Contacts of the helix formed by residues 73 - 91 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59B ILE* 4.3 4.3 - - - -
63B ASN* 4.8 1.3 - - - +
72B MET* 1.3 73.5 - - - +
74B LEU* 1.3 66.7 + - - +
75B GLU* 3.1 6.9 + - - +
76B GLU* 2.9 29.8 + - - +
77B ARG* 2.9 24.7 + - - +
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Residues in contact with LEU 74 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B ALA* 4.3 7.2 - - + -
28B LEU* 4.4 14.1 - - + -
52B LYS* 4.5 22.4 - - + +
55B LEU* 3.6 31.4 - - + -
56B GLU* 3.2 32.6 + - + +
59B ILE* 3.4 25.0 - - + +
73B SER* 1.3 73.7 - - - +
75B GLU* 1.3 58.5 + - - +
77B ARG* 3.7 1.0 - - - +
78B LYS* 3.0 51.2 + - - +
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Residues in contact with GLU 75 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29B GLU* 5.0 2.9 - - - +
73B SER* 3.2 7.2 + - - +
74B LEU* 1.3 80.5 - - - +
76B GLU* 1.3 60.2 + - - +
78B LYS* 3.3 45.1 + - - +
79B ALA* 3.6 6.1 + - - +
77C LYS* 5.7 1.2 + - - -
80C GLU* 3.9 25.9 - - + +
81C PRO* 5.1 9.3 - - + +
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Residues in contact with GLU 76 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71B ARG 3.3 5.9 - - - +
72B MET* 2.9 33.5 - - + +
73B SER* 2.9 40.2 + - - +
75B GLU* 1.3 76.1 - - - +
77B ARG* 1.3 64.3 + - - +
78B LYS 3.2 0.4 - - - -
79B ALA* 3.5 14.8 + - + +
80B ILE* 3.4 19.4 + - - +
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Residues in contact with ARG 77 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B ASN* 3.0 23.8 + - - +
21B ILE* 3.7 14.4 - - - +
22B ASN* 2.8 44.3 + - - +
25B ALA* 4.1 11.0 - - + -
59B ILE* 3.6 27.9 - - - +
62B HIS* 4.1 13.4 + - - +
63B ASN* 2.9 25.7 + - - -
66B GLU* 6.1 0.8 - - - +
70B LYS 4.4 4.8 + - - -
72B MET* 3.0 42.5 + - + +
73B SER 2.9 17.3 + - - +
74B LEU* 3.7 5.2 - - - +
76B GLU* 1.3 75.4 - - - +
78B LYS* 1.3 59.6 + - - +
80B ILE* 3.0 13.4 + - - +
81B GLY* 2.8 24.9 + - - -
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Residues in contact with LYS 78 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B ALA* 3.5 25.7 - - - +
26B GLY* 4.8 0.2 - - - -
28B LEU* 4.3 17.2 - - - +
29B GLU* 3.2 28.0 + - + +
32B GLU* 3.1 32.3 + - - -
52B LYS* 5.7 2.0 - - - +
74B LEU* 3.0 44.2 + - + +
75B GLU* 3.3 35.3 + - - +
77B ARG* 1.3 75.6 - - - +
79B ALA* 1.3 64.5 + - - +
81B GLY* 2.8 13.2 + - - -
82B VAL* 2.9 19.6 + - - +
77C LYS* 4.3 2.0 - - - +
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Residues in contact with ALA 79 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75B GLU 3.6 5.2 + - - +
76B GLU* 3.5 15.6 + - - +
77B ARG 3.3 0.2 - - - -
78B LYS* 1.3 76.7 - - - +
80B ILE* 1.3 58.7 + - + +
82B VAL* 3.2 18.4 - - - +
83B LYS* 3.0 34.2 - - - +
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Residues in contact with ILE 80 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22B ASN* 3.5 33.2 - - + +
72B MET* 4.5 25.8 - - + -
76B GLU 3.4 16.8 - - - +
77B ARG* 3.0 11.6 + - - +
79B ALA* 1.3 76.8 - - + +
81B GLY* 1.3 65.0 + - - +
83B LYS* 3.3 17.7 + - + +
84B MET* 3.1 34.4 + - + +
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Residues in contact with GLY 81 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22B ASN* 3.0 29.8 + - - -
23B PHE* 4.3 2.9 - - - -
26B GLY* 3.8 11.0 - - - -
77B ARG 2.8 7.3 + - - -
78B LYS 2.8 12.2 + - - -
80B ILE* 1.3 72.7 - - - +
82B VAL* 1.3 55.0 + - - -
84B MET* 3.2 6.4 + - - +
85B MET* 2.8 31.2 + - - +
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Residues in contact with VAL 82 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89A LEU* 3.8 21.7 - - + +
26B GLY* 4.2 4.5 - - - -
29B GLU* 3.9 33.4 - - + -
33B ARG* 4.7 5.4 - - - +
78B LYS* 2.9 17.5 + - + +
79B ALA* 3.2 19.3 - - - +
81B GLY* 1.3 73.0 - - - +
83B LYS* 1.3 62.2 + - + +
85B MET* 3.1 9.1 + - - +
86B LYS* 2.7 52.1 + - - +
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Residues in contact with LYS 83 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79B ALA* 3.0 29.1 + - - +
