Contacts of the helix formed by residues 51 - 72 (chain A) in PDB entry 2GUT
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 51 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10A TRP* 3.8 17.8 - - - +
49A ALA 3.6 0.4 - - - -
50A LYS* 1.3 98.2 - - + +
52A ARG* 1.3 68.2 + - - +
53A ASP* 2.9 18.0 + - - +
54A GLU* 3.1 18.9 + - - +
55A TYR 3.2 9.7 + - - -
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Residues in contact with ARG 52 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7A GLU* 3.1 28.5 + - - +
8A THR* 3.2 37.9 + - - +
10A TRP* 3.4 49.7 - - + +
15A PHE* 5.3 1.6 - - + -
51A THR* 1.3 77.2 - - - +
53A ASP* 1.3 61.4 + - + +
55A TYR* 4.2 0.7 - - - +
56A LEU* 2.9 46.2 + - + +
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Residues in contact with ASP 53 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A THR* 2.9 10.1 + - - +
52A ARG* 1.3 82.9 - - + +
54A GLU* 1.3 58.7 + - - +
56A LEU* 3.3 5.6 + - - +
57A SER* 2.7 44.9 + - - -
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Residues in contact with GLU 54 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48A LYS* 2.9 23.0 - - - +
49A ALA* 3.3 8.4 - - + -
50A LYS* 3.2 57.5 + - - +
51A THR* 3.1 9.6 + - - +
53A ASP* 1.3 82.4 + - - +
55A TYR* 1.3 58.7 + - - +
57A SER* 3.3 4.9 + - - -
58A LEU* 2.9 46.9 + - + +
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Residues in contact with TYR 55 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A TRP* 3.3 37.5 - + + -
15A PHE* 5.0 7.2 - + - -
16A ARG* 4.3 11.3 + - + +
19A LEU* 3.1 43.5 - - + +
20A VAL 4.4 0.5 + - - -
23A ILE* 3.9 8.3 - - - +
42A GLU* 4.0 17.9 - - - +
45A VAL* 3.4 29.2 - - + -
46A PHE* 3.8 23.3 - + - -
49A ALA* 3.3 9.8 - - + +
51A THR 3.2 4.1 + - - +
52A ARG 4.2 0.4 - - - +
54A GLU* 1.3 73.8 - - - +
56A LEU* 1.3 67.4 + - + +
57A SER 2.9 1.6 + - - -
58A LEU* 3.0 1.9 + - - -
59A VAL* 2.7 59.6 + - + +
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Residues in contact with LEU 56 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15A PHE* 4.0 31.9 - - + -
19A LEU* 4.1 21.1 - - + -
52A ARG* 2.9 33.5 + - + +
53A ASP* 3.8 5.4 - - - +
55A TYR* 1.3 85.2 - - + +
57A SER* 1.3 56.2 + - - +
59A VAL* 4.0 3.8 - - - +
60A ALA* 3.2 28.2 + - - +
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Residues in contact with SER 57 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A ASP* 2.7 27.0 + - - -
54A GLU* 3.4 7.4 - - - -
55A TYR 2.9 0.6 + - - -
56A LEU* 1.3 76.0 - - - +
58A LEU* 1.3 69.6 + - - +
59A VAL 3.3 0.3 + - - -
60A ALA* 3.3 4.8 + - - +
61A ARG* 3.2 24.8 + - - +
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Residues in contact with LEU 58 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45A VAL* 3.6 28.2 - - + +
48A LYS* 4.4 31.0 - - + -
54A GLU* 2.9 35.1 + - + +
57A SER* 1.3 80.4 - - - +
59A VAL* 1.3 61.8 + - - +
61A ARG* 3.7 11.6 + - + +
62A LEU* 3.1 22.5 + - - +
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Residues in contact with VAL 59 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19A LEU* 3.9 15.5 - - + -
23A ILE* 3.4 34.1 - - + -
45A VAL* 3.9 9.0 - - + -
55A TYR* 2.7 70.1 + - + +
56A LEU* 4.0 5.8 - - - +
58A LEU* 1.3 70.1 - - - +
60A ALA* 1.3 67.1 + - - +
62A LEU* 3.0 8.4 + - - +
63A ILE* 2.9 30.3 + - + +
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Residues in contact with ALA 60 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56A LEU 3.2 16.7 + - - +
57A SER* 3.3 4.9 + - - +
59A VAL* 1.3 79.5 - - - +
61A ARG* 1.3 65.0 + - - +
63A ILE* 3.0 9.3 + - - +
64A ILE* 2.8 41.0 + - + +
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Residues in contact with ARG 61 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57A SER* 3.2 14.9 + - - +
58A LEU* 3.8 12.3 - - - +
60A ALA* 1.3 77.0 - - - +
62A LEU* 1.3 57.2 + - - +
64A ILE* 3.7 10.6 - - + +
65A HIS* 2.9 41.7 + - - +
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Residues in contact with LEU 62 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A ILE* 3.3 41.5 - - + -
41A MET* 5.0 19.1 - - + -
