Contacts of the helix formed by residues 58 - 77 (chain J) in PDB entry 2GTL
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 HIS 58 (chain J).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52J HIS* 3.2 44.8 + + + -
55J ASP* 2.9 30.3 + - + +
56J THR 3.4 0.2 - - - -
57J SER* 1.3 77.1 - - - +
59J PRO* 1.3 87.3 - - + +
60J ALA* 2.7 45.0 + - + +
61J PHE* 2.8 14.4 + - - -
62J ILE* 2.9 10.9 + - - -
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Residues in contact with PRO 59 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57J SER 3.5 5.6 - - - +
58J HIS* 1.3 104.9 - - + +
60J ALA* 1.3 62.5 + - - +
62J ILE* 3.0 11.9 + - + +
63J ALA* 2.8 26.4 + - - +
87K ASP* 4.9 0.4 - - - +
89K PRO* 3.8 21.1 - - + +
90K ALA* 3.7 32.4 - - + +
93K ALA* 4.7 2.2 - - + -
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Residues in contact with ALA 60 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51J VAL* 3.1 21.2 - - + +
52J HIS* 3.9 16.8 - - + +
58J HIS* 2.7 29.5 + - + +
59J PRO* 1.3 73.4 - - - +
61J PHE* 1.3 56.7 + - - +
63J ALA* 3.3 4.5 - - - +
64J HIS 3.0 21.5 + - - -
67J ARG* 4.7 0.9 + - - -
93K ALA* 4.3 15.4 - - + +
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Residues in contact with PHE 61 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31J GLN* 5.2 1.6 - - - -
34J TRP* 3.7 34.5 - + + -
38J PHE* 3.6 32.1 - + - -
48J PHE* 4.6 3.6 - - + -
51J VAL* 3.5 18.3 + - + +
52J HIS 3.4 21.8 - - - +
53J GLY* 4.3 5.4 - - - -
55J ASP 4.0 4.0 - - - +
56J THR* 3.0 45.3 - - - -
58J HIS* 2.8 14.5 + - - +
60J ALA* 1.3 72.3 - - - +
62J ILE* 1.3 56.2 + - - +
63J ALA 3.1 0.2 - - - -
64J HIS* 3.0 27.7 + + - +
65J ALA* 2.7 37.4 + - + +
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Residues in contact with ILE 62 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27J GLU* 4.0 35.4 - - + +
30J SER* 5.2 1.2 + - - +
31J GLN* 3.6 42.4 - - + +
56J THR 3.9 4.7 - - - +
57J SER* 4.0 13.0 - - - +
58J HIS 2.9 16.6 + - - +
59J PRO* 3.3 11.4 - - + +
61J PHE* 1.3 75.8 - - + +
63J ALA* 1.3 63.2 + - - +
65J ALA* 3.4 6.4 + - + +
66J ASP* 2.9 24.2 + - - +
84K LEU* 4.9 6.5 - - + -
87K ASP* 5.3 2.0 - - - +
90K ALA* 4.1 17.7 - - + -
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Residues in contact with ALA 63 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59J PRO 2.8 10.8 + - - +
60J ALA 3.3 10.8 - - - +
62J ILE* 1.3 81.1 - - - +
64J HIS* 1.3 64.8 + - - +
66J ASP* 3.1 2.0 + - - +
67J ARG* 2.7 39.1 + - - +
80K LEU* 5.0 0.9 - - - +
84K LEU* 4.5 11.2 - - - -
90K ALA* 4.2 4.7 - - - +
93K ALA* 4.4 3.4 - - + -
94K ALA* 4.0 28.7 - - + +
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Residues in contact with HIS 64 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34J TRP* 4.1 3.7 - + - -
48J PHE* 3.2 20.6 - + - -
51J VAL* 3.4 26.0 - - + +
60J ALA 3.0 1.8 + - - -
61J PHE* 3.0 35.6 + + - +
63J ALA* 1.3 78.4 - - - +
65J ALA* 1.3 59.0 + - - +
67J ARG* 2.9 28.9 + - - +
68J VAL* 2.8 43.0 + - + +
160J HEM 3.8 36.8 + - + +
161J CMO 3.2 22.9 + - - -
