Contacts of the helix formed by residues 67 - 82 (chain A) in PDB entry 5H1C
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 SER 67 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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65A GLY 4.3 0.4 - - - -
66A ILE* 1.3 80.5 - - - +
68A GLU* 1.3 65.3 + - - +
69A ALA* 3.9 8.1 + - - +
70A LYS* 3.0 51.7 + - - +
71A ALA 3.4 0.5 + - - -
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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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57A LYS* 3.0 23.3 + - - +
61A ILE* 3.5 44.8 - - + +
66A ILE* 3.9 0.6 + - - +
67A SER* 1.3 74.1 - - - +
69A ALA* 1.3 58.3 + - - +
71A ALA* 2.9 16.6 + - - -
72A ASP* 2.9 14.4 + - - -
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Residues in contact with ALA 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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67A SER* 3.2 8.6 + - - +
68A GLU* 1.3 75.1 - - - +
70A LYS* 1.3 66.9 + - + +
72A ASP* 2.9 26.9 + - + +
73A LYS* 3.0 22.0 + - - +
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Residues in contact with LYS 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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37A ASP* 4.5 22.9 + - + +
40A LYS* 5.1 3.2 - - - +
65A GLY 3.5 20.3 + - - +
66A ILE* 4.2 13.2 - - + -
67A SER* 3.0 37.6 + - - +
69A ALA* 1.3 77.4 - - - +
71A ALA* 1.3 57.4 - - - +
73A LYS* 3.0 20.5 + - + +
74A ILE* 2.9 38.7 + - + +
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Residues in contact with ALA 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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57A LYS* 3.1 34.3 - - + +
60A LEU* 3.5 24.9 - - + -
61A ILE* 5.1 1.6 - - + -
66A ILE* 4.7 1.3 - - + +
67A SER 3.4 3.0 + - - +
68A GLU* 2.9 6.1 + - - +
70A LYS* 1.3 78.3 - - - +
72A ASP* 1.3 59.4 + - - +
74A ILE* 4.0 10.9 - - - +
75A LEU* 2.9 39.0 + - + +
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Residues in contact with ASP 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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57A LYS* 4.1 8.7 + - - -
68A GLU* 2.9 15.1 + - - +
69A ALA* 2.9 19.8 + - + +
71A ALA* 1.3 77.8 - - - +
73A LYS* 1.3 63.3 + - + +
75A LEU* 4.2 4.4 - - - +
76A ALA* 2.9 26.6 + - - +
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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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31A CYS* 5.4 10.3 - - - +
32A GLY 5.4 7.4 + - - +
33A ILE* 5.1 13.0 - - + -
69A ALA* 3.0 20.8 + - - +
70A LYS* 3.0 19.4 + - + +
72A ASP* 1.3 76.8 - - + +
74A ILE* 1.3 64.6 + - + +
76A ALA* 3.1 8.8 + - - +
77A GLU* 2.9 28.9 + - + +
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Residues in contact with ILE 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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28A LEU* 5.1 6.6 - - + +
33A ILE* 4.6 21.5 - - + -
41A LEU* 4.2 31.4 - - + -
52A VAL* 3.5 27.9 - - + +
60A LEU* 4.1 23.3 - - + -
66A ILE* 5.2 3.6 - - + -
70A LYS* 2.9 32.1 + - + +
71A ALA* 3.8 9.2 - - - +
72A ASP 3.3 0.2 - - - -
73A LYS* 1.3 77.8 - - + +
75A LEU* 1.3 57.4 + - - +
77A GLU* 3.0 10.0 + - - +
78A ALA* 2.9 24.4 + - - +
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Residues in contact with LEU 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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52A VAL* 4.0 23.1 - - + +
53A ALA* 5.5 2.5 - - - +
55A ALA 4.4 9.6 - - - +
57A LYS* 4.2 33.0 - - + +
60A LEU* 4.4 16.4 - - + -
71A ALA* 2.9 24.9 + - + +
72A ASP* 4.3 4.9 - - - +
74A ILE* 1.3 73.9 - - - +
76A ALA* 1.3 60.6 + - - +
78A ALA* 3.1 7.5 + - + +
79A ALA* 2.9 29.1 + - - +
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Residues in contact with ALA 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 ASP 2.9 20.5 + - - +
73A LYS* 3.3 7.9 - - - +
75A LEU* 1.3 77.7 - - - +
77A GLU* 1.3 64.9 + - - +
79A ALA* 3.5 7.8 + - - +
80A LYS* 2.9 24.0 + - - +
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Residues in contact with GLU 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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28A LEU* 3.6 22.2 - - + +
30A GLN* 5.0 5.3 - - - +
31A CYS* 3.1 39.5 - - + +
33A ILE* 4.4 15.5 - - + -
73A LYS* 2.9 20.4 + - + +
74A ILE* 3.0 8.9 + - - +
76A ALA* 1.3 80.5 - - - +
78A ALA* 1.3 59.7 + - - +
79A ALA 3.2 0.2 - - - -
80A LYS* 2.9 36.9 + - - +
81A LEU* 2.9 21.7 + - - +
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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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28A LEU* 4.6 1.3 - - + +
49A VAL* 4.5 12.8 - - + +
52A VAL* 4.3 9.6 - - + +
53A ALA* 3.7 35.5 - - + +
74A ILE 2.9 12.5 + - - +
75A LEU* 3.1 13.9 + - + +
77A GLU* 1.3 76.2 - - - +
79A ALA* 1.3 57.5 + - - +
82A VAL* 2.9 35.9 + - - +
84A MET* 6.0 0.4 - - - -
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Residues in contact with ALA 79 (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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75A LEU 2.9 15.7 + - - +
76A ALA* 3.7 7.9 - - - +
78A ALA* 1.3 75.0 - - - +
80A LYS* 1.3 63.8 + - - +
81A LEU 4.2 0.2 - - - -
82A VAL 3.3 19.8 - - - +
83A PRO* 4.4 2.9 - - - +
84A MET* 5.4 6.5 - - + +
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Residues in contact with LYS 80 (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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76A ALA 2.9 16.2 + - - +
77A GLU* 2.9 35.6 + - - +
79A ALA* 1.3 78.8 - - - +
81A LEU* 1.3 66.8 + - + +
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Residues in contact with LEU 81 (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 GLN* 4.0 20.7 + - - +
27A ARG* 4.1 25.1 - - + +
28A LEU* 3.8 16.4 - - + -
49A VAL* 3.6 37.7 - - + -
77A GLU* 2.9 12.3 + - - +
80A LYS* 1.3 91.4 - - + +
82A VAL* 1.3 63.6 + - - +
83A PRO* 3.6 9.4 - - - +
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Residues in contact with VAL 82 (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 GLN* 3.9 11.7 - - - +
49A VAL* 4.7 2.7 - - + -
50A GLU* 3.6 37.9 - - + +
53A ALA* 4.4 6.5 - - + -
54A TYR* 4.1 15.3 - - + +
78A ALA 2.9 21.7 + - - +
79A ALA* 3.3 15.5 - - - +
81A LEU* 1.3 79.1 - - + +
83A PRO* 1.3 82.1 - - + +
84A MET* 3.6 20.5 + - - +
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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