Contacts of the strand formed by residues 40 - 54 (chain A) 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 ILE 40 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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30A ASP* 4.0 2.4 - - - -
31A SER* 3.7 8.0 + - - -
32A GLY 2.5 38.0 + - - +
34A ASP* 3.8 27.6 - - + +
38A ASN 3.9 1.3 - - - +
39A PRO* 1.3 77.8 - - - +
41A LYS* 1.3 67.1 + - - +
42A ARG* 5.2 2.3 - - + +
169D ASP* 3.8 11.2 - - - +
170D PHE* 4.1 25.7 - - + -
171D TYR* 3.6 31.9 - - + -
184D TYR* 5.1 6.7 - - + -
190D LEU* 3.8 23.1 - - + -
191D TYR* 5.0 10.3 - - + +
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Residues in contact with LYS 41 (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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28A GLU* 3.3 38.2 + - - +
29A VAL 3.3 8.5 - - - +
30A ASP* 4.1 14.2 + - - +
39A PRO* 4.0 25.0 + - + +
40A ILE* 1.3 75.8 - - - +
42A ARG* 1.3 59.6 + - - +
67A PRO* 3.0 18.4 - - + +
171D TYR* 3.0 18.9 + - - -
191D TYR* 5.1 8.4 + - - +
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Residues in contact with ARG 42 (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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28A GLU* 4.5 2.5 - - - -
29A VAL* 2.9 38.8 + - + +
30A ASP* 5.1 0.2 - - - +
31A SER* 3.9 26.1 + - - +
40A ILE* 4.1 4.6 + - + +
41A LYS* 1.3 71.3 - - - +
43A ILE* 1.3 66.9 + - - +
44A GLN 3.5 0.9 + - - -
64A TYR* 3.3 38.2 - - + +
65A THR* 3.6 9.6 - - - +
67A PRO* 3.9 4.0 - - - -
91A GLU* 2.6 42.2 + - - -
95A LYS* 6.0 0.2 - - - +
97A HIS* 4.4 4.8 + - - +
170D PHE* 3.8 33.7 + - + +
171D TYR* 3.1 35.4 - - + +
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Residues in contact with ILE 43 (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 GLU* 3.9 34.8 - - + +
27A LYS 3.7 2.7 - - - +
28A GLU* 3.8 28.7 - - + +
42A ARG* 1.3 71.1 - - - +
44A GLN* 1.3 62.9 + - - +
45A TYR* 3.8 30.1 - - + +
63A ILE 3.7 0.5 - - - +
64A TYR* 3.2 7.9 - - - -
65A THR* 2.9 37.4 + - + +
66A ALA 4.1 4.9 - - - +
67A PRO* 4.0 25.0 - - + +
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Residues in contact with GLN 44 (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 SER 4.7 0.2 - - - -
26A GLU* 3.7 1.6 - - - -
27A LYS* 2.8 58.0 + - + +
29A VAL* 3.7 18.8 - - + +
42A ARG 3.5 0.6 + - - -
43A ILE* 1.3 75.9 - - - +
45A TYR* 1.3 60.8 + - - +
46A GLU* 3.9 1.7 + - - +
62A PHE* 3.8 36.4 - - + -
63A ILE 3.7 2.5 - - - -
64A TYR* 2.6 45.1 + - + -
95A LYS* 5.6 0.2 - - - +
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Residues in contact with TYR 45 (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 ALA* 4.3 2.9 - - + -
25A SER 3.4 7.6 - - - +
26A GLU* 4.1 20.1 + - + -
43A ILE* 3.8 20.1 - - + +
44A GLN* 1.3 72.6 - - - +
46A GLU* 1.3 61.1 + - - +
47A ILE* 4.3 15.0 - - + -
62A PHE* 3.2 11.0 - - - +
63A ILE* 2.7 49.8 + - + +
65A THR* 3.8 11.8 - - + +
74A VAL 2.9 20.3 + - - -
75A SER* 3.1 5.5 - - - -
76A LEU* 2.8 49.1 + - + -
78A VAL* 3.3 35.7 - - + -
98A ILE* 5.0 1.6 - - + -
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Residues in contact with GLU 46 (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 ALA* 3.6 1.4 - - - -
24A VAL* 2.9 36.5 + - + +
25A SER* 2.9 38.2 + - - +
27A LYS* 5.1 5.4 + - - +
44A GLN* 3.9 2.3 + - - +
45A TYR* 1.3 72.0 - - - +
47A ILE* 1.3 68.5 + - - +
61A GLU* 3.6 6.1 - - + +
62A PHE* 3.9 25.4 - - + -
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Residues in contact with ILE 47 (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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19A ILE* 4.2 6.5 - - + -
