Contacts of the strand formed by residues 50 - 60 (chain B) in PDB entry 2WJ7
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 PHE 50 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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56A HIS 3.9 0.4 - - - +
57A ARG* 3.4 3.4 + - - +
58A LYS* 2.9 57.2 + - + -
59A TYR 6.5 0.2 - - - -
60A ARG* 5.3 12.8 - - + -
43B GLU* 5.1 7.9 - - + -
44B ARG* 3.5 9.4 - - - +
45B GLN* 3.7 42.0 - - + -
49B GLY* 1.3 81.7 - - - -
51B ILE* 1.3 66.3 + - - +
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Residues in contact with ILE 51 (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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55A PHE* 4.2 15.5 - - + -
56A HIS 3.2 18.2 - - - +
57A ARG* 3.6 20.9 - - + +
41B HIS* 2.9 18.4 + - - +
43B GLU* 4.0 5.5 - - - +
44B ARG* 3.1 28.7 + - - +
46B ASP* 3.6 25.8 - - + +
50B PHE* 1.3 78.9 - - - +
52B SER* 1.3 74.7 + - - +
53B ARG* 3.5 40.4 - - + +
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Residues in contact with SER 52 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A PHE* 3.4 1.3 - - - -
56A HIS* 3.0 47.3 + - - +
41B HIS* 3.3 17.5 - - - -
42B GLU* 4.2 1.1 - - - -
43B GLU* 3.5 21.5 - - - +
51B ILE* 1.3 75.5 - - - +
53B ARG* 1.3 69.7 + - - +
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Residues in contact with ARG 53 (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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54A GLU 3.6 9.9 - - - +
55A PHE* 4.7 5.4 - - + -
57A ARG* 5.1 2.8 - - - +
20B HIS* 3.5 48.7 + - - +
21B PHE* 3.9 20.7 - - + -
40B LYS* 3.3 2.8 - - - +
41B HIS* 2.6 78.2 + - + +
44B ARG* 4.4 3.0 - - - +
46B ASP* 4.7 6.9 + - - -
51B ILE* 3.5 34.2 - - + +
52B SER* 1.3 80.3 - - - +
54B GLU* 1.3 62.8 + - - +
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Residues in contact with GLU 54 (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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53A ARG* 3.7 0.9 - - - +
54A GLU* 2.9 50.2 + - + +
21B PHE* 4.9 0.4 - - - -
38B HIS* 2.7 27.8 + - + -
39B GLY 3.2 14.8 - - - +
40B LYS* 3.1 32.0 + - + -
53B ARG* 1.3 77.9 - - - +
55B PHE* 1.3 71.4 + - - +
56B HIS* 5.9 0.4 - - + +
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Residues in contact with PHE 55 (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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51A ILE* 4.4 9.6 - - + -
52A SER 3.5 12.8 - - - +
53A ARG* 4.7 6.1 - - + -
16B LEU* 4.4 7.9 - - + -
17B ASP 5.9 0.7 - - - -
18B VAL* 4.3 16.8 - - + -
21B PHE* 3.7 37.9 - + - -
26B LEU* 4.3 3.6 - - + -
37B VAL* 3.6 38.6 - - + -
38B HIS* 3.2 8.3 + - - -
39B GLY* 2.9 48.1 + - - -
54B GLU* 1.3 80.0 - - - +
56B HIS* 1.3 62.8 + - - +
57B ARG* 4.0 17.5 - - + -
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Residues in contact with HIS 56 (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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43A GLU* 5.4 3.5 - - - +
50A PHE 3.9 0.9 - - - +
51A ILE* 3.4 4.5 + - - -
52A SER* 2.9 49.2 + - - +
36B GLU* 3.5 33.4 + - + -
37B VAL 3.4 10.7 + - - -
38B HIS* 4.0 24.1 - + + +
54B GLU* 6.0 0.2 - - + -
55B PHE* 1.3 74.9 - - - +
57B ARG* 1.3 58.9 + - - +
58B LYS* 2.7 33.8 + - - +
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Residues in contact with ARG 57 (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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46A ASP* 2.8 38.6 + - - -
48A HIS* 4.6 5.6 - - - +
49A GLY 3.1 29.4 - - - +
50A PHE 3.2 10.7 + - - +
51A ILE* 3.3 28.6 - - + +
53A ARG* 5.1 2.2 - - - +
16B LEU* 5.1 4.7 - - + -
35B ILE 3.5 0.2 - - - +
36B GLU* 3.3 5.4 - - - -
37B VAL* 2.9 41.8 + - + +
55B PHE* 4.0 15.7 - - + -
56B HIS* 1.3 72.0 + - - +
58B LYS* 1.3 70.9 + - - +
59B TYR* 3.4 44.5 + - + +
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Residues in contact with LYS 58 (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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43A GLU* 2.9 33.9 - - - +
49A GLY* 3.2 6.6 - - - -
50A PHE* 2.8 49.7 + - + +
34B VAL* 3.7 22.9 - - + -
35B ILE 3.1 4.3 - - - -
36B GLU* 3.9 16.8 + - + +
56B HIS* 2.7 42.1 + - - +
57B ARG* 1.3 80.6 + - - +
59B TYR* 1.3 61.6 + - - +
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Residues in contact with TYR 59 (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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48A HIS* 3.4 46.9 - + + +
49A GLY* 4.8 0.2 - - - -
14B VAL* 3.5 30.2 - - + +
15B ASN 4.9 0.3 + - - -
16B LEU* 3.1 28.4 - - + +
34B VAL* 3.3 9.7 - - - +
35B ILE* 2.9 61.3 + - + +
37B VAL* 4.2 13.9 - - + -
57B ARG* 3.4 37.4 + - + -
58B LYS* 1.3 76.7 - - - +
60B ARG* 1.3 68.4 + - - +
82B VAL* 5.9 2.7 - - + -
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Residues in contact with ARG 60 (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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45A GLN* 4.5 11.9 - - - +
46A ASP 5.0 2.4 + - - -
47A GLU 4.7 5.9 + - - -
48A HIS* 4.0 17.0 + - - +
49A GLY* 3.1 33.9 + - - +
50A PHE* 3.7 27.9 - - + -
33B ASP* 3.8 6.3 - - + +
34B VAL* 4.9 7.0 - - + +
35B ILE* 5.8 0.4 - - - +
59B TYR* 1.3 81.6 - - - +
61B ILE* 1.4 64.8 + - + +
62B PRO* 3.9 6.4 - - - +
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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