Contacts of the helix formed by residues 48 - 72 (chain H) 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 VAL 48 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47H GLN* 1.3 76.2 - - - +
49H GLU* 1.3 52.8 + - - +
51H ASP* 3.2 9.5 - - - +
52H ILE* 2.7 35.7 + - - +
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Residues in contact with GLU 49 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47H GLN 4.4 3.3 - - - +
48H VAL* 1.3 76.5 - - - +
50H ASP* 1.3 57.6 + - - +
52H ILE* 3.2 9.1 + - - +
53H GLN* 2.8 28.0 + - - +
571Z GLU* 5.4 10.1 - - + +
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Residues in contact with ASP 50 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47H GLN* 2.9 23.5 + - + +
49H GLU* 1.3 75.9 - - - +
51H ASP* 1.3 64.8 + - - +
53H GLN* 3.1 9.9 + - - +
54H GLN* 3.1 22.7 + - - +
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Residues in contact with ASP 51 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47H GLN 2.2 30.6 + - - +
48H VAL* 3.2 12.1 - - - +
50H ASP* 1.3 69.9 - - - +
52H ILE* 1.3 61.6 + - - +
54H GLN* 3.3 5.9 + - - +
55H LEU* 3.2 23.1 + - - +
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Residues in contact with ILE 52 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48H VAL 2.7 16.4 + - - +
49H GLU* 3.5 12.1 - - - +
51H ASP* 1.3 70.1 - - - +
53H GLN* 1.3 61.8 + - - +
55H LEU* 4.2 4.9 - - - +
56H LEU* 3.0 28.1 + - - +
571Z GLU* 4.8 18.6 - - + -
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Residues in contact with GLN 53 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49H GLU 2.8 13.3 + - - +
50H ASP* 3.1 15.2 + - - +
52H ILE* 1.3 77.3 - - - +
54H GLN* 1.3 63.7 + - - +
56H LEU* 3.6 5.1 - - - +
57H LYS* 3.1 22.0 + - - +
69I LYS* 6.1 4.9 - - + -
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Residues in contact with GLN 54 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50H ASP 3.1 9.0 + - - +
51H ASP* 3.3 8.5 + - - +
53H GLN* 1.3 78.4 - - - +
55H LEU* 1.3 63.6 + - - +
57H LYS* 3.1 9.8 + - - +
58H LYS* 2.9 21.2 + - - +
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Residues in contact with LEU 55 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51H ASP 3.2 12.8 + - - +
52H ILE* 4.2 4.7 - - - +
54H GLN* 1.3 76.9 - - - +
56H LEU* 1.3 64.3 - - - +
58H LYS* 3.0 11.5 + - - +
59H ILE* 2.9 20.8 + - - +
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Residues in contact with LEU 56 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52H ILE 3.0 21.7 + - - +
53H GLN* 3.6 6.1 - - - +
55H LEU* 1.3 74.6 - - - +
57H LYS* 1.3 63.8 + - - +
59H ILE* 3.0 24.5 + - - +
60H ASN* 3.6 2.8 + - - +
592Z ASN 4.2 8.6 - - - +
593Z THR* 5.8 0.9 - - - -
596Z ASP* 6.2 3.8 - - + -
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Residues in contact with LYS 57 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53H GLN 3.1 9.6 + - - +
54H GLN* 3.1 11.7 + - - +
56H LEU* 1.3 77.9 - - - +
58H LYS* 1.3 62.3 + - - +
59H ILE 3.2 0.7 + - - -
60H ASN* 3.4 5.9 + - - +
61H GLU* 3.2 19.2 + - - +
76I GLU* 5.5 11.4 - - + -
593Z THR* 5.1 11.6 - - - -
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Residues in contact with LYS 58 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54H GLN 2.9 12.7 + - - +
55H LEU* 3.0 14.8 + - - +
57H LYS* 1.3 73.8 - - - +
59H ILE* 1.3 53.3 + - - +
61H GLU* 3.3 9.1 - - + +
62H LEU* 2.6 37.7 + - - +
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Residues in contact with ILE 59 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55H LEU 2.9 10.5 + - - +
56H LEU* 3.0 15.4 + - - +
58H LYS* 1.3 74.5 - - - +
60H ASN* 1.3 52.8 + - - +
62H LEU* 3.0 8.1 + - - +
63H THR* 2.3 39.7 + - - -
592Z ASN* 4.1 7.6 - - + +
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Residues in contact with ASN 60 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56H LEU 3.6 1.4 + - - +
57H LYS 3.4 6.3 + - - +
59H ILE* 1.3 77.6 - - - +
61H GLU* 1.3 57.2 + - - +
63H THR* 3.6 0.4 - - - -
64H GLY* 2.3 38.5 + - - -
80I ARG* 6.5 0.2 - - - -
589Z SER 3.9 4.7 - - - +
