Contacts of the helix formed by residues 57 - 69 (chain A) in PDB entry 2N7Y
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 CYS 57 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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53A PRO* 3.7 11.8 + - - +
55A VAL 4.3 0.4 - - - -
56A VAL* 1.3 77.3 - - - +
58A LEU* 1.3 65.7 + - - +
59A GLN* 4.2 9.9 - - + +
60A GLN* 3.2 53.3 + - - +
61A VAL* 3.6 12.5 + - - +
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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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7A ALA* 4.3 27.8 - - + +
8A THR 5.0 0.4 - - - +
9A SER* 3.7 22.4 - - - +
49A VAL* 4.9 15.5 - - + -
51A TYR* 5.3 7.4 - - + +
53A PRO* 4.3 12.1 - - + -
56A VAL 4.3 9.2 - - - +
57A CYS* 1.3 72.6 - - - +
59A GLN* 1.3 64.6 + - - +
61A VAL* 3.1 13.7 + - + +
62A CYS* 3.0 22.5 + - - +
74A ILE* 3.6 32.5 - - + -
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Residues in contact with GLN 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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57A CYS* 3.2 11.3 - - + +
58A LEU* 1.3 78.3 - - - +
60A GLN* 1.3 62.5 + - - +
62A CYS* 3.3 18.5 + - - +
63A HIS* 2.8 36.6 + - + +
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Residues in contact with GLN 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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32A LEU* 4.7 16.8 - - + -
56A VAL* 5.6 0.2 - - + -
57A CYS* 3.2 31.3 + - - +
58A LEU 3.2 0.8 - - - -
59A GLN* 1.3 78.7 - - - +
61A VAL* 1.3 60.6 + - - +
63A HIS* 3.1 27.7 + - - +
64A GLN* 2.8 38.8 + - - +
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Residues in contact with VAL 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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11A VAL* 5.5 8.1 - - + -
25A ILE* 3.4 29.5 - - + +
29A ILE* 3.7 32.5 - - + -
32A LEU* 5.3 1.3 - - + -
38A MET* 5.5 1.6 - - + -
49A VAL* 5.2 16.4 - - + -
51A TYR* 5.2 5.6 - - + -
56A VAL* 4.5 10.5 - - + -
57A CYS 3.8 13.5 - - - +
58A LEU* 3.1 14.1 + - + +
60A GLN* 1.3 77.6 - - - +
62A CYS* 1.3 63.2 + - - +
64A GLN* 3.3 17.5 + - - +
65A ILE 3.4 9.0 + - - -
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Residues in contact with CYS 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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11A VAL* 5.8 5.6 - - + -
58A LEU 3.0 12.9 + - - +
59A GLN* 3.5 21.3 - - - +
61A VAL* 1.3 76.6 - - - +
63A HIS* 1.3 52.7 + - - +
65A ILE* 3.3 9.0 - - - +
66A GLY* 2.8 34.9 + - - -
72A ALA* 3.6 29.2 - - + -
73A SER* 5.2 2.7 - - - -
74A ILE* 5.6 6.7 - - + +
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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
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59A GLN* 2.8 23.1 + - + +
60A GLN* 3.1 33.1 + - - +
62A CYS* 1.3 77.6 - - - +
64A GLN* 1.3 63.6 + - + +
66A GLY* 4.9 0.4 - - - -
67A ASP* 2.9 70.3 + - + +
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Residues in contact with GLN 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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24A SER* 4.4 5.9 + - - -
25A ILE* 4.0 11.2 - - + +
28A ARG* 3.2 55.3 + - + +
29A ILE* 3.5 21.5 + - - +
32A LEU* 3.4 25.5 - - - +
60A GLN* 2.8 24.3 + - + +
61A VAL* 3.6 16.2 - - - +
63A HIS* 1.3 83.1 - - + +
65A ILE* 1.3 58.6 + - - +
67A ASP* 4.3 3.0 - - - +
68A MET* 3.7 15.1 + - - +
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Residues in contact with ILE 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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11A VAL* 5.7 0.9 - - + -
13A ILE* 3.6 31.0 - - + -
21A CYS* 3.9 41.7 - - + +
22A VAL* 5.7 0.4 - - - -
24A SER* 5.5 0.2 - - - -
25A ILE* 3.8 24.2 - - + +
61A VAL* 3.4 10.0 + - + +
62A CYS* 3.3 12.1 - - - +
64A GLN* 1.3 77.4 - - - +
66A GLY* 1.3 68.0 + - - +
68A MET* 3.2 20.1 + - - +
70A PHE* 3.4 17.6 + - + +
71A GLU 5.0 0.7 - - - +
72A ALA* 3.5 25.1 - - + -
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Residues in contact with GLY 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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62A CYS* 2.8 25.1 + - - -
63A HIS* 3.9 1.1 - - - -
65A ILE* 1.3 74.7 - - - +
67A ASP* 1.3 57.1 + - - +
69A GLY* 3.0 20.4 + - - -
70A PHE 3.3 14.8 - - - +
71A GLU* 5.5 0.4 - - - -
72A ALA 5.5 1.6 - - - -
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Residues in contact with ASP 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 HIS* 2.9 62.7 + - + +
64A GLN* 4.3 4.0 - - - +
66A GLY* 1.3 73.0 - - - +
68A MET* 1.3 63.6 + - - +
69A GLY* 3.2 1.6 + - - -
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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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20A SER* 4.9 10.1 - - - +
21A CYS* 4.9 0.7 - - - -
24A SER* 3.5 36.3 - - - +
64A GLN 3.7 6.5 + - - +
65A ILE* 3.2 17.8 + - + +
66A GLY 3.1 0.4 - - - -
67A ASP* 1.3 80.4 - - - +
69A GLY* 1.3 54.7 + - - +
70A PHE* 3.6 31.3 - - + -
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Residues in contact with GLY 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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66A GLY 3.0 10.8 + - - -
67A ASP 3.1 1.9 - - - -
68A MET* 1.3 80.3 - - - +
70A PHE* 1.3 69.3 + - - +
71A GLU 4.4 0.2 + - - -
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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