Contacts of the helix formed by residues 60 - 79 (chain A) in PDB entry 2GB0
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 GLU 60 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58A GLY* 3.0 2.6 + - - -
59A ARG* 1.3 114.4 + - - +
61A TYR* 1.3 62.2 + - - +
63A PRO* 3.2 11.4 - - - +
64A LEU* 3.6 13.2 + - - +
369A ASP* 3.8 37.4 - - - +
371A SER* 4.1 5.0 + - - +
372A ILE* 3.3 54.0 - - + +
373A PHE* 5.1 4.3 - - + -
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Residues in contact with TYR 61 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A TYR* 3.5 21.8 - + + -
57A GLU* 3.5 17.5 - - + -
58A GLY* 2.9 32.3 + - - +
60A GLU* 1.3 76.4 - - - +
62A VAL* 1.3 58.6 + - - +
64A LEU* 3.3 3.4 + - + -
65A ALA* 2.7 31.0 + - - +
324A HIS* 2.7 46.8 + - - -
325A PHE* 3.7 20.4 + + - -
345A HIS* 3.7 16.9 - + - -
349A PHE* 3.5 24.2 - + + -
372A ILE* 3.7 12.3 - - + -
373A PHE* 3.5 29.8 - + - -
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Residues in contact with VAL 62 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A HIS 3.6 25.8 - - - +
54A ALA* 5.0 0.4 - - - -
55A TYR 4.1 20.0 - - - +
59A ARG* 3.0 6.2 + - - +
61A TYR* 1.3 75.1 - - - +
63A PRO* 1.4 70.1 - - + +
65A ALA* 2.9 5.1 + - - +
66A LEU* 2.8 39.6 + - + +
107A ALA* 4.7 4.3 - - + +
111A HIS* 3.5 51.8 - - + +
113A LEU* 4.5 5.8 - - + -
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Residues in contact with PRO 63 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A ARG* 2.9 52.5 - - - +
60A GLU 3.2 10.5 - - - +
62A VAL* 1.4 83.9 - - + +
64A LEU* 1.3 56.3 + - - +
66A LEU* 3.3 8.9 + - + +
67A ARG* 2.9 31.6 + - - +
111A HIS* 4.8 4.0 - - + +
368A HIS* 5.7 3.1 - - + -
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Residues in contact with LEU 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 GLU 3.6 11.9 + - - +
61A TYR* 3.3 7.6 + - + +
62A VAL 3.2 0.8 - - - -
63A PRO* 1.3 78.6 - - - +
65A ALA* 1.3 58.3 + - - +
67A ARG* 3.5 2.4 + - + -
68A SER* 2.8 36.3 + - - +
325A PHE* 5.1 2.2 - - + -
327A ILE* 5.2 2.2 - - + -
349A PHE* 3.7 29.6 - - + -
352A GLY* 4.1 24.9 - - - +
353A VAL* 4.4 11.4 - - + +
356A VAL* 4.5 7.0 - - + -
368A HIS* 3.7 29.8 - - + +
370A ILE* 6.0 2.7 - - + -
373A PHE* 4.3 26.5 - - + -
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Residues in contact with ALA 65 (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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51A ILE* 4.1 7.3 - - + +
52A ARG 3.8 22.0 - - - +
53A HIS* 4.2 13.3 - - + +
55A TYR* 5.3 1.3 - - + -
61A TYR 2.7 18.5 + - - +
62A VAL* 3.4 8.3 - - - +
64A LEU* 1.3 78.3 - - - +
66A LEU* 1.3 57.9 + - - +
68A SER* 3.3 3.9 + - - -
69A GLN* 2.9 28.3 + - - +
348A LYS* 5.5 1.1 - - + -
349A PHE* 3.7 19.7 - - + -
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Residues in contact with LEU 66 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A HIS* 3.9 36.3 - - + +
62A VAL* 2.8 35.6 + - + +
63A PRO* 3.9 7.2 - - + +
65A ALA* 1.3 73.2 - - - +
67A ARG* 1.3 67.0 + - - +
69A GLN* 3.3 7.0 + - + +
70A GLU* 3.0 22.0 + - - +
111A HIS* 5.9 1.3 - - + +
113A LEU* 4.4 16.4 - - + -
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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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63A PRO 2.9 17.0 + - - +
64A LEU* 3.9 4.7 - - + +
66A LEU* 1.3 78.3 - - - +
68A SER* 1.3 63.4 + - - +
70A GLU* 3.1 28.3 + - - +
71A LEU* 2.9 48.1 + - + +
74A GLU* 4.2 8.3 + - - -
352A GLY* 4.9 2.5 - - - -
355A GLU* 2.9 42.3 + - - +
367A GLU* 5.9 0.2 + - - -
368A HIS* 3.8 18.2 - - + +
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Residues in contact with SER 68 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A ILE* 4.6 0.2 - - - -
64A LEU* 2.8 24.4 + - - +
65A ALA* 3.7 6.1 - - - -
67A ARG* 1.3 78.3 - - - +
69A GLN* 1.3 52.0 + - - +
71A LEU* 3.0 1.9 + - - -
72A TRP* 2.8 40.3 + - - -
348A LYS 3.3 21.1 - - - -
349A PHE* 3.4 12.4 + - - +
351A SER* 3.1 18.1 + - - -
352A GLY* 3.1 23.2 + - - +
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Residues in contact with GLN 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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51A ILE* 3.3 22.3 - - + +
53A HIS* 2.8 38.0 + - + +
65A ALA 2.9 14.4 + - - +
66A LEU* 3.5 11.7 - - + +
67A ARG 3.2 0.2 - - - -
68A SER* 1.3 76.6 - - - +
70A GLU* 1.3 62.9 + - - +
72A TRP* 3.1 13.9 + - - +
73A TYR* 3.0 54.2 + - + -
84A PHE* 3.5 32.8 - - - -
143A ASN 4.6 2.0 - - - +
144A SER* 4.4 0.9 - - - -
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Residues in contact with GLU 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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66A LEU 3.0 13.5 + - - +
