Contacts of the helix formed by residues 59 - 75 (chain A) in PDB entry 6P1A
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 ASN 59 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26A TRP* 3.7 3.5 + - - -
58A CYS* 1.3 85.7 - - - +
60A ASP* 1.3 65.5 + - - +
61A ASP* 3.0 12.8 + - - +
62A ASP* 2.6 53.4 + - - -
63A GLY 3.2 13.3 + - - -
31C ARG* 4.0 34.8 - - - +
57C MET* 5.0 9.3 + - - +
58C CYS 4.8 3.0 + - - -
59C ASN* 4.3 18.4 - - + +
60C ASP* 5.2 3.1 + - - +
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Residues in contact with ASP 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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26A TRP* 3.0 33.9 + - + +
31A ARG* 3.9 14.6 + - - +
58A CYS 4.8 0.5 - - - +
59A ASN* 1.3 75.5 - - - +
61A ASP* 1.3 65.5 + - - +
63A GLY 3.4 0.2 + - - -
64A MET* 2.9 33.3 + - + +
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Residues in contact with ASP 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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59A ASN* 3.0 13.6 + - - +
60A ASP* 1.3 78.1 + - - +
62A ASP* 1.3 71.2 + - - +
64A MET* 3.2 7.5 + - - +
65A LEU* 3.0 23.0 + - - +
152A ARG* 4.5 9.6 - - - +
31C ARG* 5.2 6.7 + - - -
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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
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19A TRP* 3.3 38.9 - - + -
58A CYS* 4.1 8.1 - - + +
59A ASN* 2.6 37.2 + - - +
61A ASP* 1.3 72.5 - - - +
63A GLY* 1.3 61.8 + - - +
65A LEU* 3.3 3.6 + - - +
66A ILE* 2.9 33.4 + - + +
149A PHE* 4.9 2.9 - - + -
152A ARG* 2.8 34.9 + - - +
57C MET* 4.2 12.1 - - - +
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Residues in contact with GLY 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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23A TRP* 3.7 5.6 - - - -
26A TRP* 3.3 31.6 - - - -
58A CYS* 3.6 13.8 - - - -
59A ASN 3.2 9.7 + - - -
60A ASP 3.8 1.3 - - - -
61A ASP 3.2 0.2 - - - -
62A ASP* 1.3 78.2 - - - +
64A MET* 1.3 54.5 + - - +
67A SER* 2.9 34.0 + - - -
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Residues in contact with MET 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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26A TRP* 3.6 16.9 - - + -
31A ARG 5.2 2.0 - - - +
32A LEU* 4.2 6.5 - - - -
33A GLU* 4.2 29.6 - - + +
35A ARG* 6.0 0.2 - - - +
36A MET* 3.6 39.7 - - + +
60A ASP* 2.9 18.7 + - + +
61A ASP* 3.6 6.1 - - - +
63A GLY* 1.3 75.7 - - - +
65A LEU* 1.3 58.5 + - - +
67A SER* 3.3 3.8 + - - -
68A GLN* 2.9 48.0 + - - +
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Residues in contact with LEU 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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61A ASP 3.0 16.2 + - - +
62A ASP* 3.8 5.6 - - - +
64A MET* 1.3 77.9 - - - +
66A ILE* 1.3 61.5 + - - +
68A GLN* 3.2 13.4 + - - +
69A VAL* 3.0 22.3 + - + +
145A LEU* 3.5 28.0 - - + -
148A ALA* 3.8 29.6 - - + +
149A PHE* 3.9 19.7 - - + -
152A ARG* 3.8 34.8 - - + +
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Residues in contact with ILE 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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19A TRP* 3.5 41.7 - - + +
20A LEU* 4.1 17.0 - - + -
23A TRP* 3.3 43.7 - - + -
58A CYS* 4.8 2.7 - - - -
62A ASP* 2.9 25.1 + - + +
65A LEU* 1.3 77.1 - - - +
67A SER* 1.3 56.8 + - - +
69A VAL* 3.3 1.6 + - + +
70A VAL* 2.9 30.6 + - + +
145A LEU* 3.9 28.0 - - + -
149A PHE* 4.3 6.3 - - + -
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Residues in contact with SER 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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23A TRP* 2.8 27.7 + - - +
