Contacts of the helix formed by residues 56 - 74 (chain A) in PDB entry 4I6X
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 56 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54A SER* 3.0 15.2 + - - -
55A LYS* 1.3 80.5 - - - +
57A GLU* 1.3 63.9 + - - +
58A VAL* 3.5 8.2 + - - +
59A ALA* 2.9 25.7 + - - +
60A ALA 3.2 13.5 + - - -
84A ASP* 3.3 13.7 - - - -
86A GLY* 4.8 1.3 - - - -
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Residues in contact with GLU 57 (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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56A SER* 1.3 73.6 - - - +
58A VAL* 1.3 64.9 + - + +
60A ALA* 3.2 12.1 + - - +
61A GLU* 3.4 15.9 + - + +
64A LEU* 5.1 3.0 - - + +
82A TRP* 3.7 31.4 - - + -
84A ASP* 3.6 13.1 + - - +
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Residues in contact with VAL 58 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A SER* 3.3 7.6 + - - +
57A GLU* 1.3 77.0 - - + +
59A ALA* 1.3 62.5 + - - +
60A ALA 3.2 0.9 + - - -
61A GLU* 3.2 41.2 + - - +
62A ASN 5.0 0.2 + - - -
107A LYS* 5.4 1.9 + - - -
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Residues in contact with ALA 59 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A LYS* 4.4 5.4 - - + +
56A SER* 2.9 30.2 + - - +
57A GLU 3.3 0.2 - - - -
58A VAL* 1.3 77.6 - - - +
60A ALA* 1.3 59.8 + - - +
61A GLU 3.6 0.5 + - - -
62A ASN* 4.7 2.6 + - - +
63A HIS* 4.7 3.8 + - - -
107A LYS* 3.4 55.0 + - + +
108A VAL* 3.8 9.8 - - + +
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Residues in contact with ALA 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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52A LEU* 4.0 6.7 - - + -
54A SER* 3.6 25.4 - - - -
56A SER 3.2 5.4 + - - +
57A GLU 3.2 9.8 + - - +
58A VAL 3.1 0.8 - - - -
59A ALA* 1.3 78.0 - - - +
61A GLU* 1.3 63.9 + - - +
62A ASN 3.4 0.4 - - - -
63A HIS* 3.2 6.2 + - - +
64A LEU* 2.8 39.9 + - + +
82A TRP* 3.7 11.0 - - + -
108A VAL* 4.4 5.8 - - - -
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Residues in contact with GLU 61 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A GLU* 3.5 11.1 - - + +
58A VAL* 3.2 42.8 + - - +
59A ALA 3.3 0.2 - - - -
60A ALA* 1.3 76.8 - - - +
62A ASN* 1.3 69.0 + - - +
64A LEU* 3.2 9.1 + - + +
65A ARG* 3.0 32.6 + - - +
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Residues in contact with ASN 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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58A VAL 5.0 0.2 + - - -
59A ALA 4.7 2.2 + - - +
60A ALA 3.4 0.6 - - - -
61A GLU* 1.3 84.7 - - - +
63A HIS* 1.3 66.3 + - - +
65A ARG* 3.3 18.7 + - - +
66A LEU* 3.2 21.8 + - - +
107A LYS* 4.7 17.1 - - - +
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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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52A LEU* 3.8 27.4 - - + -
59A ALA 4.7 4.8 + - - -
60A ALA* 3.2 8.4 + - - +
62A ASN* 1.3 82.1 - - + +
64A LEU* 1.3 58.3 + - - +
66A LEU* 3.3 6.4 + - + +
67A LEU* 2.8 39.7 + - + +
107A LYS* 5.7 6.1 - - + -
108A VAL* 3.3 34.8 - - + +
110A LEU* 4.6 13.7 - - + +
126A VAL* 3.9 33.5 - - + +
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Residues in contact with LEU 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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30A ILE* 3.8 23.1 - - + +
52A LEU* 3.8 14.8 - - + -
57A GLU* 5.1 3.1 - - + +
60A ALA* 2.8 36.7 + - + +
61A GLU* 3.2 7.2 + - - +
63A HIS* 1.3 76.1 - - - +
65A ARG* 1.3 59.3 + - - +
67A LEU* 4.0 3.8 - - + +
68A SER* 2.7 36.6 + - - +
82A TRP* 3.7 48.9 - - + +
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Residues in contact with ARG 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 GLU* 3.0 20.8 + - - +
62A ASN* 3.5 21.3 + - - +
64A LEU* 1.3 79.8 - - - +
66A LEU* 1.3 63.5 + - - +
68A SER* 3.6 13.3 + - - -
69A THR* 3.8 11.3 + - - +
