Contacts of the helix formed by residues 52 - 68 (chain B) in PDB entry 4WNP
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 52 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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26B ALA* 3.0 37.2 + - - +
27B PHE* 4.0 22.0 - - + -
49B ASN 3.2 6.1 + - - -
51B LYS* 1.3 89.4 - - - +
53B LEU* 1.3 64.7 + - - +
54B ALA 3.3 2.2 + - - -
55B LYS* 3.4 7.1 + - + -
56B SER* 2.9 20.8 + - - -
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Residues in contact with LEU 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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48B ILE* 3.2 35.7 - - + -
49B ASN 3.5 6.5 + - - -
50B LYS* 3.8 24.4 + - + +
51B LYS 3.6 3.2 + - - -
52B ASN* 1.3 73.4 - - - +
54B ALA* 1.3 64.7 + - - +
56B SER* 3.6 0.2 - - - -
57B GLN* 3.0 31.5 + - - +
86B ASN 5.7 2.7 - - - +
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Residues in contact with ALA 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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52B ASN 3.4 0.4 - - - -
53B LEU* 1.3 80.0 - - - +
55B LYS* 1.3 64.6 + - - +
57B GLN* 3.6 5.3 + - - +
58B THR* 3.2 26.5 + - - -
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Residues in contact with LYS 55 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27B PHE* 3.3 44.1 - - + -
52B ASN* 3.4 9.0 + - + +
53B LEU 3.4 0.2 - - - -
54B ALA* 1.3 77.8 - - - +
56B SER* 1.3 61.0 + - - +
58B THR* 3.2 7.3 + - - -
59B LEU* 2.8 52.1 + - + +
168B PHE* 4.3 11.1 - - - -
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Residues in contact with SER 56 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27B PHE* 2.8 37.2 + - - +
48B ILE* 3.3 10.8 - - - -
49B ASN 2.9 29.8 + - - -
52B ASN 2.9 19.6 + - - -
53B LEU 3.6 2.9 - - - -
55B LYS* 1.3 76.6 - - - +
57B GLN* 1.3 57.1 + - - +
59B LEU* 3.3 2.4 + - - +
60B LEU* 2.9 33.7 + - - +
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Residues in contact with GLN 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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48B ILE* 3.8 23.6 - - + +
53B LEU* 3.0 26.3 + - - +
54B ALA* 3.8 4.8 - - - +
56B SER* 1.3 75.8 - - - +
58B THR* 1.3 64.1 + - - +
60B LEU* 4.0 2.8 - - - +
61B GLY* 3.0 19.4 + - - -
84B MET 3.6 13.9 + - - -
85B ALA 3.1 26.6 + - - +
86B ASN* 4.5 5.0 - - - -
87B SER 3.8 10.1 - - - +
88B VAL* 3.8 16.5 - - + +
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Residues in contact with THR 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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54B ALA 3.2 12.5 + - - -
55B LYS* 3.2 11.4 + - - -
57B GLN* 1.3 79.2 - - - +
59B LEU* 1.3 62.3 + - + +
61B GLY* 3.3 2.5 + - - -
62B LYS* 2.9 29.4 + - + +
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Residues in contact with LEU 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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27B PHE* 3.3 50.3 - - + +
55B LYS* 2.8 34.3 + - + +
56B SER* 3.8 4.0 - - - +
58B THR* 1.3 80.5 - - + +
60B LEU* 1.3 57.6 + - + +
62B LYS* 3.2 5.9 + - + +
63B GLU* 2.8 31.5 + - - +
167B GLY* 3.4 33.7 - - - +
168B PHE* 4.2 18.2 - - + -
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Residues in contact with LEU 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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27B PHE 4.4 4.9 - - - +
28B ALA* 4.4 3.8 - - + -
46B LYS* 3.6 42.6 - - + +
47B CYS* 3.8 4.3 - - - +
48B ILE* 3.4 49.4 - - + +
56B SER* 2.9 20.0 + - - +
57B GLN 4.1 2.0 - - - +
59B LEU* 1.3 78.0 - - + +
61B GLY* 1.3 60.5 + - - +
63B GLU* 3.5 7.8 + - - +
64B ILE* 3.1 28.1 + - - +
88B VAL* 3.9 21.3 - - + +
90B LEU* 3.7 14.1 - - + +
