Contacts of the helix formed by residues 64 - 78 (chain A) in PDB entry 1SL1
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 TYR 64 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6A ILE* 4.4 25.4 - - + -
8A ALA* 3.4 24.6 + - + +
10A ALA 2.7 21.8 + - - -
11A LEU* 3.9 7.2 - - + -
12A LEU* 3.3 39.0 - - + +
15A VAL* 4.1 2.5 - - + +
60A ASN* 3.1 26.8 + - - +
61A GLY 3.6 0.4 + - - -
63A LYS* 1.3 77.6 - - - +
65A ASP* 1.3 77.0 + - - +
66A VAL 3.4 1.6 - - - -
67A PRO* 3.1 4.6 - - - +
68A ALA* 2.8 44.8 + - + +
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Residues in contact with ASP 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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5A ASP* 3.5 10.1 - - - +
6A ILE* 3.4 38.5 + - + +
58A PHE* 3.6 34.4 - - + -
59A HIS 4.0 5.6 - - - +
60A ASN* 3.5 7.4 - - - +
61A GLY* 3.5 16.0 + - - -
64A TYR* 1.3 88.8 - - - +
66A VAL* 1.3 64.0 + - - +
68A ALA* 3.9 0.2 - - - +
69A LEU* 3.0 32.1 + - - +
4003A MG 4.2 1.2 - - - -
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Residues in contact with VAL 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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58A PHE* 3.9 24.9 - - + -
61A GLY 2.8 25.3 + - - +
62A HIS* 4.8 1.6 - - - +
65A ASP* 1.3 73.9 - - - +
67A PRO* 1.3 69.6 - - + +
69A LEU* 3.3 7.8 + - - +
70A THR* 3.3 21.8 + - - +
81A PHE* 5.0 1.6 - - - -
83A LEU* 4.1 22.0 - - + +
88A CYS* 4.1 19.3 - - + -
222A TRP* 3.7 32.1 - - + -
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Residues in contact with PRO 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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12A LEU* 3.9 12.4 - - + +
61A GLY 3.5 8.1 - - - +
62A HIS 3.5 10.5 - - - +
63A LYS 3.3 21.1 - - - +
64A TYR* 3.1 15.0 - - - +
66A VAL* 1.3 95.5 - - + +
68A ALA* 1.3 62.0 + - - +
70A THR* 3.3 9.5 + - - +
71A LYS* 3.0 22.3 + - - +
229A ARG* 3.6 34.3 - - - +
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Residues in contact with ALA 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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6A ILE* 4.5 8.1 - - + -
12A LEU* 3.6 17.0 - - + +
15A VAL* 4.5 9.4 - - + -
64A TYR* 2.8 44.8 + - + +
65A ASP* 3.9 4.7 - - - +
67A PRO* 1.3 73.9 - - - +
69A LEU* 1.3 53.2 + - - +
71A LYS* 3.2 3.5 + - - +
72A LEU* 2.7 45.3 + - + +
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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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6A ILE* 4.0 20.4 - - + -
18A PHE* 4.3 3.1 - - + -
39A PHE* 3.8 29.3 - - + -
42A TYR* 3.8 19.7 - - + +
43A LEU* 4.2 2.5 - - + -
46A LEU* 3.6 30.7 - - + -
58A PHE* 4.2 13.2 - - + -
65A ASP 3.0 25.8 + - - +
66A VAL 3.6 4.5 - - - +
67A PRO 3.2 0.2 - - - -
68A ALA* 1.3 75.2 - - - +
70A THR* 1.3 58.4 + - - +
72A LEU* 4.5 2.7 - - + -
73A ALA* 2.8 33.6 + - - +
81A PHE* 3.7 19.5 - - + -
83A LEU* 4.7 2.7 - - + -
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Residues in contact with THR 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 VAL* 3.3 13.6 + - - +
67A PRO* 3.6 12.7 - - - +
68A ALA 3.3 0.4 - - - -
69A LEU* 1.3 77.7 - - - +
71A LYS* 1.3 63.2 + - - +
73A ALA* 4.0 1.7 - - - +
74A LYS* 3.3 23.1 + - + +
79A ARG 4.6 1.0 - - - +
81A PHE* 2.6 34.1 + - - +
82A HIS* 3.6 29.4 + - + +
83A LEU 5.0 1.2 + - - -
