Contacts of the strand formed by residues 17 - 30 (chain B) in PDB entry 4ILW
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 VAL 17 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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15B ALA* 3.7 0.3 - - - +
16B ASP* 1.3 86.4 - - + +
18B VAL* 1.3 67.7 + - - +
19B ILE* 3.7 24.2 - - + -
52B MET* 4.3 4.9 - - + -
54B LYS 3.4 7.0 - - - +
56B PRO* 4.2 11.9 - - + -
60B ILE* 4.1 17.5 - - + -
86B ILE 3.7 0.9 - - - +
87B ALA* 3.3 2.9 - - - -
88B GLY 2.9 32.0 + - - +
89B LYS 4.5 0.7 - - - -
90B ALA* 3.9 31.4 - - + +
96B MET* 4.0 23.1 - - + +
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Residues in contact with VAL 18 (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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12B PHE* 4.0 37.9 - - + +
15B ALA* 4.1 9.2 - - + -
17B VAL* 1.3 79.2 - - - +
19B ILE* 1.3 67.0 + - - +
53B PHE* 2.9 32.8 + - + -
54B LYS* 2.8 30.7 + - + +
85B LEU* 3.8 27.1 - - + -
86B ILE 3.3 6.1 - - - +
87B ALA* 4.0 17.5 - - + -
118B LEU* 4.7 1.8 - - + -
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Residues in contact with ILE 19 (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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17B VAL* 3.7 14.4 - - + -
18B VAL* 1.3 80.8 - - - +
20B ARG* 1.3 60.2 + - - +
21B ALA* 4.3 10.8 - - + -
47B ILE* 4.1 16.2 - - + -
49B GLN* 3.9 19.5 - - + +
51B LYS 3.2 13.2 - - - +
52B MET* 3.9 10.5 - - + -
53B PHE* 4.2 1.8 - - - -
60B ILE* 4.0 16.8 - - + -
63B ILE* 4.7 3.8 - - + -
84B TYR 3.6 0.2 - - - +
85B LEU* 3.5 8.5 - - - +
86B ILE* 2.7 51.3 + - + +
96B MET* 3.8 26.0 - - - -
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Residues in contact with ARG 20 (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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19B ILE* 1.3 71.1 - - - +
21B ALA* 1.3 65.5 + - - +
49B GLN* 3.8 1.6 - - - -
50B ILE* 2.9 46.2 + - + +
51B LYS* 2.8 25.1 + - + +
53B PHE* 3.9 14.1 - - + -
83B GLU* 2.6 30.6 + - + +
84B TYR 3.3 7.2 - - - +
85B LEU* 4.6 1.3 - - - +
107B TRP* 3.3 64.9 - - + +
108B ASP* 5.4 0.2 + - - -
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Residues in contact with ALA 21 (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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19B ILE* 4.0 13.0 - - + -
20B ARG* 1.3 78.0 - - - +
22B LYS* 1.3 62.4 + - - +
47B ILE* 4.0 22.7 - - + -
48B LYS 3.4 14.4 - - - +
49B GLN* 4.4 0.4 - - - -
50B ILE* 4.1 7.9 - - - -
83B GLU* 3.3 2.1 - - - -
84B TYR* 2.6 44.6 + - - +
86B ILE* 4.4 13.7 - - + -
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Residues in contact with LYS 22 (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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21B ALA* 1.3 73.0 - - - +
23B ALA* 1.3 59.7 + - - +
24B VAL* 3.8 12.1 + - + +
47B ILE* 3.4 5.2 - - - +
48B LYS* 3.0 41.3 + - + +
50B ILE* 4.2 6.0 - - + +
80B GLY* 3.4 15.5 - - - -
81B LYS* 3.2 38.4 - - - +
82B LYS 3.1 25.4 - - - +
83B GLU* 4.0 15.0 - - + +
84B TYR* 5.1 1.1 - - - -
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Residues in contact with ALA 23 (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 LYS* 1.3 74.4 - - - +
24B VAL* 1.3 61.3 + - - +
45B TYR* 4.3 4.3 - - + -
46B GLU 3.6 8.7 - - - +
47B ILE* 4.0 11.7 - - + -
76B LEU* 4.2 22.7 - - + -
77B ASP 4.0 6.1 + - - +
78B VAL* 3.7 26.6 - - + -
79B GLY 3.5 4.9 + - - -
80B GLY* 3.1 20.8 + - - -
81B LYS 4.6 0.3 + - - -
82B LYS 4.1 4.3 + - - +
84B TYR* 5.2 3.3 - - + -
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Residues in contact with VAL 24 (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 LYS* 4.3 17.5 - - - +
23B ALA* 1.3 73.0 - - - +
25B SER* 1.3 64.9 + - - +
46B GLU* 2.9 23.4 + - + +
47B ILE 4.7 1.6 - - - -
48B LYS* 4.4 17.0 - - + +
78B VAL* 3.0 6.0 - - - +
79B GLY* 3.0 26.5 + - - +
80B GLY* 3.9 14.8 - - - +
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Residues in contact with SER 25 (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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24B VAL* 1.3 82.5 - - - +
26B GLU* 1.3 60.2 + - - +
27B LYS* 3.5 23.4 + - - -
45B TYR* 3.4 7.6 - - - +
46B GLU* 2.9 52.4 + - - +
78B VAL* 3.2 11.8 - - - +
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Residues in contact with GLU 26 (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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25B SER* 1.3 76.1 - - - +
27B LYS* 1.3 78.4 + - - +
43B ILE* 3.8 26.0 - - + +
44B GLN 3.7 4.5 - - - -
45B TYR* 3.3 28.7 + - + -
75B SER* 5.3 2.8 + - - -
76B LEU 4.9 1.8 - - - +
78B VAL* 3.6 19.6 - - + +
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Residues in contact with LYS 27 (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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25B SER* 3.5 22.8 + - - -
26B GLU* 1.3 85.0 - - - +
28B GLU* 1.3 68.1 + - - +
29B VAL* 4.4 4.3 - - + -
43B ILE* 4.5 4.9 - - - -
44B GLN* 2.8 57.9 + - - +
46B GLU* 5.0 6.6 + - - +
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Residues in contact with GLU 28 (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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27B LYS* 1.3 74.4 - - - +
29B VAL* 1.3 71.6 + - - +
41B LYS* 3.1 43.0 + - + +
42B ARG 3.7 5.4 - - - +
43B ILE* 3.8 22.8 - - + +
67B PRO* 4.2 9.6 - - + +
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Residues in contact with VAL 29 (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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27B LYS* 4.0 5.8 - - + +
28B GLU* 1.3 81.0 - - - +
30B ASP* 1.3 78.5 + - - +
41B LYS* 3.3 10.0 - - - +
42B ARG* 3.0 42.4 + - + +
44B GLN* 3.7 35.7 - - + +
64B TYR* 4.1 20.0 - - + -
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Residues in contact with ASP 30 (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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29B VAL* 1.3 92.0 - - - +
31B SER* 1.3 63.7 + - - +
32B GLY* 3.8 22.1 - - - +
39B PRO* 4.2 4.3 - - - +
40B ILE 3.7 4.3 - - - -
41B LYS* 3.7 29.5 + - - +
42B ARG 5.6 0.7 - - - -
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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