80B ILE* 3.4 19.9 - - + +
82B VAL* 1.3 86.6 - - + +
84B MET* 1.3 63.3 + - + +
86B LYS* 3.1 19.9 + - + +
87B VAL* 3.2 19.0 + - - +
97B ILE* 3.6 47.5 - - + +
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Residues in contact with MET 84 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34A PHE* 4.0 20.0 - - + -
19B ALA* 4.1 22.9 - - + +
22B ASN* 4.5 7.4 - - + +
23B PHE* 4.1 19.3 - - + -
80B ILE* 3.1 29.8 + - + +
81B GLY 3.4 7.9 - - - +
83B LYS* 1.3 77.9 - - + +
85B MET* 1.3 63.1 + - - +
87B VAL* 3.0 12.8 - - - +
88B LEU* 2.9 27.7 + - - +
10D LEU* 3.8 39.0 - - + +
11D ALA* 4.4 13.2 - - - +
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Residues in contact with MET 85 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A CYS* 4.0 12.6 - - - -
85A MET* 3.4 24.2 - - + -
89A LEU* 3.4 15.0 - - + -
23B PHE* 3.3 50.5 - - + +
26B GLY 3.4 7.6 - - - -
27B ILE* 3.4 33.7 - - + +
30B CYS* 4.4 1.8 - - - -
81B GLY 2.8 17.4 + - - +
82B VAL* 3.1 11.0 + - - +
84B MET* 1.3 75.7 - - - +
86B LYS* 1.3 58.7 + - - +
88B LEU* 3.3 3.8 + - - +
89B LEU* 2.8 36.9 + - - +
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Residues in contact with LYS 86 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89A LEU* 3.9 35.4 + - + -
90A PHE* 3.6 38.0 - - + +
82B VAL* 2.7 30.7 + - - +
83B LYS* 3.1 14.0 + - + +
85B MET* 1.3 74.8 - - - +
87B VAL* 1.3 63.5 + - - +
89B LEU* 4.6 2.9 - - - -
90B PHE* 3.1 32.3 + - - +
96B GLY 2.9 27.4 - - - +
97B ILE* 4.7 9.9 + - - +
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Residues in contact with VAL 87 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83B LYS 3.2 6.3 + - - +
84B MET* 3.0 24.9 - - - +
86B LYS* 1.3 75.2 - - - +
88B LEU* 1.3 54.2 + - + +
90B PHE 3.5 0.2 + - - -
91B MET* 2.7 29.8 + - - -
92B ASP 2.9 24.5 + - - +
93B PRO* 3.7 20.9 - - + -
96B GLY* 4.8 0.4 - - - -
97B ILE* 3.7 35.0 - - + +
10D LEU* 3.4 28.5 - - + -
74D VAL* 5.0 8.8 - - + +
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Residues in contact with LEU 88 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30A CYS* 3.9 11.7 - - + +
33A ARG* 3.1 42.4 + - + +
34A PHE* 3.7 20.2 - - + -
37A GLN* 3.9 10.1 - - + +
23B PHE* 3.7 31.2 - - + -
84B MET 2.9 21.0 + - - +
85B MET* 3.7 5.8 - - - +
87B VAL* 1.3 78.2 - - + +
89B LEU* 1.3 62.3 + - + +
91B MET* 2.8 34.7 + - + +
10D LEU* 3.9 18.6 - - + -
74D VAL* 5.2 2.9 - - + -
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Residues in contact with LEU 89 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29A GLU* 6.2 0.2 - - + -
30A CYS* 3.5 29.2 - - - -
33A ARG* 3.1 18.8 + - - +
82A VAL* 3.8 33.9 - - + +
85A MET* 4.0 18.2 - - + -
86A LYS* 3.6 40.8 + - + +
89A LEU* 3.5 32.8 - - + -
90A PHE* 5.7 0.4 - - + -
85B MET 2.8 21.7 + - - +
86B LYS* 3.8 5.6 - - - +
88B LEU* 1.3 71.7 - - - +
90B PHE* 1.3 63.0 + - + +
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Residues in contact with PHE 90 (chain B).
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* 3.8 35.2 - - + +
90A PHE* 3.2 39.9 - + - -
95A ALA* 5.7 4.0 - - + -
86B LYS* 3.1 26.6 + - + +
87B VAL 4.2 0.4 - - - +
88B LEU 3.1 0.4 - - - -
89B LEU* 1.3 80.9 - - + +
91B MET* 1.3 71.6 + - - +
92B ASP* 3.4 21.2 - - + +
96B GLY* 5.4 2.9 - - - -
101B GLU* 3.8 16.2 - - - +
102B PRO* 4.7 7.6 - - + -
103B TYR* 3.6 46.1 - + + -
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Residues in contact with MET 91 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33A ARG* 3.6 36.1 - - - +
36A TRP* 4.3 4.3 - - + -
37A GLN* 4.1 4.7 - - - +
87B VAL 2.7 11.8 + - - -
88B LEU* 2.8 34.1 + - + +
90B PHE* 1.3 79.7 - - - +
92B ASP* 1.3 59.6 + - - +
93B PRO* 4.6 0.2 - - - -
44D ARG* 4.4 15.0 + - + +
74D VAL* 3.5 25.8 - - + -
75D VAL 3.0 33.0 - - - +
76D ASP* 3.8 30.1 - - + +
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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