Contacts of the helix formed by residues 56 - 77 (chain P) 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 THR 56 (chain P).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54P THR* 4.8 2.9 - - - -
55P ARG* 1.3 78.0 - - - +
57P ALA* 1.3 63.1 + - - +
58P SER* 3.4 11.2 - - - -
59P ASP* 2.7 35.3 + - - +
60P MET* 3.3 6.6 + - - +
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Residues in contact with ALA 57 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56P THR* 1.3 74.6 - - - +
58P SER* 1.3 58.1 + - - +
60P MET* 2.8 28.6 + - - +
61P VAL* 3.5 5.9 + - - +
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Residues in contact with SER 58 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5P GLY* 3.4 36.0 + - - -
8P ARG* 3.9 7.0 - - - +
54P THR* 4.8 9.2 - - - -
56P THR* 4.6 7.8 - - - -
57P ALA* 1.3 76.6 - - - +
59P ASP* 1.3 52.9 + - - +
60P MET 3.3 0.2 - - - -
61P VAL* 3.3 11.3 + - - +
62P SER* 2.7 38.5 + - - -
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Residues in contact with ASP 59 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51P GLU* 4.8 6.1 - - - +
54P THR* 4.4 4.2 - - - -
55P ARG* 3.5 20.9 - - - +
56P THR 2.7 42.3 + - - +
58P SER* 1.3 75.6 + - - +
60P MET* 1.3 49.3 + - - -
62P SER* 3.7 8.9 - - - -
63P THR* 2.4 36.1 + - - -
102P ALA* 5.3 0.4 - - - -
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Residues in contact with MET 60 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56P THR 3.3 6.8 + - - +
57P ALA* 2.8 12.6 + - - +
59P ASP* 1.3 74.4 - - - +
61P VAL* 1.3 60.2 + - - +
63P THR* 3.4 7.5 - - - -
64P SER* 2.9 28.1 + - - -
99P GLN* 6.4 1.1 - - + -
101P VAL* 4.2 15.0 - - + -
102P ALA* 4.2 22.2 - - + +
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Residues in contact with VAL 61 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5P GLY 5.4 3.1 - - - +
8P ARG* 5.1 7.9 - - + -
9P ALA* 5.9 4.7 - - + +
57P ALA 3.5 3.5 + - - +
58P SER* 3.3 17.6 + - - +
60P MET* 1.3 75.1 - - - +
62P SER* 1.3 59.5 + - - +
63P THR 3.1 0.9 - - - -
64P SER* 3.3 8.3 + - - -
65P ARG* 2.9 36.3 + - + +
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Residues in contact with SER 62 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8P ARG* 3.6 24.7 + - - +
50P LEU 5.2 1.0 + - - -
51P GLU* 2.7 54.3 - - - +
54P THR* 5.0 5.6 - - - -
58P SER 2.7 27.2 + - - -
59P ASP* 3.7 9.7 - - - -
61P VAL* 1.3 71.4 - - - +
63P THR* 1.3 56.1 + - - +
65P ARG* 4.6 2.2 - - - +
66P ILE 2.9 18.0 + - - +
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Residues in contact with THR 63 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51P GLU* 4.0 5.6 + - - -
59P ASP 2.4 26.8 + - - -
60P MET* 3.4 8.3 - - - -
61P VAL 3.1 0.4 - - - -
62P SER* 1.3 73.9 - - - +
64P SER* 1.3 62.2 + - - +
67P LEU* 2.8 41.9 + - - +
99P GLN* 5.0 1.6 - - - +
102P ALA* 2.6 44.4 - - - +
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Residues in contact with SER 64 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60P MET 2.9 18.5 + - - -
61P VAL* 3.3 11.9 + - - -
63P THR* 1.3 74.4 - - - +
65P ARG* 1.3 61.6 + - - +
67P LEU* 3.8 0.9 - - - +
68P VAL* 2.9 32.3 + - - +
105P VAL* 6.0 5.6 - - - -
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Residues in contact with ARG 65 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8P ARG 5.1 0.7 - - - +
9P ALA* 5.1 12.8 - - + -
12P ARG* 4.3 25.6 - - + -
61P VAL* 2.9 23.8 + - + +
62P SER* 4.5 2.7 - - - +
64P SER* 1.3 76.7 - - - +
66P ILE* 1.3 59.8 + - - +
68P VAL* 3.2 7.0 + - - +
69P ALA* 2.9 29.7 + - - +
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Residues in contact with ILE 66 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12P ARG* 5.8 0.4 - - - +
44P ILE* 6.1 2.7 - - + -
47P LEU* 4.7 19.3 - - + +
48P LEU* 5.2 7.4 - - + +
51P GLU* 2.6 49.2 + - + +
62P SER 2.9 9.1 + - - +
65P ARG* 1.3 74.3 - - - +
67P LEU* 1.3 56.0 + - + +
69P ALA* 3.2 5.4 + - + +
70P VAL* 2.7 46.0 + - + +
90P LEU* 6.2 2.0 - - + -
