Contacts of the helix formed by residues 65 - 79 (chain A) in PDB entry 2A79
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 65 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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61A GLY 6.1 0.7 - - - -
63A GLN 5.5 0.9 - - - +
64A ILE* 1.3 81.8 - - - +
66A ASP* 1.3 54.3 + - - +
67A GLU* 3.5 17.8 + - - +
68A MET* 2.9 22.6 + - + +
69A ALA* 2.7 35.3 + - - +
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Residues in contact with ASP 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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61A GLY* 4.7 6.4 + - - -
64A ILE 5.1 0.7 - - - +
65A THR* 1.3 76.3 - - - +
67A GLU* 1.3 66.8 + - - +
69A ALA* 3.5 8.2 - - - +
70A GLU* 2.8 30.5 + - - +
98A VAL* 3.6 31.9 - - + +
101A ASN* 5.3 5.9 + - - -
102A ILE* 4.8 1.9 - - - +
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Residues in contact with GLU 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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65A THR* 3.1 19.9 + - - +
66A ASP* 1.3 87.2 + - - +
68A MET* 1.3 58.8 + - - +
70A GLU* 3.6 8.2 + - - +
71A HIS* 3.1 25.5 + - - +
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Residues in contact with MET 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* 3.8 15.3 - - + -
65A THR* 2.9 23.5 + - - +
67A GLU* 1.3 79.0 - - - +
69A ALA* 1.3 56.0 + - - +
71A HIS* 3.2 16.6 + - - +
72A LEU* 2.7 45.6 + - + +
325A SER 3.2 27.6 - - - +
326A ASN* 3.8 14.6 - - + +
327A ALA* 4.2 13.7 - - + +
328A GLU* 5.7 1.6 - - - +
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Residues in contact with ALA 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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60A PHE* 4.0 18.6 - - + -
61A GLY 5.7 0.2 - - - +
64A ILE* 3.7 16.3 - - + +
65A THR 2.7 15.7 + - - +
66A ASP* 3.5 5.6 - - - +
68A MET* 1.3 75.2 - - - +
70A GLU* 1.3 62.5 + - - +
72A LEU* 3.1 4.2 + - - +
73A MET* 2.9 20.1 + - - +
98A VAL* 3.6 28.7 - - + -
102A ILE* 3.5 10.3 - - + +
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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 ASP 2.8 17.9 + - - +
67A GLU* 3.7 9.4 - - - +
68A MET 3.2 0.2 - - - -
69A ALA* 1.3 77.9 - - - +
71A HIS* 1.3 53.9 + - - +
73A MET* 3.4 1.4 + - - +
74A THR* 2.7 44.8 + - - +
102A ILE* 3.5 29.8 - - + +
105A LYS* 2.8 43.3 + - - +
106A LYS* 4.1 18.1 + - + +
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Residues in contact with HIS 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 GLU 3.1 15.1 + - - +
68A MET* 3.4 16.4 - - - +
69A ALA 3.2 0.2 - - - -
70A GLU* 1.3 76.5 - - - +
72A LEU* 1.3 66.6 + - - +
74A THR* 3.4 4.5 + - - -
75A LEU* 2.9 59.7 + - + +
327A ALA* 3.2 35.8 - - + +
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Residues in contact with LEU 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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54A LEU* 4.1 14.4 - - + -
60A PHE* 4.9 6.5 - - + -
64A ILE* 3.7 23.3 - - + -
68A MET* 2.7 28.6 + - + +
69A ALA* 3.5 4.9 - - - +
71A HIS* 1.3 73.9 - - - +
73A MET* 1.3 61.1 + - - +
75A LEU* 3.4 0.8 + - + -
76A ALA* 3.1 20.6 + - - +
324A ALA* 3.1 30.7 - - + +
325A SER 4.4 2.2 - - - -
326A ASN 3.4 23.3 - - - +
327A ALA* 3.7 17.5 - - + -
330A LEU* 3.3 30.4 - - + +
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Residues in contact with MET 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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54A LEU* 4.0 10.5 - - + +
60A PHE* 4.3 9.6 - - + -
69A ALA 2.9 14.1 + - - +
70A GLU 3.9 3.1 - - - +
72A LEU* 1.3 73.2 - - - +
74A THR* 1.3 61.8 + - - +
76A ALA* 3.3 2.0 + - - +
77A TYR* 2.8 32.1 + - - +
84A PHE* 3.4 52.3 - - + -
99A LEU* 3.2 28.0 - - + -
102A ILE* 3.8 27.8 - - + -
103A ILE* 4.4 7.2 - - + -
108A TRP* 3.4 25.6 - - + -
113A LEU* 4.2 8.5 - - + -
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Residues in contact with THR 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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70A GLU* 2.7 24.2 + - - +
71A HIS* 3.9 6.0 - - - -
73A MET* 1.3 75.1 - - - +
75A LEU* 1.3 69.5 + - + +
77A TYR* 3.2 1.4 + - - +
78A ASP* 2.8 48.9 + - - +
106A LYS* 3.1 43.7 + - - +
108A TRP* 3.9 11.5 - - + +
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Residues in contact with LEU 75 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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71A HIS* 2.9 64.2 + - + +
72A LEU* 3.6 4.5 - - - +
74A THR* 1.3 80.5 - - + +
76A ALA* 1.3 64.1 + - - +
78A ASP* 3.2 4.9 + - - +
79A ASN* 2.9 32.9 + - - +
327A ALA* 4.1 14.6 - - + +
330A LEU* 4.1 10.5 - - + -
331A MET* 3.7 36.1 - - + -
334A ILE* 5.3 0.4 - - - -
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Residues in contact with ALA 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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54A LEU* 4.2 10.1 - - + -
72A LEU 3.1 15.4 + - - +
73A MET 3.5 3.8 - - - +
75A LEU* 1.3 78.4 - - - +
77A TYR* 1.3 63.1 + - - +
79A ASN* 3.3 9.8 + - - -
80A GLY 3.4 0.3 + - - -
81A ILE* 3.0 52.7 + - + +
84A PHE* 4.1 14.4 - - + -
330A LEU* 4.2 9.6 - - + +
334A ILE* 4.8 2.5 - - - -
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Residues in contact with TYR 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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73A MET 2.8 21.3 + - - +
74A THR 3.5 3.4 - - - +
76A ALA* 1.3 69.6 - - - +
78A ASP* 1.3 64.4 + - - +
79A ASN 2.9 3.8 - - - -
80A GLY* 2.6 29.8 + - - -
81A ILE 3.6 15.4 - - - +
82A ASN* 5.9 0.7 - - - -
84A PHE* 4.4 4.0 - + + -
108A TRP* 3.3 55.8 - + + +
109A ARG* 4.6 7.1 + - - -
112A SER* 2.8 33.0 + - - -
113A LEU* 3.7 28.9 - - + -
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Residues in contact with ASP 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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74A THR* 2.8 41.6 + - - +
75A LEU* 3.8 5.7 + - - +
77A TYR* 1.3 84.7 - - - +
79A ASN* 1.3 62.0 + - - +
80A GLY 3.2 1.4 + - - -
108A TRP* 4.8 2.6 + - - -
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Residues in contact with ASN 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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38A PHE* 3.7 14.7 - - - -
75A LEU* 2.9 24.4 + - - +
76A ALA 3.8 4.7 - - - +
77A TYR 2.8 2.2 + - - -
78A ASP* 1.3 82.5 - - - +
80A GLY* 1.3 58.6 + - - +
81A ILE* 3.5 4.2 + - + +
331A MET* 4.0 30.5 - - - +
334A ILE* 4.3 27.3 - - + +
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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
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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