45A VAL* 5.4 11.9 - - + -
58A LEU 3.1 11.6 + - - +
59A VAL* 3.0 10.0 + - - +
61A ARG* 1.3 80.5 - - - +
63A ILE* 1.3 66.0 + - + +
65A HIS* 3.3 6.3 + - - +
66A PHE* 3.0 52.7 + - + -
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Residues in contact with ILE 63 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19A LEU* 6.1 0.4 - - + -
22A GLN* 3.8 30.5 - - + +
23A ILE* 3.9 31.2 - - + +
26A ALA* 3.7 13.2 - - + +
59A VAL* 2.9 23.1 + - + +
60A ALA* 3.6 8.7 - - - +
62A LEU* 1.3 78.9 - - + +
64A ILE* 1.3 67.3 + - + +
66A PHE* 3.0 17.8 + - - +
67A ARG* 3.1 37.3 + - - +
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Residues in contact with ILE 64 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60A ALA* 2.8 46.0 + - + +
61A ARG* 3.7 10.3 - - + +
63A ILE* 1.3 73.7 - - + +
65A HIS* 1.3 65.2 + - - +
67A ARG* 3.1 16.9 + - + +
68A ASP* 3.1 23.1 + - + +
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Residues in contact with HIS 65 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A ARG* 2.9 26.6 + - - +
62A LEU* 3.6 7.2 - - - +
64A ILE* 1.3 77.3 - - - +
66A PHE* 1.3 60.9 + - + +
68A ASP* 3.4 8.6 + - + +
69A ILE* 2.9 45.5 + - + +
76A ALA* 4.5 4.2 - - - -
77A SER* 3.1 44.9 + - - -
78A VAL* 5.2 2.0 - - + -
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Residues in contact with PHE 66 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A ILE* 5.2 0.4 - - + -
26A ALA* 4.3 8.3 - - + +
27A MET* 3.2 38.6 - - + -
30A ALA* 3.6 35.9 - - + +
32A VAL* 3.4 25.1 - - + -
41A MET* 4.5 10.1 - - + -
62A LEU* 3.0 57.5 + - + -
63A ILE* 3.0 10.4 + - - +
65A HIS* 1.3 75.0 - - + +
67A ARG* 1.3 64.5 + - - +
68A ASP 3.2 0.2 + - - -
69A ILE* 3.3 12.9 + - + +
70A HIS* 3.2 19.1 + - - +
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Residues in contact with ARG 67 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26A ALA* 4.8 11.7 - - + +
30A ALA* 5.3 1.6 - - - +
63A ILE* 3.1 42.2 + - + +
64A ILE* 3.1 13.2 + - - +
66A PHE* 1.3 75.7 - - - +
68A ASP* 1.3 57.6 + - - +
70A HIS* 3.7 5.6 + - - +
71A ASN* 2.8 30.5 + - - +
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Residues in contact with ASP 68 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64A ILE* 3.1 15.1 + - + +
65A HIS* 3.6 13.5 - - + +
66A PHE 3.1 0.2 - - - -
67A ARG* 1.3 75.6 - - - +
69A ILE* 1.3 67.7 + - - +
71A ASN* 2.9 22.5 + - - +
72A LYS* 3.0 12.6 + - - +
74A SER* 3.6 31.2 + - - -
75A GLN* 4.3 1.0 + - - +
76A ALA* 3.6 21.7 + - + +
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Residues in contact with ILE 69 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30A ALA 5.1 3.6 - - - +
31A GLY 5.7 1.1 - - - +
32A VAL* 5.0 14.4 - - + -
65A HIS* 2.9 35.7 + - + +
66A PHE* 3.3 22.6 + - + +
68A ASP* 1.3 75.6 - - - +
70A HIS* 1.3 61.2 + - - +
72A LYS* 3.6 13.9 + - - +
76A ALA* 3.8 25.7 - - + +
78A VAL* 3.7 31.0 - - + -
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Residues in contact with HIS 70 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29A LYS* 3.1 27.2 + - + +
30A ALA* 3.4 30.9 + - - +
31A GLY* 5.2 1.6 - - - -
66A PHE 3.2 6.0 + - - +
67A ARG* 4.2 4.5 - - - +
68A ASP 3.2 0.6 - - - -
69A ILE* 1.3 77.9 - - - +
71A ASN* 1.3 67.9 + - - +
72A LYS* 3.2 11.1 + - - +
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Residues in contact with ASN 71 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67A ARG 2.8 21.2 + - - +
68A ASP* 2.9 21.2 + - - +
70A HIS* 1.3 78.7 - - - +
72A LYS* 1.3 80.1 + - - +
73A LYS* 4.7 2.1 - - - +
74A SER* 4.7 2.9 + - - -
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Residues in contact with LYS 72 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68A ASP 3.0 9.7 + - - -
69A ILE 3.6 10.9 + - - +
70A HIS* 3.2 9.6 - - - +
71A ASN* 1.3 98.2 - - - +
73A LYS* 1.3 77.2 + - + +
74A SER* 3.1 6.7 + - - +
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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
------------------------------------------------------------
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