Contacts of the helix formed by residues 73 - 91 (chain A) in PDB entry 3SDL
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 73 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59A ILE* 4.8 1.3 - - - -
63A ASN* 5.1 0.9 - - - +
72A MET* 1.3 75.1 - - - +
74A LEU* 1.3 66.1 + - - +
75A GLU* 3.5 9.2 + - - +
76A GLU* 3.0 27.8 + - - +
77A ARG* 2.9 26.8 + - - +
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Residues in contact with LEU 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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25A ALA* 4.7 2.7 - - + -
28A LEU* 4.4 14.8 - - + -
52A LYS* 4.4 14.1 - - - -
55A LEU* 4.4 14.1 - - + -
56A GLU* 4.0 32.3 - - + +
59A ILE* 3.8 31.3 - - + +
73A SER* 1.3 73.5 - - - +
75A GLU* 1.3 71.1 + - + +
77A ARG* 3.5 1.6 + - - +
78A LYS* 3.1 54.0 + - + +
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Residues in contact with GLU 75 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A SER* 3.1 8.0 + - - +
74A LEU* 1.3 86.2 - - + +
76A GLU* 1.3 64.0 + - - +
78A LYS* 3.4 38.3 + - - +
79A ALA* 3.5 18.9 + - - +
81D PRO* 6.4 1.8 - - + -
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Residues in contact with GLU 76 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A ARG 4.3 3.5 - - - +
72A MET* 3.1 42.3 - - + +
73A SER* 3.0 30.9 + - - +
75A GLU* 1.3 79.5 - - - +
77A ARG* 1.3 60.6 + - - +
79A ALA* 3.5 14.5 + - - +
80A ILE* 3.6 15.2 + - + +
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Residues in contact with ARG 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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18A ASN* 3.1 28.0 + - - +
21A ILE* 3.9 11.7 - - - +
22A ASN* 3.0 41.9 + - - +
25A ALA* 3.9 11.7 - - + -
59A ILE* 3.5 35.3 + - - +
62A HIS* 4.2 9.4 - - - -
63A ASN* 2.8 28.9 + - - +
70A LYS 5.0 2.0 + - - -
71A ARG* 4.6 1.4 - - - +
72A MET* 3.2 39.5 + - + +
73A SER 2.9 14.4 + - - +
74A LEU 4.0 4.3 - - - +
76A GLU* 1.3 73.9 - - - +
78A LYS* 1.3 67.4 + - - +
80A ILE* 3.2 8.8 + - - +
81A GLY* 2.9 20.4 + - - -
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Residues in contact with LYS 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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25A ALA* 3.9 22.2 - - + +
26A GLY* 4.2 3.8 - - - +
28A LEU* 4.2 14.8 - - - +
29A GLU* 3.2 31.4 + - + +
32A GLU* 3.0 29.8 + - - -
52A LYS* 5.9 1.0 - - - +
74A LEU* 3.1 36.1 + - + +
75A GLU* 3.4 43.9 + - - +
76A GLU 3.3 0.2 - - - -
77A ARG* 1.3 76.0 - - - +
79A ALA* 1.3 57.3 + - - +
81A GLY* 3.1 1.6 + - - -
82A VAL* 2.8 35.7 + - + +
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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 GLU 3.5 8.8 + - - +
76A GLU* 3.7 11.4 - - - +
77A ARG 3.2 0.4 - - - -
78A LYS* 1.3 78.6 - - - +
80A ILE* 1.3 62.6 + - + +
82A VAL* 3.5 8.2 + - - +
83A LYS* 3.2 45.0 + - - +
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Residues in contact with ILE 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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22A ASN* 4.3 23.1 - - + +
72A MET* 3.5 39.0 - - + -
76A GLU* 3.7 13.2 - - + +
77A ARG* 3.2 10.0 + - - +
79A ALA* 1.3 77.8 - - + +
81A GLY* 1.3 62.8 + - - +
83A LYS* 3.4 15.5 + - + +
84A MET* 3.1 34.8 + - + +
98A GLU* 5.1 11.7 - - + +
99A GLY* 4.9 0.8 - - - -
100A PHE* 6.3 3.1 - - + -
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Residues in contact with GLY 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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22A ASN 3.3 24.0 + - - -
23A PHE* 4.4 1.9 - - - +
26A GLY* 4.0 9.4 - - - -
77A ARG 2.9 10.3 + - - -
78A LYS 3.6 2.9 - - - -
80A ILE* 1.3 76.4 - - - +
82A VAL* 1.3 58.3 + - - +
84A MET* 3.3 11.7 + - - +
85A MET* 2.9 33.4 + - - +
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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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26A GLY* 4.1 4.2 - - - +
29A GLU* 4.2 25.4 - - + -
33A ARG* 4.7 9.6 - - - +
78A LYS 2.8 23.9 + - - +
79A ALA* 3.7 8.7 - - - +
81A GLY* 1.3 76.1 - - - +
83A LYS* 1.3 65.3 + - + +
85A MET* 3.1 4.4 + - - +
86A LYS* 2.9 49.8 + - - +
89B LEU* 3.8 26.9 - - + +
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Residues in contact with LYS 83 (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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79A ALA* 3.2 34.6 + - - +