21A ALA* 4.0 17.5 - - + -
22A LYS 3.3 15.3 - - - +
23A ALA* 3.9 13.0 - - + -
24A VAL* 4.5 4.3 - - - +
45A TYR* 4.3 8.5 - - + +
46A GLU* 1.3 84.8 - - - +
48A LYS* 1.3 60.4 + - - +
49A GLN* 3.9 11.7 + - - +
60A ILE* 3.2 38.8 - - + +
61A GLU* 2.8 36.1 + - - +
62A PHE 4.1 1.3 - - - +
63A ILE* 3.8 26.0 - - + -
76A LEU* 5.2 1.3 - - + -
86A ILE* 5.6 0.9 - - + -
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Residues in contact with LYS 48 (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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21A ALA* 3.5 1.7 - - - -
22A LYS* 3.0 36.0 + - + +
24A VAL* 4.4 11.9 - - + +
47A ILE* 1.3 77.5 - - - +
49A GLN* 1.3 80.2 + - + +
50A ILE* 3.2 13.1 + - + +
59A ASP* 5.1 7.7 + - - -
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Residues in contact with GLN 49 (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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19A ILE* 3.9 11.1 - - + +
20A ARG 4.0 4.0 - - - +
21A ALA* 4.4 0.4 - - - -
47A ILE* 3.9 9.8 - - + +
48A LYS* 1.3 90.3 + - - +
50A ILE* 1.3 64.1 + - - +
51A LYS* 3.8 15.4 - - - +
52A MET* 3.5 40.4 - - - +
59A ASP* 3.4 33.5 + - + +
60A ILE* 2.8 47.9 + - - +
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Residues in contact with ILE 50 (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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20A ARG* 2.9 39.0 + - + +
21A ALA* 4.1 10.8 - - - +
22A LYS* 4.1 13.9 - - + -
48A LYS* 3.8 17.0 - - + +
49A GLN* 1.3 75.7 - - - +
51A LYS* 1.3 63.5 + - + +
83A GLU* 3.2 41.7 - - + +
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Residues in contact with LYS 51 (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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19A ILE* 3.2 6.1 - - - +
20A ARG* 2.9 44.1 + - + +
49A GLN* 3.5 8.7 - - - +
50A ILE* 1.3 86.1 - - + +
52A MET* 1.3 68.6 - - - +
53A PHE* 3.5 38.1 - - + -
119A ASN* 4.3 12.9 + - - +
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Residues in contact with MET 52 (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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17A VAL* 4.7 0.7 - - + -
18A VAL 3.7 3.8 - - - +
19A ILE* 3.9 10.1 - - + -
49A GLN* 3.5 36.6 - - - +
51A LYS* 1.3 86.7 - - - +
53A PHE* 1.3 64.4 + - - +
54A LYS* 3.3 17.0 - - - +
55A GLY* 3.3 20.0 - - - +
56A PRO* 3.2 44.2 - - + +
57A GLU* 5.5 0.2 - - - -
58A LYS 4.8 2.2 - - - +
60A ILE* 4.5 6.1 - - + -
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Residues in contact with PHE 53 (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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12A PHE* 4.1 17.6 - - + -
18A VAL* 2.9 21.2 + - + +
19A ILE* 4.2 1.1 - - - -
20A ARG* 3.9 24.2 - - + -
51A LYS* 3.5 48.9 - - + -
52A MET* 1.3 74.8 - - - +
54A LYS* 1.3 61.9 + - - +
85A LEU* 4.1 8.1 - - + -
107A TRP* 3.9 22.2 - + - -
115A LYS 4.9 2.7 - - - -
118A LEU* 3.5 54.4 - - + +
119A ASN* 4.6 6.1 - - - -
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Residues in contact with LYS 54 (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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12A PHE* 2.8 41.8 + - + +
13A CYS* 3.1 18.6 + - - +
15A ALA 2.7 27.2 + - - +
16A ASP* 4.0 8.5 - - - +
17A VAL* 3.4 1.7 - - - +
18A VAL* 2.8 45.1 + - + +
52A MET* 3.3 10.3 - - - +
53A PHE* 1.3 79.6 - - - +
55A GLY* 1.3 60.7 + - - +
123A GLN* 4.3 15.0 + - - +
126A CYS* 5.5 0.6 - - - -
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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