Contacts of the helix formed by residues 61 - 76 (chain A) in PDB entry 2AX1
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 ASP 61 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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60A LEU* 1.3 73.9 - - - +
62A ASP* 1.3 65.1 + - - +
63A HIS* 4.1 15.2 - - + -
64A TYR* 3.2 10.7 + - - +
65A ARG* 3.1 35.7 + - - +
345A ARG* 3.1 30.3 + - - +
346A TYR* 2.6 29.9 + - - -
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Residues in contact with ASP 62 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A ASP* 1.3 74.8 - - - +
63A HIS* 1.3 58.4 + - + +
65A ARG* 2.7 33.9 + - - +
66A ASP* 2.7 49.0 + - - +
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Residues in contact with HIS 63 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A ASP* 3.4 10.4 + - - +
62A ASP* 1.3 80.1 - - + +
64A TYR* 1.3 63.1 + - - +
66A ASP* 3.3 10.8 + - - +
67A VAL* 3.1 30.5 + - - +
301A ALA* 3.7 21.8 - - + +
304A ARG* 3.7 28.3 + - + +
305A ALA* 3.8 30.3 - - + -
307A LYS* 5.9 2.4 + - - -
346A TYR* 3.9 7.2 - - - +
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Residues in contact with TYR 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 LEU* 3.6 46.5 - - + +
61A ASP* 3.2 21.4 + - - +
62A ASP 3.2 0.4 - - - -
63A HIS* 1.3 79.3 - - - +
65A ARG* 1.3 66.0 + - + +
68A LEU* 3.1 41.0 + - + +
231A ASN* 4.9 0.5 + - - -
232A ASP* 4.1 11.4 + - - -
235A VAL* 3.7 22.1 - - + +
297A LEU* 3.5 40.6 - - + +
298A LYS* 4.4 20.2 - - + -
301A ALA* 3.6 9.8 - - - +
346A TYR* 4.0 22.4 - + + -
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Residues in contact with ARG 65 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A LEU* 3.1 30.6 + - + +
61A ASP* 3.1 21.6 + - - +
62A ASP* 2.7 41.7 + - - +
64A TYR* 1.3 84.5 - - + +
66A ASP* 1.3 62.6 + - - +
68A LEU* 3.4 8.3 + - + +
69A LYS* 2.9 30.4 + - - +
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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
----------------------------------------------------------
62A ASP* 2.7 33.3 + - - +
63A HIS* 3.7 12.7 + - - +
65A ARG* 1.3 74.3 - - - +
67A VAL* 1.3 63.7 + - - +
69A LYS* 3.3 9.6 + - - +
70A GLU* 3.1 31.6 + - - +
304A ARG* 3.8 17.8 + - - +
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Residues in contact with VAL 67 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A HIS 3.1 17.3 + - - +
66A ASP* 1.3 74.3 - - - +
68A LEU* 1.3 63.7 + - - +
70A GLU* 3.1 12.8 + - + +
71A MET* 2.9 35.4 + - + +
296A TYR* 4.6 3.8 - - + -
297A LEU* 3.7 22.0 - - + +
300A SER* 3.7 20.6 - - - +
301A ALA* 3.7 23.3 - - - +
304A ARG* 3.8 25.4 - - - +
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Residues in contact with LEU 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 TYR* 3.1 32.2 + - + +
65A ARG* 3.7 7.6 - - + +
67A VAL* 1.3 76.2 - - - +
69A LYS* 1.3 64.3 + - - +
71A MET* 3.3 4.4 + - + +
72A LYS* 3.0 51.1 + - + +
235A VAL* 3.7 39.7 - - + -
239A ILE* 4.0 18.8 - - + -
297A LEU* 3.5 14.3 - - + +
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Residues in contact with LYS 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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65A ARG 2.9 18.1 + - - +
66A ASP* 3.5 10.3 - - - +
68A LEU* 1.3 77.4 - - - +
70A GLU* 1.3 64.3 + - + +
72A LYS* 3.2 11.1 + - - +
73A ALA* 3.1 20.8 + - + +
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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* 3.1 15.2 + - - +
67A VAL* 3.1 8.6 + - - +
69A LYS* 1.3 76.6 - - + +
71A MET* 1.3 63.1 + - + +
73A ALA* 3.2 16.9 + - - +
74A LYS* 3.3 31.2 + - - +
304A ARG* 2.9 41.9 + - - -
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Residues in contact with MET 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 VAL* 2.9 22.0 + - + +
68A LEU* 3.5 8.7 - - - +
70A GLU* 1.3 77.2 - - + +
72A LYS* 1.3 62.6 + - - +
74A LYS* 3.2 8.3 + - - +
75A ALA* 3.1 21.7 + - - +
186A VAL* 3.7 25.1 - - + +
239A ILE* 4.0 21.5 - - + -
293A LEU* 3.7 44.9 - - + +
296A TYR* 3.8 26.2 - - + -
297A LEU* 3.7 28.9 - - + -
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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 LEU* 3.0 46.8 + - + +
69A LYS* 3.6 10.1 - - - +
71A MET* 1.3 75.9 - - - +
73A ALA* 1.3 61.1 + - - +
75A ALA* 3.2 6.0 + - - +
76A SER* 2.9 29.5 + - - -
238A SER* 3.3 33.2 + - - -
239A ILE* 4.4 9.0 - - + -
242A CYS* 3.6 25.0 - - - -
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Residues in contact with ALA 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 LYS* 3.1 11.7 + - + +
70A GLU* 3.4 13.7 - - - +
71A MET 3.2 0.2 - - - -
72A LYS* 1.3 78.3 - - - +
74A LYS* 1.3 60.4 + - + +
76A SER* 3.6 17.8 + - - -
77A THR* 3.8 10.7 - - - +
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Residues in contact with LYS 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* 3.3 25.5 + - - +
71A MET* 3.2 9.2 + - - +
72A LYS 3.2 0.2 - - - -
73A ALA* 1.3 76.1 - - + +
75A ALA* 1.3 63.5 + - - +
76A SER 3.2 0.4 - - - -
77A THR* 2.8 29.9 + - - -
78A VAL* 4.0 0.5 - - - +
185A VAL* 3.5 29.5 - - + +
186A VAL* 3.3 29.2 + - + +
187A MET 6.2 0.2 - - - -
188A GLY* 6.0 1.8 - - - +
296A TYR* 5.4 4.4 + - - -
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Residues in contact with ALA 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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71A MET 3.1 12.9 + - - +
72A LYS* 3.2 8.7 + - - +
74A LYS* 1.3 78.5 - - - +
76A SER* 1.3 61.9 + - - +
77A THR 3.1 0.9 - - - -
78A VAL* 3.1 17.5 + - - +
182A LEU* 3.7 24.9 - - + -
186A VAL* 4.0 1.7 - - + +
239A ILE* 3.6 32.5 - - + +
242A CYS* 3.6 11.7 - - + +
243A CYS* 3.6 6.5 - - - -
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Residues in contact with SER 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 LYS 2.9 16.3 + - - -
73A ALA* 3.6 14.6 + - - -
74A LYS 3.2 0.6 - - - -
75A ALA* 1.3 75.7 - - - +
77A THR* 1.3 59.5 + - - +
78A VAL 3.3 4.9 + - - +
242A CYS* 3.3 26.3 + - - +
243A CYS* 5.2 0.2 - - - -
244A ASP* 5.2 2.8 + - - +
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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