Contacts of the helix formed by residues 57 - 78 (chain g) 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 TYR 57 (chain g).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119a MET* 3.1 49.1 - - + -
121a VAL* 5.8 0.9 - - + -
6g VAL* 3.0 19.2 + - + +
7g THR* 5.2 1.6 - - - -
8g GLY 6.0 1.6 - - - -
39g ILE* 3.6 32.8 - - + +
40g SER 2.5 32.4 + - - -
41g ARG* 3.9 11.2 - - + -
53g ALA 5.9 0.7 - - - -
55g GLY 3.2 4.9 + - - +
56g ASP* 1.3 70.2 - - - +
58g ALA* 1.3 59.8 + - - +
60g PHE* 3.2 28.5 + + + +
61g GLN* 2.9 50.8 + - + +
64g LYS* 4.2 11.1 + - - -
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Residues in contact with ALA 58 (chain g).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88a TYR* 4.3 7.9 - - + -
91a ARG* 3.8 11.9 - - - +
117a GLY* 4.1 9.0 - - - +
118a GLY 4.0 5.9 - - - +
119a MET* 3.6 35.5 - - + +
6g VAL 4.7 0.2 + - - -
56g ASP* 3.3 14.6 + - - +
57g TYR* 1.3 75.3 - - - +
59g ASP* 1.3 61.4 + - - +
61g GLN* 3.2 5.4 + - - +
62g TYR* 3.0 25.5 + - - +
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Residues in contact with ASP 59 (chain g).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88a TYR* 3.2 22.3 + - - -
91a ARG* 3.3 1.0 + - - -
1g THR* 2.8 33.2 + - - +
56g ASP* 3.0 19.5 + - - +
57g TYR 3.3 0.2 - - - -
58g ALA* 1.3 72.7 - - - +
60g PHE* 1.3 59.8 + - - +
62g TYR* 3.2 8.6 + - - +
63g LEU* 2.9 31.2 + - - +
106g LEU* 3.5 17.3 - - + +
107g TRP 2.9 21.1 + - - -
108g ASN* 3.1 19.3 - - - +
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Residues in contact with PHE 60 (chain g).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40g SER 3.9 10.1 - - - -
41g ARG* 3.8 22.7 - - + -
42g ILE 4.6 0.4 - - - -
43g MET* 4.2 17.3 - - + -
51g LEU* 4.4 25.4 - - + -
53g ALA* 3.3 28.9 - - + -
56g ASP 3.2 14.4 + - - +
57g TYR* 3.4 43.5 - + - +
58g ALA 3.2 0.4 - - - -
59g ASP* 1.3 74.7 - - - +
61g GLN* 1.3 61.2 + - + +
63g LEU* 3.4 4.9 + - + +
64g LYS* 2.9 47.6 + - + +
108g ASN* 3.6 12.7 + - - +
110g MET* 5.3 2.5 - - + -
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Residues in contact with GLN 61 (chain g).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84a LYS* 4.2 19.9 - - + +
118a GLY 5.9 0.4 - - - +
119a MET* 3.9 7.0 - - + -
120a MET* 3.0 47.7 + - - +
57g TYR* 2.9 45.7 + - + +
58g ALA* 3.2 8.7 + - - +
60g PHE* 1.3 78.2 - - + +
62g TYR* 1.3 58.3 - - - +
64g LYS* 3.3 20.4 + - - +
65g GLN* 3.0 29.2 + - - +
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Residues in contact with TYR 62 (chain g).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84a LYS* 6.2 1.8 - - - +
88a TYR* 3.5 45.5 - + + +
58g ALA 3.0 12.4 + - - +
59g ASP 3.2 7.4 + - - +
61g GLN* 1.3 74.5 - - - +
63g LEU* 1.3 78.0 + - + +
65g GLN* 3.1 22.7 + - - +
66g VAL* 3.0 51.9 + - + +
99g ARG* 4.8 9.2 + - - -
106g LEU* 4.3 17.9 - - + -
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Residues in contact with LEU 63 (chain g).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51g LEU* 5.3 4.3 - - + -
59g ASP 2.9 13.2 + - - +
60g PHE* 3.8 5.4 - - + +
62g TYR* 1.3 86.4 - - + +
64g LYS* 1.3 56.6 + - - +
66g VAL* 4.0 3.5 - - + +
67g LEU* 2.9 38.2 + - + +
91g TRP* 4.7 13.2 - - + -
92g LEU* 4.0 20.9 - - + -
95g ALA* 5.0 5.6 - - + -
