Contacts of the helix formed by residues 44 - 56 (chain A) in PDB entry 4WJN
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 LEU 44 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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24A LEU* 4.5 7.4 - - + -
38A VAL* 4.6 7.9 - - + -
42A THR* 4.1 6.1 - - + +
43A HIS* 1.3 69.5 - - - +
45A LYS* 1.3 65.2 + - - +
46A LYS 3.0 2.5 - - - -
47A LEU* 3.0 33.4 + - + +
48A LYS* 3.0 26.7 + - + +
71A ILE* 3.8 33.0 - - + -
72A ALA 4.3 1.6 - - - +
73A ASP 3.4 1.4 + - - -
75A HIS 2.9 21.5 + - - +
76A THR 4.1 10.3 - - - -
77A PRO* 4.1 19.1 - - + -
80A LEU* 3.9 19.3 - - + -
82A MET* 4.2 11.7 - - + -
88A ILE* 5.2 1.6 - - + -
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Residues in contact with LYS 45 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43A HIS* 3.1 4.0 + - + +
44A LEU* 1.3 76.8 - - - +
46A LYS* 1.3 56.6 + - - +
48A LYS* 3.2 8.0 + - - +
49A GLU* 2.9 55.5 + - + +
59A MET* 4.3 11.2 - - + -
73A ASP* 2.9 55.7 + - + +
74A ASN* 5.5 2.0 - - - +
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Residues in contact with LYS 46 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42A THR* 4.7 2.7 - - + -
43A HIS 3.2 12.5 + - - +
44A LEU 3.0 0.6 - - - -
45A LYS* 1.3 80.2 - - - +
47A LEU* 1.3 60.0 + - - +
49A GLU* 3.6 15.1 + - - +
50A SER* 3.1 23.0 + - - -
14B ILE* 3.7 22.5 - - + +
15B SEP 2.8 64.5 + - - +
16B SEP 3.0 14.2 + - - -
17B SEP 4.2 10.5 + - - +
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Residues in contact with LEU 47 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A LEU* 4.2 6.5 - - + -
26A VAL* 4.1 17.5 - - + -
36A PHE* 3.6 39.1 - - + -
38A VAL* 4.2 8.5 - - + -
42A THR* 5.6 0.6 - - + +
44A LEU* 3.0 34.0 + - + +
46A LYS* 1.3 76.5 - - - +
48A LYS* 1.3 68.5 + - + +
50A SER* 3.2 2.1 + - - -
51A TYR* 2.9 27.4 + - + +
64A PHE* 4.4 14.6 - - + -
88A ILE* 4.2 21.3 - - + -
14B ILE* 4.2 16.6 - - + +
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Residues in contact with LYS 48 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44A LEU* 3.0 16.3 + - + +
45A LYS* 3.5 9.6 - - - +
47A LEU* 1.3 78.7 - - + +
49A GLU* 1.3 57.4 + - - +
51A TYR* 3.4 1.6 + - - +
52A ALA* 3.0 30.8 + - - +
59A MET* 3.6 18.6 - - + +
64A PHE* 3.3 54.8 - - + -
71A ILE* 2.9 29.7 + - + -
72A ALA* 4.0 4.0 - - - +
73A ASP* 2.8 45.3 + - - +
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Residues in contact with GLU 49 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45A LYS* 2.9 46.1 + - - +
46A LYS* 3.8 18.2 - - - +
48A LYS* 1.3 75.4 - - - +
50A SER* 1.3 63.1 + - - +
52A ALA* 3.8 2.3 - - - +
53A GLN* 3.0 25.1 + - - +
59A MET* 3.4 23.3 - - + -
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Residues in contact with SER 50 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36A PHE* 3.5 16.0 - - - -
46A LYS 3.1 16.9 + - - -
47A LEU 3.6 3.8 - - - -
49A GLU* 1.3 80.0 - - - +
51A TYR* 1.3 62.5 + - - +
53A GLN* 3.4 12.9 + - - +
54A ARG* 3.0 52.4 + - - +
12B VAL* 3.8 6.8 - - - +
14B ILE* 3.9 9.1 - - - +
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Residues in contact with TYR 51 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26A VAL* 3.6 25.8 - - + -
28A GLY* 3.4 27.2 + - - -
32A SER* 4.6 3.7 + - - -
34A ILE* 4.1 15.9 - - + -
36A PHE* 3.9 21.7 - + + -
47A LEU* 2.9 17.3 + - + +
48A LYS 3.7 3.4 - - - +
50A SER* 1.3 76.9 - - - +
52A ALA* 1.3 63.9 + - - +
54A ARG* 3.2 5.9 + - - +
55A GLN* 3.0 63.0 + - + +
62A LEU* 4.0 9.0 - - + -
64A PHE* 3.8 25.4 - + + -
90A VAL* 3.8 24.2 - - + +
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Residues in contact with ALA 52 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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48A LYS 3.0 17.1 + - - +
49A GLU 3.8 3.1 - - - +
51A TYR* 1.3 77.0 - - - +
53A GLN* 1.3 63.9 + - - +
55A GLN* 3.2 1.3 + - - +
56A GLY 2.9 18.5 + - - -
57A VAL* 3.1 30.9 + - - +
59A MET* 3.7 26.0 - - + +
62A LEU* 4.1 18.4 - - + -
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Residues in contact with GLN 53 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49A GLU 3.0 16.6 + - - +
50A SER* 3.4 16.6 + - - +
52A ALA* 1.3 76.5 - - - +
54A ARG* 1.3 72.5 + - + +
56A GLY* 3.1 13.3 + - - -
57A VAL 5.0 0.7 - - - -
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Residues in contact with ARG 54 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34A ILE* 4.2 23.1 - - + -
36A PHE* 4.8 3.1 - - - -
50A SER* 3.0 34.4 + - - +
51A TYR 3.2 4.0 + - - +
53A GLN* 1.3 87.5 + - + +
55A GLN* 1.3 62.9 + - - +
56A GLY 3.3 0.4 + - - -
10B ARG* 5.9 1.5 + - - +
12B VAL* 3.7 39.2 - - - +
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Residues in contact with GLN 55 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30A ASP* 5.6 1.9 - - - +
32A SER* 4.6 9.0 + - - -
34A ILE* 3.6 28.9 - - - +
51A TYR* 3.0 51.5 + - + +
52A ALA* 3.8 4.0 - - - +
53A GLN 3.2 0.2 - - - -
54A ARG* 1.3 80.5 + - - +
56A GLY* 1.3 61.5 + - - +
57A VAL* 3.6 21.8 + - + +
10B ARG* 4.9 5.5 - - - +
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Residues in contact with GLY 56 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52A ALA 2.9 4.6 + - - -
53A GLN* 3.1 14.0 + - - -
54A ARG 3.3 0.6 + - - -
55A GLN* 1.3 79.9 - - - +
57A VAL* 1.3 62.3 + - - +
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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