Contacts of the strand formed by residues 100 - 115 (chain B) in PDB entry 1S4Y
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 ILE 100 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13A ASN* 4.6 9.4 + - - +
17A GLU* 4.6 0.2 - - - +
42A ARG* 3.6 28.0 - - - +
51A VAL* 3.9 25.8 - - + -
52A LYS* 2.9 25.5 + - - -
77A VAL* 4.0 11.0 - - + -
30B ILE* 3.7 21.1 - - + -
92B LEU* 4.0 18.4 - - + -
93B TYR 3.5 5.8 - - - +
94B TYR* 3.4 32.8 - - + +
98B GLN 4.7 1.3 - - - +
99B ASN* 1.3 72.7 - - - +
101B ILE* 1.3 65.2 + - - +
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Residues in contact with ILE 101 (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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13A ASN* 5.9 0.7 - - - +
17A GLU* 3.9 22.7 - - + +
52A LYS* 4.1 1.3 - - - +
91B MET 3.7 0.9 - - - +
92B LEU* 3.2 9.0 - - - +
93B TYR* 2.8 66.0 + - + +
95B ASP* 3.9 30.3 - - + +
99B ASN* 3.8 16.6 - - + +
100B ILE* 1.3 79.4 - - - +
102B LYS* 1.4 69.9 + - - +
103B LYS* 4.1 14.4 - - - +
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Residues in contact with LYS 102 (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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17A GLU* 5.1 2.7 + - - +
25A GLU* 5.4 4.8 + - - -
38A TYR* 3.4 30.7 - - + +
52A LYS* 3.7 11.8 - - + +
55A CYS* 2.8 34.4 + - - +
56A TRP* 3.9 16.1 - - + +
90B SER* 3.8 11.5 + - - -
91B MET 3.3 9.0 - - - +
92B LEU* 3.8 7.9 - - + -
101B ILE* 1.4 78.2 - - - +
103B LYS* 1.4 70.6 + - - +
104B ASP* 3.2 29.8 + - - -
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Residues in contact with LYS 103 (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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89B MET 3.6 0.7 - - - +
90B SER* 3.4 0.3 - - - -
91B MET* 2.7 42.8 + - - +
93B TYR* 3.4 30.7 - - + +
101B ILE* 4.0 11.7 - - - +
102B LYS* 1.4 78.2 - - - +
104B ASP* 1.3 71.4 + - - +
105B ILE* 3.6 24.0 + - + +
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Residues in contact with ASP 104 (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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57A LEU* 3.6 28.5 - - + +
88B PRO* 5.1 0.2 - - - -
89B MET 3.5 5.2 - - - -
90B SER* 2.9 23.0 + - - -
102B LYS* 3.2 20.1 + - - +
103B LYS* 1.3 78.5 - - - +
105B ILE* 1.3 63.8 + - - +
106B GLN* 3.7 16.4 + - - +
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Residues in contact with ILE 105 (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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88B PRO* 3.1 4.3 - - - +
89B MET 2.8 39.3 + - - +
91B MET* 4.4 19.3 - - + -
93B TYR* 4.6 11.2 - - + +
103B LYS* 3.8 38.4 - - + +
104B ASP* 1.3 71.8 - - - +
106B GLN* 1.3 71.5 + - - +
108B MET* 3.3 29.3 - - + +
58D PHE* 3.9 20.4 - - + -
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Residues in contact with GLN 106 (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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57A LEU* 5.7 0.2 - - - +
88B PRO* 3.7 31.1 - - - +
104B ASP* 3.7 16.3 + - - +
105B ILE* 1.3 86.1 - - - +
107B ASN* 1.3 87.8 + - - +
108B MET* 3.3 1.4 + - - +
58D PHE 4.6 5.0 + - - -
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Residues in contact with ASN 107 (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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86B LEU* 3.7 40.8 - - + +
87B ARG 3.9 10.0 + - - +
88B PRO* 4.1 1.2 - - - +
105B ILE 3.8 0.4 + - - -
106B GLN* 1.3 90.2 + - - +
108B MET* 1.3 60.8 + - - +
109B ILE 3.7 0.9 - - - -
58D PHE 4.3 5.4 + - - +
59D HIS* 3.4 23.9 + - - +
84D THR 5.4 5.8 + - - -
