Contacts of the helix formed by residues 60 - 74 (chain A) in PDB entry 5H8Q
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 GLY 60 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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17A PRO 3.4 12.6 - - - -
18A PHE 3.4 4.0 - - - -
20A ILE* 4.5 1.3 - - - -
59A LYS* 1.3 81.1 - - - +
61A PHE* 1.3 67.0 + - - -
62A CYS 3.4 2.7 - - - -
63A ILE* 3.2 1.5 + - - +
64A ASP* 3.0 20.5 + - - -
278A TRP* 3.5 29.7 + - - -
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Residues in contact with PHE 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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17A PRO 3.0 16.9 + - - +
18A PHE* 3.7 24.2 - + + -
60A GLY* 1.3 72.0 - - - +
62A CYS* 1.4 66.4 + - - +
64A ASP* 3.3 4.3 + - - +
65A ILE* 3.2 42.4 + - + +
130A PHE* 3.9 4.7 - + - -
131A VAL* 3.5 26.5 - - + -
271A MET* 3.2 26.2 - - + -
274A LEU* 3.6 29.0 - - + +
275A GLU* 3.6 24.5 - - + -
278A TRP* 3.6 19.8 - - + -
279A LEU* 3.7 18.6 - - + -
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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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18A PHE* 2.8 36.8 + - - +
19A VAL* 4.0 4.3 - - + -
61A PHE* 1.4 73.2 - - - +
63A ILE* 1.3 62.4 + - + +
65A ILE* 3.4 9.1 + - - +
66A LEU* 3.0 26.2 + - - +
111A VAL* 3.9 10.5 - - + +
112A GLY* 3.4 47.3 - - - +
113A SER* 4.8 0.2 - - - -
130A PHE* 3.7 22.2 - - - -
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Residues in contact with ILE 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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12A THR* 4.6 5.4 - - + +
18A PHE 4.5 1.6 - - - +
19A VAL* 4.1 21.8 - - + -
34A ASN 4.9 0.4 - - - +
36A VAL* 3.6 33.2 - - + +
58A CYS* 3.8 16.4 - - + +
59A LYS* 3.5 31.9 - - - +
60A GLY 3.2 7.3 + - - +
62A CYS* 1.3 76.5 - - - +
64A ASP* 1.3 60.4 + - - +
66A LEU* 3.2 12.9 + - + +
67A LYS* 2.9 34.4 + - + +
79A LEU* 3.9 25.6 - - + -
111A VAL* 5.3 2.7 - - + -
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Residues in contact with ASP 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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34A ASN* 4.4 6.1 + - - +
60A GLY 3.0 10.8 + - - +
61A PHE 3.7 6.1 - - - +
63A ILE* 1.3 74.3 - - - +
65A ILE* 1.4 61.4 + - - +
67A LYS* 3.1 34.0 + - - +
68A LYS* 3.1 28.3 + - - +
274A LEU* 3.6 26.3 - - + +
277A LEU* 3.5 14.4 - - - +
278A TRP* 2.8 32.5 + - - +
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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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61A PHE* 3.2 44.3 + - + +
62A CYS* 3.6 9.2 - - - +
63A ILE 3.2 0.4 - - - -
64A ASP* 1.4 75.5 - - - +
66A LEU* 1.3 56.5 + - - +
68A LYS* 3.2 8.7 + - + +
69A LEU* 2.9 38.6 + - + +
111A VAL* 5.2 4.0 - - + -
130A PHE* 3.4 26.2 - - + -
246A ILE* 4.6 6.3 - - + -
262A LEU* 3.8 25.4 - - + -
265A PHE* 5.2 4.5 - - + -
271A MET* 3.8 15.3 - - - -
274A LEU* 3.7 16.8 - - + -
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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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10A ILE* 3.6 29.4 - - + -
36A VAL* 5.3 1.3 - - + -
62A CYS 3.0 15.2 + - - +
63A ILE* 3.2 13.9 + - + +
65A ILE* 1.3 77.5 - - - +
67A LYS* 1.3 55.6 + - - +
69A LEU* 3.3 9.0 + - + +
70A SER* 2.9 30.0 + - - -
