Contacts of the strand formed by residues 42 - 49 (chain E) in PDB entry 2P5W
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 ARG 42 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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33E TYR* 3.1 5.5 - - - -
34E ARG* 2.8 74.7 + - + +
35E GLN* 5.8 0.2 - - - -
36E ASP* 5.4 5.6 + - - -
40E GLY 3.8 10.8 - - - +
41E LEU* 1.3 76.4 - - - +
43E LEU* 1.3 62.9 + - - +
44E ILE* 3.5 2.8 + - - +
57E GLU* 3.0 31.1 + - - +
58E VAL* 2.6 43.2 - - + +
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Residues in contact with LEU 43 (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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101D ILE* 3.8 32.3 - - + -
29E TYR* 4.5 4.7 - - - +
31E SER* 3.8 21.8 - - - -
32E TRP 3.4 17.0 - - - +
33E TYR* 3.5 33.9 - - + +
41E LEU 4.3 0.4 + - - -
42E ARG* 1.3 70.9 - - - +
44E ILE* 1.3 58.5 + - - +
45E HIS 3.9 6.7 - - - +
46E TYR* 3.9 23.8 - - + -
56E GLY* 4.0 14.4 - - - -
57E GLU* 2.8 35.5 + - + +
58E VAL* 3.0 8.7 + - - +
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Residues in contact with ILE 44 (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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32E TRP* 2.8 17.3 + - + +
33E TYR* 3.8 15.3 - - - +
34E ARG* 4.0 5.4 - - + +
42E ARG 4.1 4.7 - - - +
43E LEU* 1.3 73.2 - - - +
45E HIS* 1.3 87.2 + - + +
56E GLY* 2.9 20.3 + - - -
58E VAL* 3.5 30.7 - - + +
59E PRO* 3.7 9.5 - - - +
62E TYR* 3.7 21.8 - - + -
74E LEU* 4.0 16.2 - - + -
87E TYR* 3.7 36.3 - - + -
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Residues in contact with HIS 45 (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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31E SER* 3.5 1.4 - - - -
32E TRP* 3.1 26.8 + - + +
43E LEU* 3.9 2.8 - - - +
44E ILE* 1.3 101.1 + - + +
46E TYR* 1.3 66.6 + - - +
53E THR* 5.4 1.2 + - - -
54E ASP 3.3 18.2 + - - +
55E GLN* 3.7 15.0 - - + +
56E GLY 4.2 1.6 - - - +
59E PRO* 3.2 29.5 + - + +
62E TYR* 3.2 28.2 + - + -
63E ASN* 4.3 2.2 + - - -
64E VAL* 3.5 46.0 - - + +
72E PHE* 4.0 2.4 - - + -
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Residues in contact with TYR 46 (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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65A ARG* 3.2 34.6 + - - -
99D THR* 3.3 27.5 + - - +
101D ILE* 3.8 22.5 - - + +
29E TYR* 3.7 24.0 - + + +
30E MET 3.3 14.1 - - - +
31E SER* 3.8 10.5 - - - -
43E LEU* 3.9 16.6 - - + -
45E HIS* 1.3 76.2 - - - +
47E SER* 1.3 64.1 + - - +
48E VAL* 4.2 9.2 - - + -
52E MET* 4.2 4.0 - - + -
53E THR* 3.3 6.1 - - - -
54E ASP* 2.9 49.3 + - + -
55E GLN 3.7 21.5 + - - -
72E PHE* 3.7 5.3 - - - -
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Residues in contact with SER 47 (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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28E GLU 3.4 1.6 - - - +
29E TYR* 3.3 7.4 - - - -
30E MET 2.9 27.2 + - - +
46E TYR* 1.3 77.9 - - - +
48E VAL* 1.3 60.7 + - - +
49E SER 2.9 14.8 + - - -
52E MET* 2.6 29.6 + - - -
66E ARG* 3.0 18.7 + - - +
72E PHE* 3.5 23.6 - - - -
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Residues in contact with VAL 48 (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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65A ARG* 3.8 22.2 - - + +
68A LYS* 4.2 2.2 - - + -
69A ALA* 3.8 11.4 - - + +
72A GLN* 3.8 4.0 - - - +
100D TYR* 3.9 26.2 - - + -
28E GLU* 3.4 29.4 - - - +
29E TYR* 4.5 3.1 - - + -
46E TYR* 4.2 11.9 - - + -
47E SER* 1.3 73.0 - - - +
49E SER* 1.3 68.0 + - - +
52E MET* 3.3 39.8 - - + -
94E LEU* 3.7 17.9 - - + -
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Residues in contact with SER 49 (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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19A GLU* 5.0 2.1 + - - -
68A LYS* 3.6 26.2 + - - +
71A SER* 3.9 6.6 + - - -
72A GLN* 3.4 18.8 + - - +
28E GLU 3.7 3.5 + - - -
47E SER* 2.9 19.6 + - - -
48E VAL* 1.3 91.0 - - - +
50E VAL* 1.3 78.7 + - - +
52E MET* 3.1 16.5 + - - +
66E ARG* 3.4 5.5 - - - +
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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