Contacts of the strand formed by residues 21 - 30 (chain E) in PDB entry 1W72
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 ASN 21 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11E SER* 3.8 7.6 - - - -
12E ARG* 3.5 2.1 + - - +
13E HIS* 2.7 60.4 + - - +
14E PRO 3.8 9.7 + - - -
15E ALA* 4.3 5.5 - - - +
16E GLU 4.9 1.0 - - - +
19E LYS 4.1 4.5 + - - +
20E SER* 1.3 79.7 + - - +
22E PHE* 1.3 87.4 + - - +
69E GLU* 3.3 6.4 - - - +
70E PHE* 2.7 44.9 + - + +
72E PRO* 4.3 6.3 - - + +
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Residues in contact with PHE 22 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11E SER* 3.2 7.3 - - - -
12E ARG* 2.9 83.5 + - + +
13E HIS* 5.7 2.5 - + - -
20E SER* 5.2 1.3 - - - -
21E ASN* 1.3 89.6 + - - +
23E LEU* 1.3 59.7 + - - +
24E ASN* 4.0 8.1 - - - +
67E TYR* 4.0 20.9 - + - -
68E THR* 3.3 15.7 - - - +
69E GLU* 3.3 45.1 - - + -
70E PHE* 3.5 2.9 - - - -
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Residues in contact with LEU 23 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9E VAL* 3.9 20.6 - - + -
10E TYR 3.7 14.8 - - - +
22E PHE* 1.3 72.5 - - - +
24E ASN* 1.3 61.9 + - - +
39E LEU* 4.0 31.7 - - + +
46E ILE* 4.8 0.2 - - + -
67E TYR* 3.1 6.9 - - - -
68E THR* 2.8 39.3 + - + +
70E PHE* 3.4 23.3 - - + -
78E TYR* 3.6 36.6 - - + -
79E ALA 4.6 5.6 - - - +
95E TRP* 4.1 21.1 - - + -
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Residues in contact with ASN 24 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236D ALA 2.7 29.8 + - - +
237D GLY* 5.1 0.7 - - - -
8E GLN 4.2 0.4 - - - -
9E VAL* 3.2 8.5 - - - +
10E TYR* 2.6 70.8 + - + +
12E ARG* 3.7 17.2 + - - +
22E PHE* 4.3 6.1 - - - +
23E LEU* 1.3 75.8 - - - +
25E CYS* 1.3 61.8 + - - +
26E TYR 4.0 0.7 - - - -
39E LEU* 4.6 2.5 - - - -
65E LEU* 3.7 13.0 - - + +
66E TYR 3.5 2.2 - - - -
67E TYR* 3.1 24.1 - - - +
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Residues in contact with CYS 25 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7E ILE* 3.9 18.2 - - - -
8E GLN 3.3 3.1 - - - -
9E VAL* 4.0 1.3 - - - -
24E ASN* 1.3 74.3 - - - +
26E TYR* 1.3 62.6 + - - +
27E VAL* 3.7 3.2 + - - -
37E VAL* 4.3 2.9 - - - -
39E LEU* 3.6 15.2 - - + +
64E LEU 3.6 2.4 - - - +
65E LEU* 4.1 1.1 - - - -
66E TYR* 2.8 44.5 + - + +
80E CYS* 2.0 51.4 - - + -
82E VAL* 4.3 4.7 - - - -
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Residues in contact with TYR 26 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232D GLU* 3.5 28.2 + - + -
233D THR 4.1 11.3 + - - -
234D ARG* 4.1 11.4 - - + -
235D PRO* 3.4 36.6 - - + +
6E LYS 3.7 1.4 - - - +
7E ILE* 3.6 3.1 - - - -
8E GLN* 2.7 40.8 + - + +
10E TYR* 3.4 24.7 - - + +
24E ASN 4.0 0.4 - - - -
25E CYS* 1.3 72.0 - - - +
27E VAL* 1.3 59.3 + - - +
28E SER* 3.8 14.7 + - - -
63E TYR* 3.8 40.1 - + + +
64E LEU 3.6 15.3 - - - -
65E LEU* 4.0 4.3 - - + -
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Residues in contact with VAL 27 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5E PRO* 3.2 34.3 - - + -
6E LYS 3.2 6.7 - - - +
7E ILE* 4.5 5.2 - - + +
25E CYS* 3.7 3.9 + - - +
26E TYR* 1.3 74.1 - - - +
28E SER* 1.3 62.2 + - - +
30E PHE* 3.6 16.4 - - + -
35E ILE* 3.6 17.0 - - + -
37E VAL* 4.5 5.6 - - + -
63E TYR* 3.2 2.9 - - - +
64E LEU* 2.9 53.7 + - + +
66E TYR* 4.4 14.1 - - + -
82E VAL* 4.4 10.8 - - + -
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Residues in contact with SER 28 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232D GLU* 3.3 33.0 + - - -
5E PRO* 3.3 2.9 - - - +
6E LYS* 2.7 43.2 + - - +
26E TYR* 3.8 10.7 + - - -
27E VAL* 1.3 78.0 - - - +
29E GLY* 1.3 64.8 + - - +
30E PHE* 3.2 5.2 - - - -
62E PHE 3.3 8.3 - - - -
63E TYR* 3.6 16.2 - - - -
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Residues in contact with GLY 29 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3E ARG* 3.3 19.4 - - - +
4E THR 3.5 9.3 - - - +
6E LYS* 3.4 21.2 - - - +
28E SER* 1.3 76.6 - - - +
30E PHE* 1.3 55.3 + - - +
61E SER* 2.7 25.4 + - - -
62E PHE 3.0 7.1 + - - -
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Residues in contact with PHE 30 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3E ARG 3.3 12.1 - - - +
5E PRO* 3.6 21.1 - - + -
27E VAL* 3.6 38.6 - - + -
28E SER* 3.6 12.1 - - - -
29E GLY* 1.3 79.8 - - - +
31E HIS* 1.3 65.6 + - - +
32E PRO 3.2 24.5 - - - -
33E SER* 3.8 8.3 - - - -
35E ILE* 3.8 30.5 - - + -
54E LEU* 4.7 0.9 - - + -
61E SER* 3.1 2.5 + - - -
62E PHE* 3.1 65.9 + - + -
63E TYR* 3.8 2.2 - - - -
64E LEU* 4.2 11.0 - - + -
84E HIS* 3.8 3.8 - + - +
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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