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Residues in contact with MET 108 (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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35B TYR* 3.3 24.8 + - + -
87B ARG 3.0 7.2 + - - +
89B MET* 3.2 49.6 - - + -
91B MET* 4.4 6.1 - - - -
105B ILE* 3.3 34.1 - - + +
106B GLN 3.9 0.2 - - - +
107B ASN* 1.3 81.0 - - - +
109B ILE* 1.3 63.2 + - + +
58D PHE* 3.3 55.0 - - + -
59D HIS* 2.9 24.9 - - - +
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Residues in contact with ILE 109 (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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58A ASP 5.3 3.6 - - - +
35B TYR* 3.8 15.3 - - + -
36B HIS* 3.4 27.6 - - + +
37B ALA 4.0 2.5 - - - -
38B ASN* 4.4 3.4 - - - +
86B LEU* 3.2 8.1 - - - -
87B ARG* 3.0 75.5 + - + +
88B PRO 4.4 4.3 - - - +
89B MET* 4.3 20.6 - - + -
108B MET* 1.3 80.1 - - + +
110B VAL* 1.3 72.6 + - - +
111B GLU* 3.4 1.2 + - - +
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Residues in contact with VAL 110 (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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13B LYS* 3.6 7.8 - - + +
37B ALA 3.0 12.6 + - - +
38B ASN* 2.9 33.3 + - + +
39B TYR* 4.7 4.3 - - - -
40B CYS* 3.9 6.1 - - - -
83B PRO* 3.9 14.1 - - + -
85B LYS 4.0 3.4 - - - -
86B LEU* 3.8 15.9 - - + -
108B MET 4.1 0.2 - - - -
109B ILE* 1.3 72.3 - - - +
111B GLU* 1.3 60.9 + - - +
112B GLU 4.0 9.9 - - - +
113B CYS* 3.9 28.7 - - - -
59D HIS* 3.2 32.8 - - + +
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Residues in contact with GLU 111 (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 LYS* 3.0 34.7 + - - +
13B LYS* 3.3 24.5 + - - +
85B LYS* 2.9 35.4 + - + +
86B LEU* 4.9 0.2 - - - -
87B ARG* 3.1 49.7 + - - +
109B ILE* 3.4 5.0 + - + +
110B VAL* 1.3 75.1 - - - +
112B GLU* 1.3 82.3 + - - +
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Residues in contact with GLU 112 (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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2B LEU* 4.5 25.5 - - + +
13B LYS* 4.9 4.1 + - - -
83B PRO* 3.4 6.2 - - - +
84B THR* 2.8 39.1 + - - +
85B LYS* 3.2 23.7 + - + +
110B VAL* 3.7 1.7 - - - +
111B GLU* 1.3 101.2 - - - +
113B CYS* 1.3 60.4 + - - +
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Residues in contact with CYS 113 (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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2B LEU* 3.7 24.6 + - - +
11B CYS* 4.0 11.2 - - - +
12B CYS* 3.8 16.4 - - - -
13B LYS* 3.6 28.0 - - - +
40B CYS* 2.0 57.0 - - + -
82B VAL 3.4 4.9 - - - -
84B THR* 3.8 5.9 + - - -
110B VAL* 3.9 2.0 - - - -
112B GLU* 1.3 77.3 - - - +
114B GLY* 1.3 56.6 + - - +
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Residues in contact with GLY 114 (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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11B CYS* 3.6 11.8 - - - -
82B VAL* 2.9 34.1 + - - +
84B THR* 3.9 14.9 - - - +
113B CYS* 1.3 75.2 - - - +
115B CYS* 1.3 64.1 + - - -
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Residues in contact with CYS 115 (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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10B ILE* 5.9 0.2 - - - -
11B CYS* 3.5 19.7 - - - -
43B GLU 3.8 0.7 - - - -
44B CYS* 2.1 55.4 - - + -
45B PRO* 4.5 5.4 - - + +
53B GLY* 4.7 9.2 - - - -
54B SER* 4.1 19.8 + - - -
79B SER* 4.5 1.1 - - - -
80B CYS 3.2 4.9 - - - -
114B GLY* 1.3 71.9 - - - -
116B SER* 1.3 68.1 + - - +
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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
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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