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Residues in contact with LYS 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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12A LEU* 2.8 34.5 + - + +
13A GLU* 2.9 23.4 + - - +
14A SER* 3.7 1.8 - - - +
15A VAL* 3.4 27.4 + - + +
16A THR* 5.9 0.4 - - - -
67A PRO 3.0 13.3 + - - +
68A ALA* 3.5 8.3 - - - +
70A THR* 1.3 80.1 - - - +
72A LEU* 1.3 57.6 + - - +
74A LYS* 3.4 4.7 + - - +
75A LEU* 3.1 43.4 + - + +
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Residues in contact with LEU 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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6A ILE* 4.9 4.0 - - + -
8A ALA* 4.1 6.7 - - + -
15A VAL* 4.0 25.1 - - + +
16A THR* 3.3 45.3 - - - +
17A LYS 3.4 1.3 - - - +
18A PHE* 4.0 27.8 - - + +
39A PHE* 3.4 15.9 - - + -
68A ALA* 2.7 30.1 + - + +
69A LEU* 4.1 1.3 - - - +
71A LYS* 1.3 72.1 - - - +
73A ALA* 1.3 59.1 + - - +
75A LEU* 4.4 4.5 - - + +
76A GLN* 2.8 41.6 + - + +
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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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39A PHE* 3.6 11.1 - - - -
43A LEU* 3.7 18.6 - - + -
69A LEU 2.8 24.0 + - - +
70A THR 4.0 1.6 - - - +
72A LEU* 1.3 71.4 - - - +
74A LYS* 1.3 59.6 + - - +
77A LEU* 3.0 20.7 + - - +
79A ARG* 2.9 32.6 + - + +
81A PHE* 3.6 21.1 - - + -
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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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70A THR* 3.3 15.8 + - + +
71A LYS* 3.6 4.7 - - - +
72A LEU 3.2 0.2 - - - -
73A ALA* 1.3 80.2 - - - +
75A LEU* 1.3 64.1 + - + +
78A ASN* 2.9 56.8 + - - +
79A ARG 3.2 12.0 + - - +
80A GLU* 2.7 37.1 + - - +
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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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15A VAL 4.0 19.7 - - - +
16A THR* 4.2 21.3 - - + +
71A LYS* 3.1 33.7 + - + +
72A LEU* 4.1 4.9 - - + +
74A LYS* 1.3 82.2 - - + +
76A GLN* 1.3 64.3 + - + +
78A ASN 4.7 0.5 + - - -
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Residues in contact with GLN 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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16A THR 3.8 16.2 - - - +
17A LYS* 3.4 14.1 - - - +
18A PHE* 2.7 46.1 + - - +
36A PRO 5.5 2.3 - - - +
39A PHE* 3.9 20.5 - - + +
72A LEU* 2.8 27.7 + - + +
75A LEU* 1.3 76.6 - - + +
77A LEU* 1.3 66.7 + - + +
78A ASN 3.7 0.4 - - - -
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Residues in contact with LEU 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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39A PHE* 3.7 31.0 - - + -
40A GLY* 3.8 21.1 - - - +
43A LEU* 3.8 22.4 - - + -
73A ALA 3.0 10.5 + - - +
76A GLN* 1.3 87.4 - - + +
78A ASN* 1.3 73.6 + - - +
79A ARG* 3.1 15.4 + - + +
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Residues in contact with ASN 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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74A LYS* 2.9 43.2 + - - +
75A LEU 4.6 0.6 + - - -
76A GLN 3.7 0.8 - - - -
77A LEU* 1.3 80.0 - - - +
79A ARG* 1.3 58.2 + - - +
80A GLU 4.4 0.2 + - - -
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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