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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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62A ASN 3.2 10.2 + - - +
63A HIS* 3.7 7.9 - - + +
65A ARG* 1.3 81.5 - - - +
67A LEU* 1.3 64.8 + - + +
69A THR* 2.7 30.1 + - - +
70A VAL* 3.1 10.3 + - + +
126A VAL* 3.7 44.9 - - + +
127A THR* 4.1 2.0 - - - -
128A PHE* 3.7 32.8 - - + +
131A ILE* 4.0 12.3 - - + -
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Residues in contact with LEU 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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30A ILE* 3.6 8.3 - - + +
50A LEU* 4.3 13.0 - - + -
52A LEU* 4.1 31.4 - - + -
63A HIS* 2.8 34.2 + - + +
64A LEU* 4.0 5.8 - - + +
66A LEU* 1.3 75.2 - - + +
68A SER* 1.3 57.3 + - - +
70A VAL* 3.6 4.3 - - + +
71A ALA* 2.8 32.4 + - - +
80A ILE* 3.9 36.7 - - + +
110A LEU* 4.2 12.6 - - + -
131A ILE* 4.1 27.4 - - + -
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Residues in contact with SER 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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28A MET 2.9 47.5 + - - +
29A LEU* 4.9 1.1 - - - -
30A ILE* 3.7 12.4 + - - +
64A LEU* 2.7 24.1 + - - +
65A ARG* 3.7 7.9 - - - -
66A LEU 3.2 0.2 - - - -
67A LEU* 1.3 76.1 - - - +
69A THR* 1.3 63.1 + - - +
71A ALA* 3.6 0.7 + - - +
72A GLN* 3.3 10.0 + - - +
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Residues in contact with THR 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 ARG 3.9 12.6 - - - +
66A LEU* 2.7 24.4 + - - +
68A SER* 1.3 76.8 - - - +
70A VAL* 1.3 63.7 + - - +
72A GLN* 3.3 8.0 + - - +
73A ALA* 3.2 16.1 + - - +
128A PHE* 3.6 27.1 - - - -
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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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66A LEU* 3.1 17.9 + - + +
67A LEU* 3.6 11.4 - - + +
69A THR* 1.3 76.5 + - - +
71A ALA* 1.3 63.8 + - - +
73A ALA* 2.9 13.3 + - - +
74A VAL* 3.0 12.6 + - + +
80A ILE* 3.7 18.2 - - + -
128A PHE* 4.0 30.3 - - + -
131A ILE* 3.8 34.8 - - + -
132A VAL* 4.0 13.7 - - + +
135A LEU* 4.1 10.3 - - + -
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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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28A MET* 3.4 35.2 - - + +
30A ILE* 3.7 15.0 - - + -
67A LEU 2.8 17.0 + - - +
68A SER 3.7 2.7 - - - +
69A THR 3.3 0.2 - - - -
70A VAL* 1.3 75.5 - - - +
72A GLN* 1.3 63.4 + - - +
74A VAL* 3.4 8.2 + - - +
75A LYS* 3.2 18.0 + - - -
78A GLY 5.1 1.7 - - - +
79A THR* 6.4 0.2 - - - -
80A ILE* 3.9 18.3 - - + +
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Residues in contact with GLN 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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28A MET* 3.2 33.5 + - - +
68A SER 3.3 9.0 + - - +
69A THR* 3.3 12.0 + - - +
70A VAL 3.2 0.8 - - - -
71A ALA* 1.3 79.9 - - - +
73A ALA* 1.3 63.4 + - - +
74A VAL 3.3 0.9 + - - -
75A LYS* 3.4 45.2 + - - +
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Residues in contact with ALA 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 THR 3.2 3.9 + - - +
70A VAL 2.9 9.7 + - - +
72A GLN* 1.3 79.4 - - - +
74A VAL* 1.3 62.3 + - - +
75A LYS 3.5 0.2 - - - -
77A GLN* 4.1 8.7 + - - -
128A PHE* 3.7 30.7 - - + -
132A VAL* 4.0 12.8 - - + -
136A LYS* 4.2 12.0 + - - +
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Residues in contact with VAL 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* 3.0 18.9 + - + +
71A ALA* 3.8 11.7 - - - +
72A GLN 3.2 0.4 - - - -
73A ALA* 1.3 83.0 - - - +
75A LYS* 1.3 64.4 + - - -
76A GLY 3.2 0.2 + - - -
77A GLN* 2.8 28.0 + - + +
78A GLY* 3.0 28.6 + - - +
80A ILE* 4.9 1.6 - - + -
132A VAL* 4.1 25.8 - - + +
135A LEU* 4.0 39.0 - - + -
136A LYS* 4.5 8.7 - - + -
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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
------------------------------------------------------------
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