Contacts of the helix formed by residues 59 - 78 (chain A) in PDB entry 4Y2P
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 59 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53A LEU* 3.4 8.3 - - - +
58A ILE* 1.3 74.4 - - - +
60A LEU* 1.3 64.0 + - - +
62A GLN* 2.9 36.8 + - - +
63A TRP* 3.0 18.2 + - - +
127A LEU* 3.6 24.7 - - + +
129A ASP* 2.6 34.6 + - + +
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Residues in contact with LEU 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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53A LEU* 3.4 20.7 - - + +
59A THR* 1.3 71.6 - - - +
61A SER* 1.3 59.2 + - - +
63A TRP* 3.0 42.0 + - + +
64A ILE* 3.0 21.4 + - + +
92A PHE* 5.7 8.7 - - + -
96A ILE* 4.2 8.3 - - + -
126A TRP* 3.6 35.0 - - + +
127A LEU 2.9 19.4 + - - +
128A ASP* 3.8 3.1 - - - +
129A ASP* 4.2 3.4 - - - +
130A ARG* 2.8 39.5 - - + +
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Residues in contact with SER 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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60A LEU* 1.3 75.5 - - - +
62A GLN* 1.3 63.3 + - - +
64A ILE* 3.7 11.7 + - - +
65A PRO* 3.3 17.8 - - - +
129A ASP* 2.8 45.0 + - - -
130A ARG* 4.0 10.6 + - - +
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Residues in contact with GLN 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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57A GLU 4.8 0.2 - - - +
58A ILE* 3.3 25.9 - - + +
59A THR* 2.9 42.6 + - - +
61A SER* 1.3 78.7 - - - +
63A TRP* 1.4 62.0 + - - +
65A PRO* 3.4 14.7 - - - +
66A LEU* 3.7 15.3 - - + +
129A ASP* 5.2 0.4 - - - +
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Residues in contact with TRP 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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41A PHE* 3.5 38.8 - + - -
49A ALA* 3.5 35.8 - - + +
50A THR* 2.8 24.2 + - - +
53A LEU* 3.8 27.0 - - + +
58A ILE* 3.8 9.6 - - + +
59A THR 3.0 13.0 + - - +
60A LEU* 3.0 27.3 + - + +
62A GLN* 1.4 77.5 - - - +
64A ILE* 1.3 74.9 + - + +
66A LEU* 2.9 16.3 + - - +
67A MET* 3.0 45.6 + - + +
88A ILE* 4.1 13.5 - - + -
92A PHE* 4.0 19.7 - + - -
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Residues in contact with ILE 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* 3.0 30.4 + - + +
61A SER* 4.0 12.1 - - - +
63A TRP* 1.3 95.1 - - + +
65A PRO* 1.4 71.0 - - + +
67A MET* 3.4 3.7 + - - +
68A GLU* 2.9 39.9 + - + +
88A ILE* 4.3 7.0 - - + +
89A LYS* 4.2 39.0 - - + +
92A PHE* 5.8 4.7 - - + -
93A ASP* 6.0 0.2 - - - +
130A ARG* 4.7 11.0 - - + -
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Residues in contact with PRO 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 SER 3.3 18.2 - - - +
62A GLN* 3.4 13.2 - - - +
64A ILE* 1.4 90.1 - - + +
66A LEU* 1.3 68.0 + - + +
68A GLU* 3.3 13.8 - - + +
69A GLU* 3.1 22.3 + - - +
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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
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49A ALA* 3.6 24.5 - - + -
52A ARG* 5.5 7.2 - - - +
58A ILE* 3.7 30.5 - - + -
62A GLN* 3.7 14.6 - - + +
63A TRP* 2.9 7.0 + - - +
65A PRO* 1.3 81.0 - - + +
67A MET* 1.3 59.4 + - - +
69A GLU* 3.1 8.9 + - - +
70A ASN* 2.9 32.8 + - - +
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Residues in contact with MET 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 LEU* 4.1 14.6 - - + -
37A LEU* 3.6 25.1 - - + +
40A ALA* 3.8 5.8 - - - +
41A PHE* 3.6 34.5 - - + +
49A ALA* 5.1 0.8 - - - +
50A THR* 5.3 0.2 - - - -
63A TRP* 3.0 45.3 + - + +
64A ILE 3.6 8.3 - - - +
66A LEU* 1.3 75.2 - - - +
68A GLU* 1.3 57.2 + - - +
70A ASN* 3.2 10.0 + - - +
71A CYS* 2.9 42.0 + - - -
88A ILE* 3.6 26.2 - - + -
92A PHE* 4.8 0.2 - - + -
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Residues in contact with GLU 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* 2.9 31.9 + - + +
65A PRO* 3.3 16.8 - - + +
67A MET* 1.3 72.2 - - - +
69A GLU* 1.3 66.0 + - - +
71A CYS* 3.1 14.9 + - - +
72A ARG* 3.1 14.6 + - - +