80A ILE* 3.7 11.7 - - + +
82A VAL* 1.3 81.7 - - + +
84A MET* 1.3 63.7 + - - +
86A LYS* 3.2 13.8 + - + +
87A VAL* 3.1 28.0 + - - +
95A ALA 5.1 2.5 - - - +
96A GLY* 4.3 12.0 - - - +
98A GLU* 3.2 42.5 - - + +
99A GLY* 4.1 13.5 - - - +
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Residues in contact with MET 84 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A ALA* 3.8 7.6 - - - +
22A ASN* 3.8 13.0 - - + -
23A PHE* 3.3 47.3 - - + +
80A ILE* 3.1 23.0 + - + +
81A GLY* 3.6 8.5 - - - +
82A VAL 3.2 0.2 - - - -
83A LYS* 1.3 75.5 - - - +
85A MET* 1.3 62.3 + - - +
87A VAL* 3.2 6.4 + - - +
88A LEU* 3.2 26.2 + - - +
99A GLY* 3.8 11.9 - - - +
34B PHE* 4.1 15.7 - - + -
10C LEU* 3.8 31.6 - - + +
11C ALA* 4.4 17.7 - - - -
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Residues in contact with MET 85 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A PHE* 4.0 22.4 - - + +
26A GLY 3.9 11.9 - - - +
27A ILE* 3.6 25.6 - - + -
30A CYS* 3.5 25.1 - - - -
81A GLY 2.9 18.4 + - - +
82A VAL 3.6 4.3 - - - +
84A MET* 1.3 73.4 - - - +
86A LYS* 1.3 60.8 - - - +
88A LEU* 3.2 7.6 + - - +
89A LEU* 2.9 34.4 + - + +
27B ILE* 4.7 0.2 - - + -
30B CYS* 3.7 19.7 - - + -
85B MET* 3.4 35.2 - - + -
89B LEU* 4.0 11.7 - - + -
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Residues in contact with LYS 86 (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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82A VAL* 2.9 39.0 + - + +
83A LYS* 3.2 12.8 + - + +
85A MET* 1.3 75.6 - - - +
87A VAL* 1.3 56.9 + - - +
89A LEU* 4.7 0.4 - - - -
90A PHE* 3.0 43.7 + - + +
95A ALA* 3.4 30.7 + - + +
89B LEU* 3.6 36.1 + - + -
90B PHE* 3.8 36.6 - - + +
103B TYR* 5.8 1.6 - - - -
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Residues in contact with VAL 87 (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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83A LYS 3.1 11.7 + - - +
84A MET* 3.5 9.2 - - - +
85A MET 3.2 0.4 - - - -
86A LYS* 1.3 77.4 - - - +
88A LEU* 1.3 54.5 + - + +
91A MET* 2.6 35.3 + - - +
92A ASP 3.6 21.3 - - - +
93A PRO* 4.8 0.2 - - + -
96A GLY* 3.2 42.8 - - - +
101A GLU* 3.2 38.6 - - - +
10C LEU* 4.7 6.5 - - + -
74C VAL* 4.8 7.6 - - + -
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Residues in contact with LEU 88 (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 PHE* 4.0 10.8 - - + -
84A MET 3.2 14.3 + - - +
85A MET* 3.2 8.1 + - - +
87A VAL* 1.3 75.4 - - + +
89A LEU* 1.3 62.2 + - + +
91A MET* 3.2 11.2 - - - +
30B CYS* 3.8 12.3 - - + +
33B ARG* 2.8 63.2 + - + +
34B PHE* 3.7 40.6 - - + +
37B GLN* 4.0 12.8 - - + +
10C LEU* 3.6 19.1 - - + -
74C VAL* 4.7 7.2 - - + -
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Residues in contact with LEU 89 (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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85A MET* 2.9 15.9 + - + +
86A LYS 4.1 2.7 - - - +
88A LEU* 1.3 78.6 - - - +
90A PHE* 1.3 64.4 + - + +
91A MET* 4.5 0.2 - - - +
30B CYS* 3.4 26.7 - - - -
33B ARG* 3.5 22.5 + - - +
82B VAL* 3.8 33.1 - - + +
85B MET* 3.4 35.0 - - + -
86B LYS* 3.9 26.0 + - + +
89B LEU* 3.5 25.1 - - + -
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Residues in contact with PHE 90 (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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86A LYS* 3.0 33.2 + - + +
89A LEU* 1.3 77.7 - - + +
91A MET* 1.3 73.6 + - - +
92A ASP* 3.3 14.3 + - + +
95A ALA* 5.1 3.8 - - + -
86B LYS* 3.6 45.5 - - + +
89B LEU* 5.7 0.7 - - + -
90B PHE* 3.2 39.9 - + - -
96B GLY* 4.1 8.5 - - - -
100B PHE* 4.4 14.6 - + - -
101B GLU* 5.5 1.3 - - - -
102B PRO* 3.4 37.9 - - + -
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Residues in contact with MET 91 (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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87A VAL* 2.6 22.1 + - - +
88A LEU* 3.2 24.2 - - - +
89A LEU 3.3 0.2 - - - -
90A PHE* 1.3 76.7 - - - +
92A ASP* 1.3 58.4 + - - +
93A PRO* 4.5 2.2 - - - +
33B ARG* 3.3 32.1 - - - +
37B GLN* 5.7 0.4 - - - -
44C ARG* 4.5 6.9 - - + +
74C VAL* 3.6 42.8 - - + +
75C VAL 4.4 1.8 - - - +
76C ASP* 4.0 39.3 - - + +
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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
------------------------------------------------------------
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