26A TRP* 3.5 11.4 - - - -
32A LEU* 3.5 31.3 - - - +
36A MET* 5.4 4.5 - - - -
37A SER* 5.6 0.8 - - - -
40A ILE* 4.9 3.9 - - - +
63A GLY 2.9 20.0 + - - -
64A MET 3.6 4.3 - - - -
66A ILE* 1.3 74.5 - - - +
68A GLN* 1.3 67.0 + - - +
70A VAL* 3.8 2.0 - - - +
71A ASP* 2.9 28.4 + - - +
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Residues in contact with GLN 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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36A MET* 4.5 26.6 - - + +
64A MET* 2.9 34.8 + - + +
65A LEU* 3.5 13.6 - - - +
67A SER* 1.3 75.5 - - - +
69A VAL* 1.3 64.4 + - + +
71A ASP* 3.8 3.9 - - - +
72A SER* 2.9 26.0 + - - -
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Residues in contact with VAL 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 LEU* 3.0 18.7 + - + +
66A ILE* 3.7 6.7 - - + +
68A GLN* 1.3 76.7 - - + +
70A VAL* 1.3 62.8 + - + +
72A SER* 2.8 22.1 + - - -
73A VAL* 3.0 15.3 + - + +
141A ILE* 4.2 13.5 - - + -
144A VAL* 3.6 27.6 - - + -
145A LEU* 3.6 28.7 - - + +
148A ALA* 3.8 28.7 - - + -
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Residues in contact with VAL 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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20A LEU* 4.1 26.7 - - + -
23A TRP* 3.9 23.8 - - + -
40A ILE* 5.3 0.4 - - + -
66A ILE* 2.9 25.7 + - + +
67A SER 4.0 2.5 - - - +
69A VAL* 1.3 75.7 - - + +
71A ASP* 1.3 58.3 + - - +
73A VAL* 3.3 1.3 + - - -
74A MET* 2.9 35.0 + - + +
81A PHE* 3.7 25.4 - - + -
84A LEU* 3.9 13.9 - - + -
141A ILE* 4.2 17.3 - - + -
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Residues in contact with ASP 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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36A MET 3.7 11.6 - - - +
37A SER* 2.4 40.8 + - - +
38A SER 4.6 1.0 + - - -
39A VAL* 4.8 2.8 - - - +
40A ILE* 5.1 0.2 - - + -
67A SER 2.9 17.7 + - - +
68A GLN* 3.9 3.6 - - - +
70A VAL* 1.3 77.9 - - - +
72A SER* 1.3 63.7 + - - +
75A TYR* 3.2 33.7 + - - +
81A PHE* 3.8 16.2 - - + -
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Residues in contact with SER 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 GLN 2.9 15.9 + - - -
69A VAL* 2.8 19.4 + - - -
71A ASP* 1.3 78.6 + - - +
73A VAL* 1.3 64.8 + - - +
75A TYR* 3.1 26.7 - - - -
144A VAL* 4.4 6.8 - - - +
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Residues in contact with VAL 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 VAL* 3.0 21.3 + - + +
70A VAL 4.0 2.0 - - - +
71A ASP 3.2 0.2 - - - -
72A SER* 1.3 86.6 - - - +
74A MET* 1.3 65.8 + - - +
75A TYR* 3.6 0.6 - - - -
76A ILE* 3.9 19.6 - - - +
140A MET* 4.1 28.3 - - + +
141A ILE* 3.9 24.2 - - + -
144A VAL* 3.8 30.5 - - + -
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Residues in contact with MET 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 VAL* 2.9 26.2 + - + +
73A VAL* 1.3 87.4 - - - +
75A TYR* 1.3 64.8 + - - +
76A ILE* 3.0 5.2 + - - -
77A ASP* 3.1 26.6 + - + +
80A ALA* 3.4 35.4 - - + +
81A PHE* 3.5 24.6 - - + +
84A LEU* 4.3 6.5 - - + -
137A SER* 3.1 41.3 - - - +
140A MET* 5.9 0.7 - - - -
141A ILE* 4.0 21.5 - - + -
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Residues in contact with TYR 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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39A VAL* 5.0 8.8 - - + +
71A ASP* 3.2 37.7 + - - +
72A SER* 3.1 24.0 - - - -
73A VAL 4.6 0.7 - - - -
74A MET* 1.3 76.6 - - - +
76A ILE* 1.3 85.7 + - + +
77A ASP 4.7 0.2 - - - -
78A LYS* 3.9 15.7 - - - +
81A PHE* 4.0 9.1 - - + -
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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