Contacts of the helix formed by residues 56 - 71 (chain A) in PDB entry 4WPN
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 ASP 56 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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34A SER* 5.8 6.4 - - - -
36A LYS* 5.0 10.4 + - - -
54A GLU* 4.7 10.3 - - - +
55A GLY* 1.3 73.7 - - - -
57A LYS* 1.3 75.3 + - - +
58A GLU* 3.1 17.8 - - + +
59A ASP* 2.8 14.2 + - - +
60A VAL* 2.8 27.8 + - - +
228A THR* 3.3 31.7 - - - +
229A ALA* 4.7 5.4 - - - +
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Residues in contact with LYS 57 (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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56A ASP* 1.3 79.9 + - - +
58A GLU* 1.3 77.5 - - + +
60A VAL* 3.1 1.6 + - - +
61A ASP* 3.0 55.4 + - - +
228A THR 4.3 1.7 + - - +
232A ALA* 3.7 31.5 + - + +
235A SER* 5.9 0.8 + - - -
236A HIS* 3.3 22.4 + - - +
237A MET 5.7 0.4 - - - +
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Residues in contact with GLU 58 (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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33A VAL* 4.3 20.9 - - + -
56A ASP* 3.1 21.1 - - + +
57A LYS* 1.3 90.1 + - + +
59A ASP* 1.3 60.1 + - - +
61A ASP* 3.5 20.6 + - - +
62A LYS* 3.6 13.2 + - - +
605A YB 3.7 18.3 - - - -
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Residues in contact with ASP 59 (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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23A ILE* 4.1 15.6 - - + +
25A ILE* 3.9 4.9 - - + +
31A ASP 4.4 1.6 - - - +
32A SER* 3.6 3.5 - - - -
33A VAL* 2.8 36.2 + - - +
34A SER* 5.1 1.2 + - - -
54A GLU 3.7 5.2 - - - +
55A GLY* 3.2 13.9 - - - -
56A ASP* 2.8 38.6 + - - +
58A GLU* 1.3 69.2 - - - +
60A VAL* 1.3 64.2 + - - +
61A ASP 3.0 1.8 - - - -
62A LYS* 3.3 17.5 + - + +
63A ALA* 3.1 21.3 + - - +
222A VAL* 4.4 9.2 - - + +
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Residues in contact with VAL 60 (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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56A ASP 2.8 19.0 + - - +
57A LYS 3.6 7.2 - - - +
59A ASP* 1.3 72.1 - - - +
61A ASP* 1.3 56.7 + - - +
63A ALA* 3.4 6.9 + - - +
64A VAL* 3.0 39.0 + - + +
191A VAL* 4.9 3.4 - - + -
222A VAL* 4.4 14.1 - - + -
229A ALA* 3.7 31.6 - - + +
232A ALA* 4.0 21.5 - - + -
233A ILE* 4.0 25.6 - - + -
236A HIS* 4.2 8.3 - - + -
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Residues in contact with ASP 61 (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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57A LYS* 3.0 44.5 + - - +
58A GLU* 3.5 12.8 - - - +
59A ASP 3.0 1.2 - - - -
60A VAL* 1.3 75.2 - - - +
62A LYS* 1.3 60.4 + - + +
64A VAL* 4.0 1.0 - - - +
65A LYS* 3.0 43.2 + - + +
236A HIS* 2.8 30.5 + - - +
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Residues in contact with LYS 62 (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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25A ILE* 3.8 16.5 - - + +
30A HIS* 3.1 42.4 + - - +
31A ASP 4.5 7.9 + - - -
33A VAL* 5.5 7.9 - - + +
58A GLU 3.6 13.1 + - - +
59A ASP* 3.3 19.6 + - + +
61A ASP* 1.3 76.0 - - + +
63A ALA* 1.3 64.4 + - - +
65A LYS* 4.0 7.2 - - + +
66A ALA* 3.2 23.6 + - - +
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Residues in contact with ALA 63 (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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25A ILE* 3.7 15.2 - - + +
59A ASP 3.1 7.2 + - - +
60A VAL 3.7 7.4 - - - +
61A ASP 3.3 0.2 - - - -
62A LYS* 1.3 77.6 - - - +
64A VAL* 1.3 54.7 + - - +
66A ALA* 3.4 3.5 + - - +
67A ALA* 2.9 28.1 + - - +
