + -
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Residues in contact with ALA 58 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54Q GLY 2.4 31.9 + - - +
55Q SER* 3.0 12.8 + - - +
57Q LEU* 1.3 67.7 - - - +
59Q LYS* 1.3 56.5 - - - +
60Q THR 3.5 1.2 + - - -
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Residues in contact with LYS 59 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55Q SER 2.3 29.3 + - - +
56Q LEU* 3.6 5.6 - - - +
58Q ALA* 1.3 67.2 - - - +
60Q THR* 1.3 59.5 + - - +
61Q GLY* 2.6 18.2 + - - +
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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
------------------------------------------------------------
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