75A PHE* 4.0 15.7 - - + -
77A TYR* 3.8 34.3 - - + +
79A LEU* 4.1 28.7 - - + -
109A MET* 5.1 4.0 - - - -
111A VAL* 4.2 18.8 - - + +
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Residues in contact with LYS 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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33A ARG 5.3 0.4 + - - -
34A ASN* 3.3 35.9 + - - +
35A THR 5.4 0.4 + - - +
36A VAL* 3.8 27.8 - - + -
63A ILE* 2.9 15.6 + - - +
64A ASP* 3.1 38.3 + - - +
65A ILE 3.3 0.2 - - - -
66A LEU* 1.3 75.0 - - - +
68A LYS* 1.3 62.6 + - + +
70A SER* 3.6 6.7 + - - -
71A ARG* 3.3 24.1 + - - +
77A TYR* 4.1 7.6 - - - +
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Residues in contact with LYS 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 ASP* 3.1 15.0 + - - +
65A ILE* 3.5 7.4 - - - +
67A LYS* 1.3 74.6 - - + +
69A LEU* 1.3 57.9 + - - +
71A ARG* 3.5 26.1 + - - +
72A THR* 3.0 33.6 + - - -
265A PHE* 3.6 26.0 - - + -
270A GLU* 2.8 43.4 + - + +
273A GLU* 5.0 8.5 + - - -
274A LEU* 3.9 38.6 - - + -
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Residues in contact with LEU 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 ILE* 2.9 28.5 + - + +
66A LEU* 3.7 10.3 - - + +
68A LYS* 1.3 74.0 - - - +
70A SER* 1.4 58.1 + - - +
73A VAL* 2.8 44.9 + - + +
75A PHE* 3.7 16.4 - - + -
109A MET* 5.4 2.2 - - - -
111A VAL* 5.8 0.9 - - + -
246A ILE* 3.3 33.7 - - + -
258A ILE* 4.0 23.8 - - + +
261A ALA* 3.7 27.6 - - + -
262A LEU* 4.2 5.8 - - + -
265A PHE* 3.8 13.9 - - + -
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Residues in contact with SER 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 LEU 2.9 20.4 + - - -
67A LYS* 3.7 6.3 - - - -
69A LEU* 1.4 71.9 - - - +
71A ARG* 1.3 56.6 + - - +
74A LYS* 3.1 9.4 + - - -
75A PHE* 2.6 58.3 + - - +
76A THR* 4.4 1.7 - - - +
77A TYR* 3.7 27.6 - - - -
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Residues in contact with ARG 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 LYS 3.3 14.9 + - - +
68A LYS* 3.6 35.3 + - - +
69A LEU 3.3 0.2 - - - -
70A SER* 1.3 81.8 - - - +
72A THR* 1.4 84.1 + - - +
74A LYS* 3.6 19.4 + - - +
264A GLN* 5.7 0.6 + - - -
265A PHE* 3.9 4.8 - - - -
270A GLU* 3.7 21.4 + - - -
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Residues in contact with THR 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 LYS 3.0 17.6 + - - -
69A LEU 4.3 0.7 - - - -
71A ARG* 1.4 95.3 + - - +
73A VAL* 1.3 62.4 + - + +
74A LYS* 3.5 12.3 + - - +
257A GLN* 5.5 0.5 + - - -
261A ALA* 4.1 17.0 - - + -
264A GLN* 3.9 25.8 + - - +
265A PHE* 3.6 10.9 - - + -
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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 LEU* 2.8 26.0 + - + +
72A THR* 1.3 72.1 - - + +
74A LYS* 1.3 70.5 + - - +
75A PHE* 3.8 11.4 - - + -
254A TRP* 3.7 31.9 - - + -
257A GLN* 3.7 57.9 + - + +
258A ILE* 4.2 15.3 - - + +
261A ALA* 4.0 14.8 - - + -
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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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6A ASN* 2.9 21.2 + - - +
70A SER 3.1 12.5 + - - -
71A ARG 3.6 15.9 + - - +
72A THR* 3.3 8.2 - - - +
73A VAL* 1.3 82.7 - - - +
75A PHE* 1.3 60.5 + - - +
254A TRP* 4.5 2.3 - - - -
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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