Contacts of the strand formed by residues 42 - 49 (chain B) in PDB entry 2E3V
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 LYS 42 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14A SER* 3.0 19.3 + - - -
16A ASP* 3.6 18.6 - - - +
30A ASP* 2.8 30.8 + - - +
40B ILE* 3.5 7.7 - - - +
41B LEU* 1.3 92.6 - - - +
43B TYR* 1.3 62.4 + - - +
59B TRP* 3.8 20.6 - - + -
60B TYR 3.3 13.9 - - - +
61B ASP* 3.1 21.0 + - - -
62B ALA* 3.7 2.9 - - - +
88B ALA* 3.6 0.5 - - - -
89B LEU* 2.7 48.2 + - + +
1005B PEG 3.6 24.9 + - - -
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Residues in contact with TYR 43 (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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13B PRO* 4.1 8.3 - - + -
29B PHE* 3.4 39.8 - + + -
31B GLU* 3.5 26.7 - - + +
40B ILE* 3.6 13.7 - - + +
42B LYS* 1.3 73.8 - - - +
44B LYS* 1.3 62.6 + - - +
45B ALA 4.2 0.7 - - - -
59B TRP* 3.4 8.1 - - - -
60B TYR* 2.8 41.0 + - + +
62B ALA* 3.7 34.3 - - + -
65B ALA* 3.9 13.2 - - + -
66B SER* 5.3 3.2 - - - -
71B VAL* 4.5 8.5 - - + -
86B LEU* 5.8 3.8 - - + -
87B ALA 3.3 13.2 - - - +
88B ALA* 3.8 21.5 - - + -
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Residues in contact with LYS 44 (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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17A GLN* 2.9 23.8 + - - -
43B TYR* 1.3 76.0 - - - +
45B ALA* 1.3 67.1 + - - +
46B GLU* 4.2 8.3 + - + +
57B SER* 3.6 9.6 - - - -
58B LYS 3.5 10.1 - - - +
59B TRP* 3.5 35.7 - - + +
85B ARG 4.1 0.2 - - - +
86B LEU* 3.3 5.2 - - - +
87B ALA* 2.8 38.9 + - + +
94B LEU* 4.3 21.5 - - + +
97B ILE* 4.4 2.7 - - + +
1009B BTB 2.9 53.0 + - - -
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Residues in contact with ALA 45 (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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43B TYR 4.2 0.4 - - - -
44B LYS* 1.3 74.5 - - - +
46B GLU* 1.3 61.5 + - - +
47B TRP* 3.7 2.9 - - + -
57B SER* 3.1 8.3 - - - -
58B LYS 2.9 30.2 + - - +
60B TYR* 3.7 23.4 - - + -
71B VAL* 4.4 1.3 - - + -
73B ILE* 3.7 21.8 - - + -
84B VAL* 4.9 0.9 - - + -
85B ARG 3.5 4.0 - - - -
86B LEU* 3.5 22.0 - - + -
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Residues in contact with GLU 46 (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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44B LYS* 4.3 9.1 + - + +
45B ALA* 1.3 78.8 - - - +
47B TRP* 1.3 63.0 + - - +
55B TRP* 3.8 13.0 - - + -
56B HIS 3.1 11.0 - - - +
57B SER* 4.0 1.8 - - - -
84B VAL* 3.2 4.2 - - - +
85B ARG* 2.7 80.7 + - + +
97B ILE* 3.8 18.1 - - + +
1009B BTB 2.5 38.2 + - - +
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Residues in contact with TRP 47 (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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67A MSE 3.1 40.6 - - + +
68A GLU* 4.5 0.2 - - + -
45B ALA 3.7 4.3 - - - -
46B GLU* 1.3 81.0 - - - +
48B ARG* 1.3 61.6 + - - +
55B TRP* 3.4 3.9 - - - -
56B HIS* 2.7 67.0 + + + +
57B SER* 3.6 15.9 - - - -
58B LYS* 3.6 27.4 - - + -
60B TYR* 4.8 1.3 - - - -
73B ILE* 3.4 41.7 - - + -
74B VAL 4.4 0.6 + - - -
76B LEU* 3.5 28.1 - - + +
82B TYR* 3.9 16.8 - + + -
83B ALA 3.1 14.6 - - - +
84B VAL* 4.2 10.8 - - + -
103B PHE* 5.3 1.6 - - + -
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Residues in contact with ARG 48 (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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47B TRP* 1.3 79.3 - - - +
49B ALA* 1.3 75.8 + - - +
52B GLU* 3.3 25.5 + - + +
53B GLU* 3.0 38.2 + - - +
54B VAL 3.5 12.8 - - - +
55B TRP* 3.5 38.5 - - + +
82B TYR* 3.4 5.1 - - - -
83B ALA* 2.9 31.7 + - + +
1006B PGE 3.0 34.3 + - - -
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Residues in contact with ALA 49 (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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48B ARG* 1.3 84.0 + - - +
50B VAL* 1.3 66.3 + - - +
52B GLU* 2.8 41.6 + - + +
77B LYS* 4.5 2.7 - - - +
80B THR* 3.8 8.3 - - + -
81B THR 3.4 6.7 - - - -
82B TYR* 3.4 19.6 - - + -
1007B PGE 3.4 23.1 - - - +
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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