Contacts of the helix formed by residues 72 - 89 (chain D) in PDB entry 1SCF
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 ASN 72 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21C ASN* 3.0 41.4 + - - +
18D LEU* 3.8 22.5 - - + +
21D ASN* 2.8 46.6 + - - +
22D LEU* 3.8 5.5 - - - +
63D PHE* 3.4 25.9 - - + -
70D LEU* 4.7 2.6 - - - +
71D SER* 1.3 67.6 - - - +
73D TYR* 1.3 67.9 + - - +
75D ILE* 3.3 3.3 + - - +
76D ILE* 2.9 30.9 + - - +
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Residues in contact with TYR 73 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21C ASN* 4.4 1.4 + - - -
60D LEU* 3.4 48.3 - - + +
63D PHE* 3.6 32.3 - - + +
64D SER* 3.7 19.3 - - - +
65D ASN* 3.4 35.4 - - - +
71D SER* 3.2 10.2 + - - +
72D ASN* 1.3 78.7 - - - +
74D SER* 1.3 58.6 + - - +
76D ILE* 5.0 0.2 - - - -
77D ASP* 2.9 48.8 + - + +
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Residues in contact with SER 74 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65D ASN* 4.4 8.1 + - - -
71D SER* 3.3 22.7 + - - -
73D TYR* 1.3 80.2 - - - +
75D ILE* 1.3 63.1 + - - +
77D ASP* 3.8 4.9 - - - +
78D LYS* 3.2 39.5 + - - +
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Residues in contact with ILE 75 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14D ASP* 3.9 47.3 - - + +
17D LYS* 4.5 10.5 - - + -
18D LEU* 4.1 29.8 - - + +
70D LEU* 3.6 30.1 - - + -
71D SER 3.1 14.8 + - - +
72D ASN* 3.7 4.5 - - - +
74D SER* 1.3 75.7 - - - +
76D ILE* 1.3 64.3 + - - +
78D LYS* 3.4 12.3 + - - +
79D LEU* 3.2 30.5 + - + +
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Residues in contact with ILE 76 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18D LEU* 3.6 26.5 - - + -
22D LEU* 5.2 0.2 - - + -
56D LEU* 3.5 36.3 - - + +
59D LEU* 3.9 18.4 - - + -
60D LEU* 3.9 16.2 - - + +
63D PHE* 3.6 36.3 - - + -
72D ASN 2.9 19.9 + - - +
73D TYR* 5.1 0.4 - - - -
75D ILE* 1.3 73.9 - - - +
77D ASP* 1.3 53.4 + - - +
79D LEU* 2.9 11.1 + - - +
80D VAL* 2.8 35.5 + - + +
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Residues in contact with ASP 77 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60D LEU* 3.5 22.7 - - + +
73D TYR* 2.9 38.8 + - + +
74D SER* 3.8 7.6 - - - +
76D ILE* 1.3 77.9 - - - +
78D LYS* 1.3 56.6 + - - +
80D VAL* 3.3 7.5 + - - +
81D ASN* 3.1 47.0 + - - +
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Residues in contact with LYS 78 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14D ASP* 4.2 17.1 + - - +
74D SER* 3.2 29.7 + - - +
75D ILE* 3.9 8.3 - - - +
76D ILE 3.3 0.4 - - - -
77D ASP* 1.3 74.2 - - + +
79D LEU* 1.3 66.0 + - + +
81D ASN* 3.6 9.1 + - - +
82D ILE* 3.3 28.4 + - + +
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Residues in contact with LEU 79 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11D ASN* 4.1 26.0 - - + +
14D ASP* 5.9 1.6 - - + -
15D VAL* 4.2 14.8 - - + +
18D LEU* 4.3 11.7 - - + -
56D LEU* 4.3 14.1 - - + -
75D ILE* 3.2 21.2 + - + +
76D ILE* 2.9 8.5 + - - +
78D LYS* 1.3 75.6 - - + +
80D VAL* 1.3 65.1 + - - +
82D ILE* 3.3 11.2 + - + +
83D VAL* 3.2 26.5 + - - +
116D PHE* 3.7 28.9 - - + -
119D PHE* 4.0 24.2 - - + -
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Residues in contact with VAL 80 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53D SER* 5.1 3.7 + - - +
56D LEU* 3.7 42.6 - - + +
57D THR* 3.6 20.9 - - + +
60D LEU* 4.5 11.7 - - + -