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Residues in contact with ALA 65 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30J SER* 3.9 15.5 - - - +
31J GLN* 5.0 2.0 - - - +
34J TRP* 3.5 35.9 - - + +
61J PHE* 2.7 24.6 + - + +
62J ILE* 3.6 8.7 - - + +
64J HIS* 1.3 72.8 - - - +
66J ASP* 1.3 56.6 + - - +
68J VAL* 2.8 22.8 + - - +
69J LEU* 3.0 19.5 + - - +
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Residues in contact with ASP 66 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20J TYR* 4.3 2.6 + - - -
23J GLY 5.2 0.7 - - - +
26J ARG* 3.3 31.0 + - - +
27J GLU* 3.7 29.8 + - - +
30J SER* 4.3 9.0 + - - +
62J ILE* 2.9 15.0 + - - +
63J ALA* 3.6 3.8 - - - +
65J ALA* 1.3 79.1 - - - +
67J ARG* 1.3 60.2 + - - +
69J LEU* 3.9 5.0 + - - +
70J GLY* 3.3 17.0 + - - -
80K LEU* 3.7 22.5 - - + +
83K ASN* 5.2 2.3 - - - +
84K LEU* 3.8 24.4 - - + +
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Residues in contact with ARG 67 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50J ARG* 4.9 2.4 - - - +
51J VAL* 4.5 7.3 - - - +
60J ALA 4.7 1.2 + - - -
63J ALA* 2.7 26.4 + - - +
64J HIS* 3.1 57.1 + - - +
66J ASP* 1.3 73.7 - - - +
68J VAL* 1.3 63.7 + - + +
70J GLY* 3.3 8.9 + - - -
71J GLY 3.5 6.8 + - - -
160J HEM 3.9 36.9 + - + +
80K LEU* 4.2 24.2 - - + +
93K ALA 5.2 0.8 + - - -
94K ALA* 4.6 5.5 - - - +
97K HIS* 3.6 55.3 + - - +
98K LEU* 6.1 3.4 - - - -
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Residues in contact with VAL 68 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34J TRP* 4.3 4.7 - - + +
64J HIS* 2.8 38.7 + - + +
65J ALA* 2.8 8.1 + - - +
67J ARG* 1.3 74.6 - - - +
69J LEU* 1.3 71.8 + - + +
70J GLY 2.9 1.1 - - - -
71J GLY* 2.8 15.1 + - - -
72J LEU* 3.2 9.0 + - + +
109J PHE* 4.2 19.3 - - + -
160J HEM 3.7 40.8 - - + +
161J CMO 3.2 28.7 - - - +
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Residues in contact with LEU 69 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16J TRP* 3.7 26.4 - - + -
20J TYR* 3.9 22.7 - - + +
26J ARG* 5.8 0.4 - - + -
29J PHE* 3.9 16.6 - - + -
30J SER* 3.5 28.0 - - - -
33J ILE* 4.0 15.3 - - + -
34J TRP* 4.4 9.6 - - + +
65J ALA 3.0 18.3 + - - +
66J ASP* 4.1 4.5 - - - +
68J VAL* 1.3 84.9 - - + +
70J GLY* 1.3 52.1 + - - +
72J LEU* 3.0 15.9 + - + +
73J ASP* 2.7 36.0 + - - +
109J PHE* 5.4 6.1 - - + -
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Residues in contact with GLY 70 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20J TYR* 3.8 10.7 + - - -
66J ASP 3.3 11.3 + - - -
67J ARG* 3.6 7.2 - - - -
68J VAL 2.9 1.8 - - - -
69J LEU* 1.3 77.9 - - - +
71J GLY* 1.3 62.3 + - - +
73J ASP* 3.0 19.3 + - - +
74J ILE* 3.1 11.1 + - - +
76K ASN* 3.6 22.1 + - - -
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Residues in contact with GLY 71 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67J ARG 3.5 6.7 + - - -
68J VAL 2.8 12.9 + - - -
70J GLY* 1.3 67.5 - - - -
72J LEU* 1.3 64.2 + - - -
74J ILE* 2.9 19.5 + - - +
75J ALA* 2.9 21.8 + - - +
88J GLU* 4.3 11.3 - - - +
