Contacts of the helix formed by residues 52 - 68 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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26D ALA* 2.5 49.1 + - - +
27D PHE* 4.1 15.2 - - + -
49D ASN* 3.1 5.6 + - - -
51D LYS* 1.3 88.0 - - - +
53D LEU* 1.3 64.4 + - - +
54D ALA 3.4 2.0 + - - -
55D LYS* 3.4 6.0 + - + -
56D SER* 2.9 21.8 + - - -
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Residues in contact with LEU 53 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48D ILE* 3.6 34.3 - - + -
49D ASN 3.8 7.2 - - - -
50D LYS* 3.4 23.5 + - + +
51D LYS 3.5 1.2 + - - -
52D ASN* 1.3 75.1 - - - +
54D ALA* 1.3 66.3 + - - +
56D SER* 3.6 0.7 - - - -
57D GLN* 2.9 38.2 + - - +
86D ASN* 4.8 6.3 - - - +
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Residues in contact with ALA 54 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52D ASN 3.4 0.4 - - - -
53D LEU* 1.3 81.3 - - + +
55D LYS* 1.3 61.3 + - - +
57D GLN* 3.8 7.1 - - - +
58D THR* 2.9 27.6 + - - -
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Residues in contact with LYS 55 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27D PHE* 3.2 36.9 - - + -
52D ASN* 3.4 7.4 + - + +
53D LEU 3.4 0.2 - - - -
54D ALA* 1.3 75.6 - - - +
56D SER* 1.3 59.4 + - - +
58D THR* 3.3 8.2 + - + -
59D LEU* 2.9 58.7 + - + +
168D PHE* 4.1 15.2 - - - -
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Residues in contact with SER 56 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27D PHE* 2.6 37.8 + - - +
48D ILE* 3.3 10.1 - - - -
49D ASN 3.0 29.8 + - - -
52D ASN 2.9 19.1 + - - -
53D LEU 3.6 3.1 - - - -
55D LYS* 1.3 77.9 - - - +
57D GLN* 1.3 61.9 + - - +
59D LEU* 3.3 2.3 + - - +
60D LEU* 3.0 30.5 + - - +
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Residues in contact with GLN 57 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48D ILE* 3.7 19.6 - - + +
53D LEU* 2.9 32.3 + - - +
54D ALA* 3.8 6.5 - - - +
56D SER* 1.3 76.5 - - - +
58D THR* 1.3 63.9 + - - +
60D LEU* 4.0 1.3 - - - +
61D GLY* 3.0 20.6 + - - -
83D GLU* 5.0 2.5 - - - +
84D MET 3.7 8.3 + - - -
85D ALA 2.5 36.7 + - - +
86D ASN* 3.8 9.2 - - - +
87D SER 3.9 0.6 - - - +
88D VAL* 3.5 21.7 - - + +
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Residues in contact with THR 58 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54D ALA 2.9 16.4 + - - -
55D LYS* 3.5 13.4 - - + +
57D GLN* 1.3 75.5 - - - +
59D LEU* 1.3 69.8 + - + +
61D GLY* 3.3 2.3 + - - -
62D LYS* 3.0 25.0 + - + +
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Residues in contact with LEU 59 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27D PHE* 3.4 45.5 - - + +
55D LYS* 2.9 41.4 + - + +
56D SER* 3.9 2.9 - - - +
58D THR* 1.3 81.8 - - + +
60D LEU* 1.3 61.2 + - + +
62D LYS* 3.4 1.9 + - + +
63D GLU* 2.9 29.2 + - - +
167D GLY* 3.5 32.6 - - - +
168D PHE* 4.0 25.4 - - + -
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Residues in contact with LEU 60 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27D PHE 4.2 3.6 - - - +
28D ALA* 4.2 8.7 - - + -
46D LYS* 3.8 35.9 - - + +
47D CYS* 3.7 9.9 - - - +
48D ILE* 3.6 39.5 - - + +
56D SER* 3.0 25.0 + - - +
57D GLN 4.0 1.8 - - - +
59D LEU* 1.3 76.5 - - + +
61D GLY* 1.3 66.2 + - - +
63D GLU* 3.3 8.7 + - - +
64D ILE* 3.0 29.2 + - - +
88D VAL* 4.0 22.2 - - + +
90D LEU* 3.9 10.8 - - + +