96g MET* 4.0 16.4 - - - -
106g LEU* 3.7 22.0 - - + -
108g ASN* 4.0 17.3 - - - +
110g MET* 3.6 31.2 - - - -
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Residues in contact with LYS 64 (chain g).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40g SER* 4.7 5.1 + - - -
42g ILE 5.7 2.8 + - - -
43g MET* 3.5 49.8 - - + +
57g TYR* 4.2 17.8 + - - -
60g PHE* 2.9 33.7 + - + +
61g GLN* 3.3 19.1 - - - +
63g LEU* 1.3 76.8 - - - +
65g GLN* 1.3 56.5 + - - +
68g GLY* 2.9 26.3 + - - -
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Residues in contact with GLN 65 (chain g).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99X ARG* 5.3 1.2 + - + -
100X SER* 3.4 41.5 + - - +
84a LYS* 3.2 29.1 + - - +
85a GLU* 3.5 7.0 + - - +
61g GLN 3.0 13.6 + - - +
62g TYR* 3.1 29.2 + - - +
64g LYS* 1.3 74.9 - - - +
66g VAL* 1.3 68.8 - - - +
68g GLY* 3.3 2.1 + - - -
69g GLN* 3.0 24.2 + - + +
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Residues in contact with VAL 66 (chain g).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62g TYR* 3.0 50.4 + - + +
63g LEU* 4.0 4.9 - - + +
65g GLN* 1.3 82.8 - - + +
67g LEU* 1.3 63.0 + - - +
69g GLN* 3.2 8.7 + - + +
70g MET* 3.0 26.0 + - + +
91g TRP* 3.6 30.1 - - + -
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Residues in contact with LEU 67 (chain g).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43g MET* 3.8 12.8 - - + -
45g VAL* 4.1 13.5 - - + -
51g LEU* 3.8 29.8 - - + -
63g LEU 2.9 20.6 + - - +
64g LYS 4.0 2.5 - - - +
66g VAL* 1.3 73.6 - - - +
68g GLY* 1.3 64.4 + - - +
70g MET* 3.1 12.5 + - + +
71g VAL* 2.9 28.1 + - - +
88g ILE* 4.0 36.8 - - + -
91g TRP* 3.8 30.5 - - + -
92g LEU* 4.5 9.4 - - + -
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Residues in contact with GLY 68 (chain g).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99X ARG* 6.0 0.7 - - - -
43g MET* 5.0 5.0 - - - -
45g VAL* 6.3 0.4 - - - -
64g LYS 2.9 18.9 + - - -
65g GLN* 3.7 2.0 - - - -
66g VAL 3.3 0.2 - - - -
67g LEU* 1.3 74.9 - - - +
69g GLN* 1.3 57.8 - - - +
71g VAL* 3.2 7.2 + - - +
72g ILE* 2.9 37.1 + - - +
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Residues in contact with GLN 69 (chain g).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96X SER* 2.7 33.3 + - - +
99X ARG* 2.0 53.5 + - + +
100X SER* 3.8 19.1 - - - +
65g GLN* 3.0 14.0 + - + +
66g VAL* 3.2 10.7 + - + +
68g GLY* 1.3 74.9 - - - +
70g MET* 1.3 59.6 + - + +
72g ILE* 3.8 3.9 - - - +
73g ASP* 2.9 62.5 + - - +
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Residues in contact with MET 70 (chain g).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99G PHE* 3.8 35.4 - - + -
66g VAL* 3.0 18.0 + - + +
67g LEU* 3.1 16.3 + - + +
69g GLN* 1.3 76.2 - - + +
71g VAL* 1.3 63.4 + - + +
73g ASP* 3.6 7.6 - - - +
74g GLU* 3.0 24.6 + - - +
83g TYR* 3.9 22.2 + - + +
88g ILE* 5.4 2.0 - - + -
91g TRP* 3.4 48.0 - - + +
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Residues in contact with VAL 71 (chain g).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45g VAL* 3.7 28.3 - - + -
46g ASN* 4.0 27.6 - - + +
67g LEU 2.9 14.5 + - - +
68g GLY* 3.7 8.7 - - - +
70g MET* 1.3 79.1 - - + +
72g ILE* 1.3 65.8 + - + +
74g GLU* 3.2 8.4 + - - +