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Residues in contact with LEU 67 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51P GLU* 5.3 1.3 - - - +
63P THR* 2.8 33.5 + - - +
64P SER* 4.2 0.9 - - - +
66P ILE* 1.3 80.2 - - + +
68P VAL* 1.3 56.9 + - - +
70P VAL* 3.1 15.0 - - + +
71P VAL* 2.8 31.8 - - + +
87P ILE* 5.9 3.6 - - + -
90P LEU* 5.0 22.2 - - + -
91P SER* 5.8 2.0 - - - +
102P ALA* 2.8 35.2 - - + +
103P LYS* 4.7 0.2 - - - -
105P VAL* 5.6 1.8 - - + -
106P GLN* 2.9 32.4 - - + +
109P CYS* 5.1 1.7 - - - +
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Residues in contact with VAL 68 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64P SER 2.9 19.8 + - - +
65P ARG* 3.6 5.8 - - - +
66P ILE 3.1 0.2 - - - -
67P LEU* 1.3 76.7 - - - +
69P ALA* 1.3 54.8 + - - +
71P VAL* 2.5 28.9 - - + +
72P LYS* 2.7 18.6 + - - +
109P CYS* 6.0 1.3 - - - -
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Residues in contact with ALA 69 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16P MET* 6.2 5.4 - - + -
19P ASP* 6.0 4.7 - - + -
47P LEU* 6.0 6.1 - - + -
65P ARG 2.9 16.5 + - - +
66P ILE* 3.9 5.6 - - + +
68P VAL* 1.3 74.2 - - - +
70P VAL* 1.3 57.5 + - - +
72P LYS* 3.3 8.3 - - - +
73P MET* 2.7 35.9 + - - +
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Residues in contact with VAL 70 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44P ILE* 4.9 17.3 - - + -
66P ILE* 2.7 32.6 + - + +
67P LEU* 3.1 35.0 - - + +
69P ALA* 1.3 77.4 - - - +
71P VAL* 1.3 63.0 + - + +
73P MET* 3.4 9.6 + - - +
74P CYS* 3.4 17.2 + - - +
83P LEU* 5.4 3.8 - - - +
87P ILE* 5.0 16.5 - - + +
90P LEU* 5.7 5.4 - - + -
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Residues in contact with VAL 71 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67P LEU* 2.8 19.7 - - + +
68P VAL* 2.5 41.5 - - + +
70P VAL* 1.3 79.8 - - + +
72P LYS* 1.3 59.7 + - + +
74P CYS* 2.2 42.5 - - - -
75P TYR* 3.2 1.7 + - - +
87P ILE* 5.8 6.3 - - + -
106P GLN* 4.6 11.7 - - + +
109P CYS* 4.2 29.4 - - + +
110P THR* 4.7 11.9 - - - -
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Residues in contact with LYS 72 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68P VAL 2.7 18.6 + - - +
69P ALA* 3.3 11.2 - - - +
71P VAL* 1.3 77.7 - - + +
73P MET* 1.3 64.5 + - - +
75P TYR* 3.0 19.0 + - + +
76P GLU* 3.3 12.1 + - - +
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Residues in contact with MET 73 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23P THR* 5.3 5.8 - - - -
40P LEU* 3.7 37.0 - - + +
41P GLN* 4.8 6.1 - - + +
44P ILE* 6.5 0.2 - - + -
69P ALA 2.7 19.2 + - - +
70P VAL* 3.5 9.9 - - - +
72P LYS* 1.3 72.5 - - - +
74P CYS* 1.3 60.0 + - - +
76P GLU* 2.6 32.7 - - + +
77P ALA 4.1 0.3 + - - -
79P GLU* 4.4 13.0 - - + +
83P LEU* 6.3 1.8 - - + -
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Residues in contact with CYS 74 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70P VAL 3.4 7.1 + - - +
71P VAL* 2.2 37.4 + - - +
72P LYS 3.1 0.4 - - - -
73P MET* 1.3 80.7 - - - +
75P TYR* 1.3 63.7 + - - +
78P LYS* 2.5 42.8 + - - +
79P GLU 3.8 11.2 - - - +
80P TRP* 4.7 7.2 - - + -
83P LEU* 4.2 21.3 - - + -
110P THR* 6.6 0.2 - - - -
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Residues in contact with TYR 75 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71P VAL 4.1 6.5 - - - +
72P LYS* 3.0 15.1 + - + +
74P CYS* 1.3 86.1 - - - +
76P GLU* 1.3 68.9 + - - +
77P ALA 4.7 0.2 - - - +
78P LYS* 4.3 6.5 - - - +
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Residues in contact with GLU 76 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23P THR* 4.9 17.3 - - - +
72P LYS 3.3 4.9 + - - +
73P MET* 2.6 37.7 - - + +
75P TYR* 1.3 83.5 - - - +
77P ALA* 1.3 71.8 + - + +
79P GLU* 5.3 1.1 - - + -
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Residues in contact with ALA 77 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75P TYR 4.7 0.2 - - - +
76P GLU* 1.3 85.5 - - + +
78P LYS* 1.3 76.0 + - - +
79P GLU* 3.3 20.5 + - + +
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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