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Residues in contact with GLY 61 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57D GLN 3.0 13.6 + - - -
58D THR* 3.3 3.3 + - - -
60D LEU* 1.3 77.0 - - - +
62D LYS* 1.3 60.5 + - - +
64D ILE* 3.3 7.0 + - - +
65D LYS* 3.2 20.8 + - - +
83D GLU* 3.7 29.6 - - - +
88D VAL* 4.5 1.2 - - - +
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Residues in contact with LYS 62 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58D THR* 3.0 19.0 + - + +
59D LEU* 3.7 5.6 - - + +
61D GLY* 1.3 75.5 - - - +
63D GLU* 1.3 61.6 + - - +
65D LYS* 3.2 40.6 + - - +
66D ILE* 3.2 28.2 + - + +
166D PHE 4.5 0.4 - - - +
167D GLY 3.6 20.9 - - - +
169D ALA 2.9 27.3 + - - +
170D ARG* 4.2 14.2 - - - +
171D TYR* 4.8 2.8 - - - +
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Residues in contact with GLU 63 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46D LYS* 2.5 34.5 + - - +
59D LEU 2.9 16.3 + - - +
60D LEU* 3.6 10.5 - - - +
61D GLY 3.2 0.2 - - - -
62D LYS* 1.3 76.2 - - - +
64D ILE* 1.3 59.5 + - - +
66D ILE* 3.3 0.9 + - - +
67D LEU* 2.8 48.6 + - + +
90D LEU* 3.7 19.2 - - + +
92D MET* 5.0 2.5 - - - +
165D ASP* 3.3 12.6 + - - +
166D PHE* 2.8 39.8 + - + +
167D GLY* 4.0 8.2 + - - -
401D 3RJ 5.9 0.2 - - - -
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Residues in contact with ILE 64 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60D LEU 3.0 15.5 + - - +
61D GLY 3.5 7.4 - - - +
62D LYS 3.3 0.2 - - - -
63D GLU* 1.3 76.6 - - - +
65D LYS* 1.3 64.2 + - - +
68D LYS* 3.0 31.6 + - + +
78D LEU* 4.2 7.3 - - + +
81D PHE* 3.9 55.6 - - + -
83D GLU* 4.1 17.3 - - + +
88D VAL* 3.6 30.3 - - + -
89D TYR 4.4 0.4 - - - +
90D LEU* 3.6 22.7 - - + -
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Residues in contact with LYS 65 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61D GLY 3.2 10.6 + - - +
62D LYS* 3.2 44.9 + - - +
64D ILE* 1.3 81.1 - - - +
66D ILE* 1.3 77.2 + - - +
68D LYS* 3.8 16.1 - - - +
69D GLU* 3.6 18.7 - - - +
171D TYR* 3.9 17.6 + - + -
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Residues in contact with ILE 66 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62D LYS* 3.2 34.1 + - + +
63D GLU 3.9 2.5 - - - +
64D ILE 3.2 0.4 - - - -
65D LYS* 1.3 96.3 - - - +
67D LEU* 1.3 66.5 + - - +
68D LYS 3.2 0.2 - - - -
69D GLU* 3.0 21.8 + - - +
70D LEU* 3.7 15.7 - - + +
134D ILE* 4.1 15.5 - - + -
166D PHE* 3.8 32.5 - - + +
169D ALA* 4.3 18.2 - - + +
170D ARG* 4.5 3.6 - - - -
171D TYR* 3.8 22.8 + - + +
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Residues in contact with LEU 67 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63D GLU* 2.8 47.0 + - + +
66D ILE* 1.3 68.7 - - - +
68D LYS* 1.3 61.0 + - - +
69D GLU 2.9 7.0 + - - -
70D LEU* 3.1 29.6 + - + +
71D LYS* 5.6 0.3 - - - +
75D ILE* 3.8 28.7 - - + -
76D VAL 4.0 5.8 - - - +
78D LEU* 4.0 24.0 + - + +
90D LEU* 4.7 2.2 - - + -
92D MET* 3.6 34.8 - - + -
166D PHE* 3.8 22.0 - - + -
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Residues in contact with LYS 68 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64D ILE* 3.0 32.8 + - + +
65D LYS* 3.8 18.4 - - - +
67D LEU* 1.3 77.5 - - - +
69D GLU* 1.3 76.5 + - - +
70D LEU 3.5 0.4 - - - -
71D LYS* 5.5 5.4 - - - +
78D LEU* 4.2 14.1 - - + +
81D PHE* 4.4 20.2 - - + -
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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