76D ILE* 2.8 24.4 + - + +
77D ASP* 3.5 13.2 - - - +
79D LEU* 1.3 69.7 - - - +
81D ASN* 1.3 68.6 + - - +
83D VAL* 3.2 4.7 + - - +
84D ASP* 3.0 36.5 + - - +
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Residues in contact with ASN 81 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77D ASP* 3.1 36.5 + - - +
78D LYS* 3.6 8.6 + - - +
79D LEU 3.3 0.2 - - - -
80D VAL* 1.3 80.0 - - - +
82D ILE* 1.4 56.0 + - + +
84D ASP* 3.6 16.5 - - - +
85D ASP* 3.2 33.9 + - - +
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Residues in contact with ILE 82 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11D ASN* 4.7 19.3 - - + +
78D LYS* 3.3 19.8 + - + +
79D LEU* 3.3 21.0 + - + +
80D VAL 3.3 1.0 - - - -
81D ASN* 1.4 70.2 - - + +
83D VAL* 1.3 63.2 + - + +
84D ASP 3.2 1.3 - - - -
85D ASP* 3.4 12.3 + - + +
86D LEU* 3.2 36.1 + - + +
119D PHE* 5.6 2.5 - - + -
123D ILE* 4.8 13.7 - - + -
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Residues in contact with VAL 83 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49D VAL* 3.1 42.4 - - + +
52D LEU* 4.1 5.4 - - + -
53D SER* 3.7 18.8 - - - +
56D LEU* 3.8 10.1 - - + -
79D LEU 3.2 17.5 + - - +
80D VAL 4.0 2.9 - - - +
82D ILE* 1.3 75.2 - - + +
84D ASP* 1.3 56.8 + - - +
86D LEU* 3.8 5.1 - - - -
87D VAL* 2.9 36.4 + - - +
119D PHE* 3.5 29.2 - - + -
123D ILE* 4.0 7.9 - - + -
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Residues in contact with ASP 84 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53D SER* 3.4 18.9 + - - -
57D THR* 5.4 0.5 + - - -
80D VAL* 3.0 25.7 + - - +
81D ASN* 3.6 21.0 - - - +
83D VAL* 1.3 72.1 - - - +
85D ASP* 1.3 67.3 + - - +
87D VAL* 3.3 7.4 + - - +
88D GLU* 3.1 34.8 + - - +
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Residues in contact with ASP 85 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81D ASN* 3.2 16.4 + - - +
82D ILE* 3.6 15.5 - - + +
84D ASP* 1.3 77.6 - - - +
86D LEU* 1.3 59.3 + - + +
88D GLU* 3.0 13.6 + - - +
89D CYS* 2.9 27.4 + - - +
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Residues in contact with LEU 86 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49D VAL* 4.1 9.7 - - + +
82D ILE* 3.2 23.8 + - + +
83D VAL* 4.0 4.3 - - - +
85D ASP* 1.3 78.6 - - + +
87D VAL* 1.3 60.8 + - - +
89D CYS* 3.5 12.4 + - + +
90D VAL* 3.4 17.0 + - - +
123D ILE* 3.8 34.5 - - + +
126D PHE* 3.5 57.4 - - + -
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Residues in contact with VAL 87 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49D VAL* 3.4 40.4 - - + +
50D VAL* 4.0 20.9 - - + +
53D SER* 4.2 9.2 - - - +
83D VAL 2.9 27.7 + - - +
84D ASP* 3.7 7.4 - - - +
85D ASP 3.2 0.2 - - - -
86D LEU* 1.3 78.1 - - - +
88D GLU* 1.3 61.3 + - + +
90D VAL* 3.3 20.5 + - - +
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Residues in contact with GLU 88 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84D ASP* 3.1 21.6 + - - +
85D ASP* 3.0 12.7 + - - +
87D VAL* 1.3 74.4 - - + +
89D CYS* 1.3 64.8 - - - +
90D VAL 3.3 4.3 + - - -
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Residues in contact with CYS 89 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85D ASP 2.9 13.0 + - - +
86D LEU* 3.6 18.2 - - + +
87D VAL 3.3 0.2 - - - -
88D GLU* 1.3 79.0 - - - +
90D VAL* 1.3 58.5 + - - +
126D PHE* 4.9 14.8 - - + -
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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