67A ARG* 3.1 31.4 + - - +
69A GLN* 1.3 76.4 - - - +
71A LEU* 1.3 57.1 + - - +
73A TYR* 3.1 16.9 + - - +
74A GLU* 2.9 50.7 + - - +
77A LYS* 5.9 0.3 + - - -
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Residues in contact with LEU 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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20A TYR* 6.2 1.8 - - + -
21A GLN* 4.3 14.1 - - - +
24A LYS* 5.8 2.9 - - - +
67A ARG* 2.9 55.5 + - + +
68A SER 3.4 7.2 - - - +
70A GLU* 1.3 77.4 - - - +
72A TRP* 1.3 57.6 + - - +
74A GLU* 3.2 22.6 + - + +
75A LEU* 2.9 27.5 + - - +
156A TYR* 4.6 5.3 + - - +
351A SER* 3.5 42.2 - - - +
352A GLY* 3.8 9.6 - - - +
355A GLU* 4.3 9.4 - - + +
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Residues in contact with TRP 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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51A ILE* 3.7 13.2 - - + -
68A SER 2.8 28.0 + - - -
69A GLN* 3.1 12.1 + - - +
71A LEU* 1.3 70.7 - - - +
73A TYR* 1.3 62.4 + - - +
75A LEU* 3.1 14.8 + - + +
76A GLU* 2.9 28.1 + - - +
83A ILE* 3.8 8.6 - - + +
84A PHE* 5.0 3.8 - - + -
147A LEU* 3.4 32.3 - - + +
152A CYS* 3.4 38.6 - - + -
156A TYR* 3.7 22.7 - + - -
347A PHE* 3.7 18.8 - + - -
348A LYS 3.0 19.2 + - - -
350A SER* 3.3 27.6 - - - -
351A SER* 3.4 25.8 + - - -
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Residues in contact with TYR 73 (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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69A GLN* 3.0 43.2 + - + -
70A GLU* 3.5 20.0 - - - +
72A TRP* 1.3 76.3 - - - +
74A GLU* 1.3 61.8 + - - +
76A GLU* 3.4 14.5 + - + +
77A LYS* 3.3 35.7 + - - +
84A PHE* 3.3 39.8 - + + -
86A LYS* 4.0 16.6 - - - +
143A ASN 4.5 3.4 + - - -
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Residues in contact with GLU 74 (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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20A TYR* 5.4 1.2 + - - +
24A LYS* 4.8 9.2 + - - -
67A ARG* 4.2 8.8 + - - -
70A GLU* 2.9 40.6 + - - +
71A LEU* 3.5 30.8 - - + +
72A TRP 3.1 0.2 - - - -
73A TYR* 1.3 78.1 - - - +
75A LEU* 1.3 62.5 + - - +
77A LYS* 3.1 21.0 + - + +
78A GLU* 3.2 33.6 + - - +
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Residues in contact with LEU 75 (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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20A TYR* 5.4 0.4 - - + -
71A LEU 2.9 14.0 + - - +
72A TRP* 3.5 35.7 - - + +
74A GLU* 1.3 77.4 - - - +
76A GLU* 1.3 61.6 + - - +
78A GLU* 3.0 17.1 + - - +
79A THR* 3.2 17.7 + - + +
83A ILE* 3.7 28.3 - - + -
152A CYS* 4.0 13.9 - - - +
155A ALA* 4.0 9.0 - - + -
156A TYR* 3.9 28.3 - - + -
159A LEU* 3.6 30.3 - - + -
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Residues in contact with GLU 76 (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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72A TRP 2.9 12.7 + - - +
73A TYR* 3.4 20.1 - - + +
75A LEU* 1.3 76.9 - - - +
77A LYS* 1.3 63.0 + - + +
79A THR 3.3 17.0 - - - +
81A HIS 3.6 10.6 - - - +
82A LYS* 3.6 15.1 + - - +
83A ILE* 2.9 30.7 + - + +
84A PHE* 2.8 40.7 + - + +
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Residues in contact with LYS 77 (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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70A GLU* 5.9 0.6 + - - -
73A TYR* 3.3 23.7 + - - +
74A GLU* 3.1 14.5 + - + +
76A GLU* 1.3 78.8 - - + +
78A GLU* 1.3 63.0 + - + +
79A THR 4.7 1.1 - - - +
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Residues in contact with GLU 78 (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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20A TYR* 2.6 38.2 + - - -
24A LYS* 5.1 2.8 + - - +
74A GLU* 3.3 31.3 - - - +
75A LEU* 3.0 9.6 + - - +
77A LYS* 1.3 82.9 - - + +
79A THR* 1.3 58.3 + - - +
159A LEU* 3.9 27.9 - - + +
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Residues in contact with THR 79 (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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75A LEU* 3.2 16.8 + - + +
76A GLU 3.3 15.7 - - - +
77A LYS 4.7 1.2 - - - +
78A GLU* 1.3 79.2 + - - +
80A HIS* 1.3 69.3 + - - +
81A HIS* 3.2 43.4 + - - +
83A ILE* 4.0 8.1 - - + -
155A ALA* 3.7 26.1 - - + +
158A GLU* 4.5 1.6 + - - -
159A LEU* 4.7 8.5 - - - -
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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) + - + + + + + -
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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