92J LEU* 4.8 4.3 - - - -
160J HEM 4.6 17.0 - - - +
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Residues in contact with LEU 72 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16J TRP* 3.7 27.1 - - + -
68J VAL* 3.2 7.5 + - + +
69J LEU* 3.0 20.5 + - + +
71J GLY* 1.3 73.5 - - - +
73J ASP* 1.3 62.8 + - - +
75J ALA* 3.3 4.2 + - - +
76J ILE* 2.9 43.9 + - + +
109J PHE* 5.1 4.0 - - + -
113J ILE* 3.5 27.4 - - + -
134J ILE* 4.1 12.6 - - + -
137J ILE* 4.1 22.0 - - + -
160J HEM 3.9 24.6 - - + +
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Residues in contact with ASP 73 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16J TRP* 3.2 24.9 + - + +
20J TYR* 3.6 28.4 - - + +
69J LEU 2.7 15.5 + - - +
70J GLY* 3.0 13.0 - - - +
72J LEU* 1.3 71.6 - - - +
74J ILE* 1.3 68.8 + - - +
75J ALA 2.9 0.9 + - - -
76J ILE* 4.8 0.2 - - - -
77J SER* 2.6 37.7 + - - -
28K SER* 5.4 1.4 + - - -
32K LYS* 3.1 27.4 + - - -
76K ASN* 3.6 7.1 + - - +
79K ASP* 5.3 0.7 - - - +
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Residues in contact with ILE 74 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70J GLY 3.4 12.8 - - - +
71J GLY* 2.9 12.6 + - - +
73J ASP* 1.3 73.1 - - - +
75J ALA* 1.3 59.9 + - - +
77J SER* 2.8 17.5 + - - -
78J THR* 2.8 22.1 + - + +
84J THR* 6.2 0.4 - - + -
88J GLU* 3.5 41.5 - - + +
69K ALA* 5.1 1.6 - - - +
72K LEU* 3.5 31.2 - - + -
73K ARG* 3.9 30.5 - - + +
76K ASN* 4.3 18.2 - - - +
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Residues in contact with ALA 75 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71J GLY 2.9 11.6 + - - +
72J LEU* 3.4 11.7 - - - +
73J ASP 2.9 0.4 + - - -
74J ILE* 1.3 74.9 - - - +
76J ILE* 1.3 66.3 + - - +
78J THR* 2.9 18.5 + - - -
79J LEU* 3.5 4.5 + - - +
85J LEU* 3.5 22.4 - - + +
88J GLU* 4.3 7.3 - - + +
89J LEU* 4.4 5.2 - - + -
92J LEU* 5.3 2.7 - - + -
137J ILE* 3.5 35.2 - - + -
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Residues in contact with ILE 76 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12J VAL* 4.2 6.3 - - + -
13J LYS* 3.7 34.7 - - - +
16J TRP* 3.4 50.0 - - + -
72J LEU* 2.9 30.8 + - + +
73J ASP 3.8 1.3 - - - +
75J ALA* 1.3 75.5 - - - +
77J SER* 1.3 55.3 + - - +
78J THR 2.6 12.8 + - - -
79J LEU* 2.9 35.3 + - + +
130J TRP* 4.5 9.0 - - + -
133J CYS* 6.4 0.2 - - + -
134J ILE* 4.5 4.9 - - + -
137J ILE* 3.5 17.7 - - + +
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Residues in contact with SER 77 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13J LYS* 3.4 25.5 + - - +
16J TRP* 5.5 1.5 - - - -
73J ASP* 2.6 40.0 + - - -
74J ILE* 2.8 19.8 + - - +
76J ILE* 1.3 70.5 - - - +
78J THR* 1.3 59.4 + - - +
79J LEU 3.8 0.2 - - - -
80J ASP* 3.9 0.2 - - - +
28K SER* 4.4 15.5 - - - -
29K SER* 3.2 27.6 + - - -
32K LYS* 5.8 1.1 + - - -
72K LEU* 4.8 3.5 - - - +
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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
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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