Contacts of the strand formed by residues 17 - 28 (chain A) in PDB entry 3E17
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 LEU 17 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6A LEU* 4.6 3.6 - - + -
15A TYR* 4.2 15.9 - - + +
16A GLY* 1.3 76.6 - - - +
18A ARG* 1.3 60.9 + - - +
19A LEU* 3.8 24.0 + - + +
25B VAL* 3.9 28.5 - - + -
27B GLU 3.7 2.0 - - - +
28B MET* 4.3 4.0 - - + -
34B ALA* 4.5 2.9 - - + -
40B LEU* 3.7 22.0 - - + -
46B ILE* 5.5 1.1 - - + -
66B ILE* 4.3 13.7 - - + +
73B LEU* 4.1 18.8 - - + -
75B LEU* 4.0 26.7 - - + -
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Residues in contact with ARG 18 (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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16A GLY 4.2 0.2 - - - -
17A LEU* 1.3 73.3 - - - +
19A LEU* 1.3 72.8 + - - +
56A ASN* 6.2 0.2 - - - +
25B VAL* 3.8 3.1 - - - -
26B LYS* 2.8 58.4 + - + +
27B GLU* 2.8 52.8 + - + +
29B THR* 6.2 1.7 - - + +
63B ARG* 4.2 12.5 - - - +
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Residues in contact with LEU 19 (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 LEU* 3.8 35.5 + - + +
18A ARG* 1.3 79.9 - - - +
20A GLY* 1.3 58.9 + - - +
56A ASN* 5.1 1.0 + - - -
23B ILE* 3.7 23.1 - - + -
24B PHE 3.4 9.2 - - - +
25B VAL* 4.8 0.2 - - - -
26B LYS* 4.0 4.6 - - - +
46B ILE* 4.5 12.1 - - + -
49B ILE* 4.6 4.3 - - + -
59B LEU* 3.6 13.8 - - + +
62B ALA* 4.4 15.3 - - + +
63B ARG* 3.1 40.5 + - + +
66B ILE* 3.3 29.8 - - + -
75B LEU* 6.5 0.2 - - + -
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Residues in contact with GLY 20 (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 LEU* 1.3 73.9 - - - +
21A SER* 1.3 60.2 + - - -
56A ASN* 3.2 14.4 - - - -
23B ILE* 3.4 9.5 - - - +
24B PHE* 3.0 45.9 + - - -
26B LYS* 4.0 7.5 - - - +
59B LEU* 3.8 8.9 - - - +
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Residues in contact with SER 21 (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 GLY* 1.3 75.1 - - - -
22A GLN* 1.3 63.7 + - - +
54A THR 5.2 0.2 - - - -
55A GLU* 3.7 8.3 - - - +
56A ASN* 2.8 56.7 + - - +
57A MET 3.6 10.6 + - - -
21B SER* 4.9 7.2 - - - -
22B GLN 3.2 11.0 - - - -
23B ILE* 4.0 16.2 - - - -
24B PHE* 3.7 3.3 - - - -
57B MET 5.0 1.1 - - - -
58B SER* 5.7 0.4 - - - -
59B LEU* 4.2 12.7 + - - +
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Residues in contact with GLN 22 (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 SER* 1.3 75.8 - - - +
23A ILE* 1.3 66.0 + - - +
24A PHE 4.0 0.3 + - - -
45A ILE* 3.5 35.3 - - + +
46A ILE 5.5 0.4 - - - +
54A THR 5.0 2.2 - - - -
55A GLU* 5.1 4.7 - - + +
78A LEU* 6.0 1.2 - - - +
21B SER* 3.2 5.0 - - - -
22B GLN* 2.3 80.0 + - + +
24B PHE* 4.0 22.4 - - + -
45B ILE* 3.6 12.9 - - - +
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Residues in contact with ILE 23 (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 GLN* 1.3 73.8 - - - +
24A PHE* 1.3 61.6 + - - +
45A ILE* 3.5 8.1 - - - +
46A ILE* 2.9 41.5 + - + +
49A ILE* 5.2 0.7 - - + -
54A THR* 3.9 36.8 + - - +
57A MET* 3.4 22.7 - - + +
59A LEU* 4.0 11.0 - - + -
62A ALA* 3.8 20.9 - - + -
19B LEU* 3.8 30.1 - - + -
20B GLY 3.4 7.6 - - - +
21B SER* 4.0 17.5 - - - -
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Residues in contact with PHE 24 (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 ILE* 1.3 74.6 - - - +
25A VAL* 1.3 69.3 - - - +
26A LYS* 3.2 28.3 + - + -
43A GLY* 4.4 10.5 - - - +
44A ASP 3.2 12.8 - - - +
45A ILE* 3.8 17.5 - - + -
46A ILE* 4.4 1.6 - - - +
19B LEU* 3.4 10.6 - - - +
20B GLY* 3.0 56.6 + - - -
21B SER* 3.7 21.1 - - - -
22B GLN* 4.0 25.6 - - + -
55B GLU* 3.6 24.5 - - + -
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Residues in contact with VAL 25 (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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24A PHE* 1.3 73.0 - - - +
26A LYS* 1.3 63.2 + - - +
27A GLU 4.2 5.6 - - - +
28A MET* 3.8 29.4 - - + -
40A LEU* 4.0 14.8 - - + -
41A HIS 3.5 23.6 - - - +
42A GLU* 3.9 5.6 - - - +
43A GLY* 2.7 29.2 + - - +
44A ASP* 2.9 23.5 + - + +
46A ILE* 3.8 23.3 - - + -
17B LEU* 3.8 13.5 - - + -
18B ARG 4.0 2.7 - - - -
19B LEU* 4.6 1.8 - - + -
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Residues in contact with LYS 26 (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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24A PHE* 3.2 20.7 + - + -
25A VAL* 1.3 71.9 - - - +
27A GLU* 1.3 58.5 + - + +
42A GLU* 3.2 21.6 - - - +
18B ARG* 2.8 47.6 + - + +
19B LEU 4.1 2.2 - - - +
20B GLY* 4.1 13.9 - - - +
55B GLU* 2.7 35.3 + - - +
56B ASN* 6.2 0.7 - - - +
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Residues in contact with GLU 27 (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 VAL* 3.5 3.0 - - - +
26A LYS* 1.3 83.5 - - + +
28A MET* 1.3 83.6 - - - +
29A THR* 4.3 18.1 + - - +
42A GLU* 4.4 10.8 - - - +
16B GLY 4.0 0.2 - - - +
17B LEU* 3.7 2.4 - - - -
18B ARG* 2.9 54.3 + - + +
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Residues in contact with MET 28 (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 VAL* 3.8 14.6 - - + -
27A GLU* 1.3 88.7 - - - +
29A THR* 1.3 64.9 + - - +
30A ARG* 3.8 1.0 + - - +
34A ALA* 4.0 24.7 - - + +
35A THR* 3.5 20.0 + - - +
40A LEU* 3.3 45.8 - - - +
41A HIS* 4.0 1.3 - - + -
42A GLU* 3.7 25.9 + - + +
16B GLY 3.2 7.6 - - - +
17B LEU* 4.5 2.2 - - + -
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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