590Z PHE 4.5 1.1 - - - +
592Z ASN* 2.9 32.3 - - + +
593Z THR* 3.3 28.0 - - - +
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Residues in contact with GLU 61 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57H LYS 3.2 12.3 + - - +
58H LYS* 3.3 13.9 - - - +
60H ASN* 1.3 78.2 - - - +
62H LEU* 1.3 64.4 + - - +
64H GLY* 4.2 0.5 - - - -
65H ILE* 3.5 17.3 + - - +
80I ARG* 5.9 7.6 - - + +
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Residues in contact with LEU 62 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58H LYS 2.6 22.0 + - - +
59H ILE* 3.3 5.8 - - - +
61H GLU* 1.3 74.6 - - - +
63H THR* 1.3 66.7 - - - +
65H ILE* 3.4 13.6 + - - +
66H LYS* 3.8 4.3 + - - +
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Residues in contact with THR 63 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59H ILE* 2.3 31.6 + - - -
60H ASN* 2.9 13.2 + - - -
62H LEU* 1.3 65.4 - - - +
64H GLY* 1.3 52.9 + - - -
66H LYS* 2.5 41.8 + - - +
581Z GLU* 5.6 5.4 - - - -
589Z SER* 3.4 17.2 - - - -
592Z ASN* 3.8 13.0 - - - -
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Residues in contact with GLY 64 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60H ASN 2.3 25.4 + - - -
61H GLU 4.2 0.9 - - - -
63H THR* 1.3 66.8 - - - +
65H ILE* 1.3 61.6 + - - +
66H LYS 3.1 1.2 + - - -
68H SER* 3.2 19.8 + - - -
589Z SER* 3.1 22.8 - - - -
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Residues in contact with ILE 65 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61H GLU 3.5 11.2 + - - +
62H LEU* 3.4 12.5 + - - +
63H THR 2.8 2.6 + - - -
64H GLY* 1.3 73.8 - - - +
66H LYS* 1.3 65.7 + - - +
68H SER* 3.2 16.6 - - - -
69H ASP* 3.3 8.7 + - - +
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Residues in contact with LYS 66 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62H LEU 3.8 4.2 + - - +
63H THR* 2.5 24.5 + - - +
65H ILE* 1.3 67.8 - - - +
67H GLU* 1.3 60.1 + - - +
68H SER 3.0 2.9 - - - -
69H ASP* 2.8 29.4 + - - +
70H THR* 3.4 4.0 + - - -
589Z SER* 5.5 0.7 - - - -
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Residues in contact with GLU 67 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63H THR 4.1 1.8 + - - -
64H GLY 4.1 0.2 + - - -
66H LYS* 1.3 76.6 - - - +
68H SER* 1.3 62.9 + - - +
70H THR* 2.8 33.5 + - - -
71H GLY* 3.2 6.8 + - - -
584Z SER* 4.6 19.5 - - - -
585Z GLU 4.6 14.4 - - - +
588Z ARG* 5.6 0.7 - - + -
589Z SER* 4.7 14.4 - - - +
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Residues in contact with SER 68 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64H GLY 3.2 17.6 + - - -
65H ILE* 3.2 16.4 - - - -
67H GLU* 1.3 78.1 - - - +
69H ASP* 1.3 63.4 + - - +
71H GLY* 3.8 5.4 + - - -
72H LEU* 3.9 12.1 + - - +
83I GLU 5.8 3.8 - - - -
618Z GLU* 5.6 12.5 - - - -
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Residues in contact with ASP 69 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65H ILE 3.3 6.6 + - - +
66H LYS* 2.8 15.4 + - - +
68H SER* 1.3 76.4 - - - +
70H THR* 1.3 63.3 + - - +
72H LEU* 3.7 14.3 + - - +
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Residues in contact with THR 70 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66H LYS 3.4 2.5 + - - -
67H GLU* 2.8 26.8 + - - -
69H ASP* 1.3 81.2 - - - +
71H GLY* 1.3 61.7 + - - -
72H LEU 3.2 6.2 + - - +
584Z SER* 6.1 2.7 - - - -
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Residues in contact with GLY 71 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67H GLU 3.2 8.4 + - - -
68H SER 3.8 1.1 + - - -
70H THR* 1.3 79.9 - - - +
72H LEU* 1.3 63.5 + - - +
618Z GLU 6.1 6.1 - - - -
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Residues in contact with LEU 72 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68H SER 3.9 11.1 + - - +
69H ASP* 3.7 13.9 + - - +
70H THR 3.2 8.4 - - - +
71H GLY* 1.3 85.1 - - - +
618Z GLU 6.1 2.9 - - - -
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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
------------------------------------------------------------
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