Contacts of the helix formed by residues 52 - 68 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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26C ALA* 2.8 37.4 - - - +
27C PHE* 4.1 18.5 - - + -
49C ASN* 3.0 7.7 + - - +
51C LYS* 1.3 89.0 + - - +
53C LEU* 1.3 53.3 + - - +
54C ALA 3.5 1.6 - - - -
55C LYS* 3.3 8.0 + - + +
56C SER* 2.8 30.7 + - - -
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Residues in contact with LEU 53 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48C ILE* 3.9 24.0 - - + +
49C ASN 3.8 6.7 - - - -
50C LYS* 3.5 28.7 + - + +
51C LYS 3.7 0.2 - - - -
52C ASN* 1.3 73.8 - - - +
54C ALA* 1.3 65.8 + - + +
56C SER* 3.7 1.3 - - - -
57C GLN* 3.0 42.4 + - - +
86C ASN* 4.6 14.4 - - + +
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Residues in contact with ALA 54 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52C ASN 3.5 0.2 - - - -
53C LEU* 1.3 82.9 - - + +
55C LYS* 1.3 58.0 + - - +
57C GLN* 3.4 8.1 + - - +
58C THR* 3.0 33.4 + - - -
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Residues in contact with LYS 55 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27C PHE* 3.2 42.9 - - + -
52C ASN* 3.3 10.1 + - + +
53C LEU 3.3 0.2 - - - -
54C ALA* 1.3 77.6 - - - +
56C SER* 1.3 60.7 + - - +
58C THR* 3.4 6.8 + - - -
59C LEU* 3.0 48.9 + - + +
168C PHE* 4.3 10.1 - - - -
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Residues in contact with SER 56 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27C PHE* 2.6 39.8 + - - +
48C ILE* 3.4 9.9 - - - -
49C ASN 3.0 30.3 + - - -
52C ASN 2.8 19.0 + - - -
53C LEU 3.7 2.7 - - - -
55C LYS* 1.3 77.4 - - - +
57C GLN* 1.3 63.0 + - - +
59C LEU* 3.2 2.1 + - - +
60C LEU* 3.0 27.8 + - - +
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Residues in contact with GLN 57 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48C ILE* 3.7 22.6 - - + +
53C LEU* 3.0 32.9 + - - +
54C ALA* 3.5 7.8 - - - +
56C SER* 1.3 77.5 - - - +
58C THR* 1.3 61.8 + - - +
60C LEU* 3.5 1.2 + - - +
61C GLY* 3.0 20.4 + - - -
83C GLU* 5.0 2.6 - - - +
84C MET 3.8 4.8 + - - -
85C ALA 2.6 37.6 + - - +
86C ASN* 3.4 13.8 - - - +
87C SER 3.6 2.2 - - - +
88C VAL* 3.7 15.6 - - + +
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Residues in contact with THR 58 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54C ALA* 3.0 19.0 + - - +
55C LYS* 3.6 8.1 - - - -
57C GLN* 1.3 77.1 - - - +
59C LEU* 1.3 61.3 + - + +
61C GLY* 3.4 2.0 + - - -
62C LYS* 2.9 29.8 + - + +
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Residues in contact with LEU 59 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27C PHE* 3.4 47.3 - - + +
55C LYS* 3.0 32.0 + - + +
56C SER* 3.2 4.7 + - - +
58C THR* 1.3 78.1 - - + +
60C LEU* 1.3 62.5 + - + +
62C LYS* 3.3 4.3 + - + +
63C GLU* 3.0 28.1 + - - +
167C GLY* 3.2 36.9 - - - +
168C PHE* 3.8 24.9 - - + -
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Residues in contact with LEU 60 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27C PHE 4.4 4.7 - - - +
28C ALA* 4.3 3.1 - - + -
46C LYS* 3.4 43.5 - - + +
47C CYS* 3.5 34.1 - - - +
48C ILE* 3.6 17.0 - - + +
56C SER* 3.0 17.2 + - - +
57C GLN 4.1 1.3 - - - +
59C LEU* 1.3 78.5 - - + +
61C GLY* 1.3 58.0 + - - +
63C GLU* 3.2 8.4 + - - +
64C ILE* 3.0 33.3 + - - +
88C VAL* 3.7 27.8 - - + +
90C LEU* 3.9 11.0 - - + +