82A LEU* 5.2 1.6 - - - +
86A PHE* 5.0 9.8 - - - +
87A SER* 4.6 4.1 + - - -
88A ILE* 3.4 39.4 + - + +
89A LYS* 4.2 1.6 + - - +
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Residues in contact with GLU 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 PRO 3.1 10.5 + - - +
66A LEU* 3.1 10.3 + - - +
68A GLU* 1.3 78.5 - - - +
70A ASN* 1.3 70.5 + - - +
71A CYS 3.0 0.7 + - - -
72A ARG* 3.0 42.0 + - - +
73A LYS* 2.9 46.1 + - + +
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Residues in contact with ASN 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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40A ALA* 3.2 38.0 + - + +
41A PHE 5.1 1.6 + - - -
43A LYS* 3.5 30.4 + - + +
49A ALA* 4.6 16.7 - - - +
50A THR* 5.6 1.2 + - - -
66A LEU* 2.9 16.9 + - - +
67A MET* 3.3 14.9 - - - +
69A GLU* 1.3 81.3 - - - +
71A CYS* 1.3 54.8 + - - +
73A LYS* 3.3 9.0 + - - +
74A CYS* 3.0 27.9 + - - +
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Residues in contact with CYS 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 LEU* 3.9 7.3 - - - +
37A LEU* 3.7 26.2 - - + -
40A ALA* 3.6 20.2 - - - -
67A MET* 2.9 30.8 + - - +
68A GLU 3.1 10.5 + - - +
70A ASN* 1.3 73.1 - - - +
72A ARG* 1.3 65.6 - - - +
74A CYS 3.7 0.2 + - - -
75A SER* 3.2 24.8 + - - -
82A LEU* 3.9 18.3 - - + +
86A PHE* 4.2 7.6 - - + -
88A ILE* 3.9 13.0 - - - -
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Residues in contact with ARG 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 GLU 3.1 11.3 + - - +
69A GLU* 3.0 40.4 + - - +
71A CYS* 1.3 73.2 - - - +
73A LYS* 1.3 68.2 + - - +
75A SER* 3.1 10.6 + - - +
76A GLU* 2.9 42.8 + - - +
82A LEU* 4.0 10.1 - - + +
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Residues in contact with LYS 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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43A LYS* 3.8 33.0 - - - +
69A GLU* 2.9 38.3 + - + +
70A ASN* 3.7 10.3 + - - +
72A ARG* 1.3 76.8 - - - +
74A CYS* 1.3 62.1 + - - +
76A GLU* 3.5 22.0 + - - +
77A THR* 3.1 28.6 + - - +
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Residues in contact with CYS 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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36A LEU* 3.4 26.1 - - + +
39A ASP* 3.6 15.5 - - + +
40A ALA* 3.4 32.5 - - + -
43A LYS* 3.9 17.3 - - - -
70A ASN 3.0 14.9 + - - +
71A CYS 4.1 2.9 - - - +
73A LYS* 1.3 75.0 - - - +
75A SER* 1.3 57.0 + - - +
77A THR* 3.3 12.8 - - - +
78A ALA* 3.0 30.0 + - - +
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Residues in contact with SER 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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36A LEU* 3.5 11.4 - - - +
71A CYS 3.2 15.7 + - - -
72A ARG* 3.1 14.9 + - - +
74A CYS* 1.3 73.7 - - - +
76A GLU* 1.3 59.3 + - - +
78A ALA 3.5 0.7 - - - +
79A LYS 3.0 7.4 + - - -
80A VAL* 2.8 59.2 + - - +
81A CYS* 4.6 0.3 - - - -
82A LEU* 4.0 23.1 + - - +
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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 ARG* 2.9 30.7 + - - +
73A LYS* 3.7 26.4 - - - +
75A SER* 1.3 76.8 + - - +
77A THR* 1.3 58.8 + - - +
79A LYS* 3.0 27.1 + - - +
80A VAL 4.7 2.2 - - - -
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Residues in contact with THR 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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43A LYS* 6.4 1.3 - - - -
73A LYS* 3.1 20.4 + - - +
74A CYS* 3.3 18.8 - - - +
76A GLU* 1.3 77.4 - - - +
78A ALA* 1.3 56.4 + - - +
79A LYS* 3.3 11.3 + - - +
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Residues in contact with ALA 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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33A PRO* 4.7 15.3 - - + +
36A LEU* 4.5 12.1 - - + -
74A CYS 3.0 19.0 + - - +
75A SER* 4.1 3.1 - - - +
77A THR* 1.3 73.2 - - - +
79A LYS* 1.4 70.2 + - - +
80A VAL* 3.3 9.4 + - + +
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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