75g GLU* 2.9 46.6 + - + +
83g TYR* 4.4 15.5 - - + -
88g ILE* 4.8 2.5 - - + -
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Residues in contact with ILE 72 (chain g).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70X ASP* 3.7 21.5 - - - +
71X ARG* 3.0 56.1 - - + +
99X ARG* 3.6 30.3 - - - +
68g GLY 2.9 21.0 + - - +
69g GLN* 3.8 5.6 - - - +
71g VAL* 1.3 79.5 - - + +
73g ASP* 1.3 68.1 + - - +
75g GLU* 3.1 10.7 + - - +
76g LEU* 3.1 33.8 + - + +
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Residues in contact with ASP 73 (chain g).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92X ARG* 5.1 7.6 + - - +
96X SER* 4.2 10.2 + - - -
69g GLN* 2.9 47.3 + - - +
70g MET* 3.6 8.1 - - - +
72g ILE* 1.3 79.7 - - - +
74g GLU* 1.3 61.9 + - - +
76g LEU* 3.5 23.2 + - - +
77g LEU* 3.9 12.0 + - - +
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Residues in contact with GLU 74 (chain g).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101G ARG* 4.3 1.0 + - - -
107G ARG* 3.0 45.1 + - - +
46g ASN* 5.3 1.9 + - - -
70g MET 3.0 16.5 + - - +
71g VAL* 3.6 7.1 - - - +
72g ILE 3.1 0.2 - - - -
73g ASP* 1.3 73.8 - - - +
75g GLU* 1.3 66.1 + - - +
76g LEU 3.1 4.5 - - - -
77g LEU* 3.1 25.2 + - - +
78g GLY 3.9 2.1 + - - -
79g ASP* 4.6 1.2 - - - +
81g HIS* 4.0 5.2 - - - +
82g SER* 3.3 13.8 + - - -
83g TYR* 3.0 61.7 + - + +
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Residues in contact with GLU 75 (chain g).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68X ASN* 5.0 3.1 + - - -
71X ARG* 6.1 2.5 - - + +
46g ASN* 4.1 13.0 - - - +
71g VAL* 2.9 37.8 + - + +
72g ILE* 3.1 9.4 + - - +
74g GLU* 1.3 80.6 - - + +
76g LEU* 1.3 64.8 + - + +
77g LEU 3.3 0.2 - - - -
78g GLY* 3.6 12.8 + - - +
81g HIS 5.8 1.3 - - - -
82g SER* 6.4 2.2 - - - -
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Residues in contact with LEU 76 (chain g).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68X ASN* 3.3 47.7 + - + +
69X VAL 3.2 27.6 - - - +
70X ASP* 3.3 13.5 - - - +
71X ARG* 3.2 37.7 - - + +
92X ARG* 3.3 20.0 + - + +
72g ILE* 3.1 22.8 + - + +
73g ASP* 3.5 19.1 - - - +
74g GLU 3.1 0.4 - - - -
75g GLU* 1.3 79.6 - - + +
77g LEU* 1.3 64.9 + - - +
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Residues in contact with LEU 77 (chain g).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107G ARG* 3.5 31.2 - - + +
110G SER* 5.8 4.0 - - - +
64X LYS* 6.1 1.0 - - - +
68X ASN* 5.1 2.0 + - - -
92X ARG* 3.2 33.7 - - - +
73g ASP 4.0 10.5 - - - +
74g GLU* 3.1 13.8 + - - +
76g LEU* 1.3 80.3 - - - +
78g GLY* 1.3 63.6 + - - +
79g ASP* 3.5 27.9 + - + +
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Residues in contact with GLY 78 (chain g).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64X LYS* 5.4 6.4 + - - -
68X ASN* 5.7 2.2 - - - -
74g GLU 3.9 3.6 + - - -
75g GLU* 3.6 12.0 + - - -
76g LEU 3.4 2.2 - - - -
77g LEU* 1.3 80.1 - - - +
79g ASP* 1.3 58.2 + - - +
80g GLY 3.2 7.6 + - - -
81g HIS 6.1 0.2 - - - -
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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) + - + + + + + -
------------------------------------------------------------
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