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Residues in contact with GLY 61 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57C GLN 3.0 15.9 + - - -
58C THR* 3.7 2.9 - - - -
60C LEU* 1.3 76.3 - - - +
62C LYS* 1.3 60.7 + - - +
64C ILE* 3.3 7.7 + - - +
65C LYS* 3.2 20.3 + - - +
83C GLU* 4.0 27.0 - - - +
88C VAL* 4.5 1.6 - - - +
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Residues in contact with LYS 62 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58C THR* 2.9 19.3 + - + +
59C LEU* 3.7 4.3 - - + +
60C LEU 3.3 0.2 - - - -
61C GLY* 1.3 74.9 - - - +
63C GLU* 1.3 62.7 + - - +
65C LYS* 3.2 33.1 + - - +
66C ILE* 3.1 26.5 + - + +
137C ARG* 6.0 0.9 - - - +
166C PHE 4.3 2.0 - - - +
167C GLY 3.4 23.3 - - - +
169C ALA 3.1 25.2 + - - +
170C ARG* 4.0 17.3 - - - +
171C TYR* 4.8 2.4 - - - +
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Residues in contact with GLU 63 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46C LYS* 2.4 41.6 + - - +
59C LEU 3.0 14.2 + - - +
60C LEU* 3.2 11.1 + - - +
62C LYS* 1.3 76.4 - - - +
64C ILE* 1.3 58.7 + - - +
66C ILE* 3.4 1.5 + - - +
67C LEU* 2.9 51.0 + - + +
90C LEU* 3.7 14.9 - - + +
92C MET* 4.3 5.5 - - - +
165C ASP* 3.4 8.3 + - - -
166C PHE* 3.0 38.3 + - + +
167C GLY* 3.9 7.7 + - - +
401C 3RJ 5.8 0.2 - - - -
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Residues in contact with ILE 64 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60C LEU 3.0 16.0 + - - +
61C GLY* 3.5 7.4 - - - +
62C LYS 3.3 0.2 - - - -
63C GLU* 1.3 76.6 - - - +
65C LYS* 1.3 63.7 + - - +
68C LYS* 3.0 34.7 + - + +
78C LEU* 4.2 7.8 - - + +
81C PHE* 3.8 56.3 - - + -
82C GLN 5.1 0.2 - - - +
83C GLU* 3.8 23.8 - - + +
88C VAL* 3.9 25.4 - - + -
89C TYR 4.5 0.4 - - - +
90C LEU* 3.6 18.8 - - + -
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Residues in contact with LYS 65 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61C GLY 3.2 9.3 + - - +
62C LYS* 3.2 39.7 + - - +
64C ILE* 1.3 80.3 - - - +
66C ILE* 1.3 66.0 + - - +
68C LYS* 3.2 26.1 - - + +
69C GLU* 3.6 11.8 - - - +
171C TYR* 4.0 26.1 + - + -
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Residues in contact with ILE 66 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62C LYS* 3.1 35.0 + - + +
63C GLU 3.9 3.1 - - - +
65C LYS* 1.3 83.9 - - - +
67C LEU* 1.3 62.8 + - - +
69C GLU* 3.2 15.2 + - - +
70C LEU* 3.5 30.8 - - + +
134C ILE* 4.3 12.4 - - + +
166C PHE* 3.8 24.9 - - + +
169C ALA* 4.3 17.0 - - + +
170C ARG* 4.4 7.2 - - - +
171C TYR* 3.8 33.2 - - + -
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Residues in contact with LEU 67 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63C GLU* 2.9 42.4 + - + +
66C ILE* 1.3 72.6 - - - +
68C LYS* 1.3 59.2 + - - +
69C GLU 2.9 5.4 - - - -
70C LEU* 2.8 30.6 + - + +
71C LYS* 3.0 12.3 + - - -
75C ILE* 4.0 11.4 - - + -
76C VAL 3.9 16.4 - - - +
78C LEU* 4.0 24.3 - - + +
90C LEU* 4.8 2.7 - - + -
92C MET* 3.6 31.4 - - + -
166C PHE* 3.7 28.5 - - + -
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Residues in contact with LYS 68 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64C ILE* 3.0 28.5 + - + +
65C LYS* 3.2 22.7 - - + +
67C LEU* 1.3 77.4 - - - +
69C GLU* 1.3 72.9 + - - +
70C LEU 3.5 0.2 - - - -
71C LYS* 3.3 22.2 - - - +
78C LEU* 4.1 11.1 - - + +
81C PHE* 4.5 24.3 - - + -
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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