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Residues in contact with GLY 61 (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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57B GLN 3.0 16.0 + - - -
58B THR* 3.6 3.8 - - - -
59B LEU 3.2 0.2 - - - -
60B LEU* 1.3 78.0 - - - +
62B LYS* 1.3 60.5 + - - +
64B ILE* 3.4 6.6 + - - +
65B LYS* 3.3 31.8 + - - +
83B GLU* 4.0 22.1 - - - +
88B VAL* 4.5 3.1 - - - +
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Residues in contact with LYS 62 (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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58B THR* 2.9 17.1 + - + +
59B LEU* 3.5 8.1 - - + +
61B GLY* 1.3 73.5 - - - +
63B GLU* 1.3 65.8 + - - +
65B LYS* 3.1 11.8 + - + +
66B ILE* 3.1 35.6 + - + +
166B PHE 4.1 1.6 - - - +
167B GLY 3.4 27.4 - - - +
169B ALA 3.5 22.9 + - - +
170B ARG* 4.4 11.9 - - - +
171B TYR* 5.2 4.2 - - - +
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Residues in contact with GLU 63 (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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46B LYS* 2.7 35.2 + - - +
59B LEU 2.8 20.4 + - - +
60B LEU* 3.8 9.0 - - - +
62B LYS* 1.3 72.8 - - - +
64B ILE* 1.3 58.5 + - - +
66B ILE* 3.4 1.8 + - - +
67B LEU* 2.9 52.0 + - + +
90B LEU* 3.9 12.3 - - + +
92B MET* 5.2 3.8 - - - +
165B ASP* 3.2 13.7 + - - +
166B PHE* 2.9 39.0 + - + +
167B GLY* 4.0 8.6 + - - +
401B 3RJ 6.0 0.3 - - - -
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Residues in contact with ILE 64 (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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60B LEU 3.1 14.9 + - - +
61B GLY 3.6 7.6 - - - +
62B LYS 3.2 0.2 - - - -
63B GLU* 1.3 77.6 - - - +
65B LYS* 1.3 65.9 + - + +
67B LEU* 4.0 0.3 - - - -
68B LYS* 3.0 44.2 + - + +
78B LEU* 4.1 7.7 - - + +
81B PHE* 3.7 44.4 - - + -
82B GLN 5.0 0.2 - - - +
83B GLU* 4.2 20.2 - - + +
88B VAL* 3.8 28.7 - - + -
89B TYR 4.2 0.4 - - - +
90B LEU* 3.6 19.5 - - + -
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Residues in contact with LYS 65 (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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175A ASN* 5.7 1.4 + - - -
61B GLY 3.3 18.4 + - - +
62B LYS* 3.1 12.1 + - + +
64B ILE* 1.3 83.2 - - + +
66B ILE* 1.3 63.3 + - + +
68B LYS* 3.9 16.1 - - - +
69B GLU* 3.7 18.2 - - - +
83B GLU* 4.4 17.8 + - - +
171B TYR* 5.1 1.5 + - - -
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Residues in contact with ILE 66 (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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62B LYS* 3.1 38.3 + - + +
63B GLU 3.9 3.6 - - - +
65B LYS* 1.3 76.3 - - + +
67B LEU* 1.3 60.6 + - - +
68B LYS 3.2 1.6 - - - -
69B GLU* 3.0 22.5 + - - +
70B LEU* 3.5 31.1 - - + +
134B ILE* 4.4 14.3 - - + +
166B PHE* 4.0 26.5 - - + +
169B ALA* 4.5 17.5 - - + +
170B ARG* 4.7 1.1 - - - -
171B TYR* 3.9 31.2 - - + -
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Residues in contact with LEU 67 (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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63B GLU* 2.9 48.1 + - + +
66B ILE* 1.3 70.0 - - - +
68B LYS* 1.3 66.3 + - - +
70B LEU* 3.0 27.8 + - + +
71B LYS* 5.5 0.7 - - - +
75B ILE* 4.0 20.2 - - + -
76B VAL 4.2 5.8 - - - +
78B LEU* 4.0 27.0 + - + +
90B LEU* 4.5 3.8 - - + -
92B MET* 3.7 34.5 - - + -
166B PHE* 3.6 29.6 - - + -
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Residues in contact with LYS 68 (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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64B ILE* 3.0 30.8 + - + +
65B LYS* 3.9 16.1 - - - +
66B ILE 3.2 0.2 - - - -
67B LEU* 1.3 76.8 - - - +
69B GLU* 1.3 72.2 + - - +
71B LYS* 4.0 19.8 + - - +
78B LEU* 4.4 6.9 - - + +
81B PHE* 3.8 37.6 - - + -
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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