191A VAL* 3.8 17.0 - - + -
220A ASN* 3.7 13.5 + - + -
222A VAL* 3.7 30.3 - - + -
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Residues in contact with VAL 64 (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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60A VAL* 3.0 26.1 + - + +
61A ASP 4.0 1.8 - - - +
62A LYS 3.4 0.2 - - - -
63A ALA* 1.3 73.6 - - - +
65A LYS* 1.3 56.7 - - + +
67A ALA* 3.2 2.0 + - - +
68A ARG* 2.7 33.6 + - - +
162A VAL* 4.5 4.0 - - + -
191A VAL* 4.1 15.0 - - + -
236A HIS* 3.4 33.2 - - + +
238A ASP* 3.9 27.4 - - + +
239A ILE* 3.6 31.9 - - + -
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Residues in contact with LYS 65 (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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61A ASP* 3.0 29.2 + - + +
62A LYS* 4.0 7.0 - - + +
64A VAL* 1.3 76.5 - - + +
66A ALA* 1.3 56.5 + - - +
68A ARG* 3.4 7.2 + - - +
69A GLN* 3.0 29.1 + - - +
236A HIS* 6.5 0.2 - - + -
238A ASP* 5.9 0.2 - - - -
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Residues in contact with ALA 66 (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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25A ILE* 3.8 10.3 - - + -
26A ASN* 3.5 36.5 - - - +
62A LYS 3.2 19.7 + - - +
63A ALA 3.5 4.9 - - - +
65A LYS* 1.3 73.7 - - - +
67A ALA* 1.3 64.5 + - - +
69A GLN* 3.2 6.8 + - - +
70A ALA* 3.0 25.5 + - - +
217A GLY* 3.9 4.5 - - - -
220A ASN* 3.8 7.2 - - - +
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Residues in contact with ALA 67 (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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63A ALA 2.9 17.4 + - - +
64A VAL 3.6 1.6 - - - +
66A ALA* 1.3 75.4 - - - +
68A ARG* 1.3 62.6 + - - +
70A ALA 3.5 1.0 + - - -
71A PHE* 3.1 15.6 + - - +
162A VAL* 3.5 24.0 - - + -
189A THR* 2.9 30.7 + - - +
190A VAL 4.4 1.3 - - - +
191A VAL* 3.9 5.6 - - + -
217A GLY 3.4 12.9 + - - +
220A ASN* 3.8 10.3 - - - +
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Residues in contact with ARG 68 (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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64A VAL 2.7 20.9 + - - +
65A LYS* 3.7 7.9 - - - +
67A ALA* 1.3 74.0 - - - +
69A GLN* 1.3 62.0 + - - +
71A PHE* 3.2 34.9 + - - +
72A GLN* 3.2 44.7 + - + +
160A ILE 5.4 0.2 + - - -
162A VAL* 3.6 15.6 - - + +
238A ASP* 2.8 59.0 + - - +
240A ASP* 2.8 34.9 + - - -
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Residues in contact with GLN 69 (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 ASN* 6.1 0.2 - - - +
65A LYS 3.0 17.5 + - - +
66A ALA* 3.2 7.4 + - - +
68A ARG* 1.3 79.1 - - - +
70A ALA* 1.3 62.0 + - - +
72A GLN* 3.2 30.6 + - - +
75A SER* 4.2 5.5 - - - -
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Residues in contact with ALA 70 (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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66A ALA 3.0 16.1 + - - +
67A ALA 3.9 2.5 - - - +
68A ARG 3.3 0.2 - - - -
69A GLN* 1.3 77.1 - - - +
71A PHE* 1.3 56.6 + - - +
75A SER* 2.9 22.6 + - - -
76A PRO* 6.4 0.2 - - - -
77A TRP* 3.8 14.7 - - + +
78A ARG* 4.3 0.2 - - - +
189A THR* 4.0 7.5 - - + +
215A PRO* 5.9 0.9 - - + -
216A PRO 3.5 25.1 - - - +
217A GLY 3.6 16.4 - - - +
218A VAL* 3.9 7.4 - - + +
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Residues in contact with PHE 71 (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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67A ALA 3.1 15.9 + - - +
68A ARG* 3.6 29.4 - - - +
69A GLN 3.1 1.2 - - - -
70A ALA* 1.3 77.2 - - - +
72A GLN* 1.3 61.4 + - - +
77A TRP* 5.1 0.2 - + - -
78A ARG* 2.8 59.7 + - - +
159A PRO* 3.5 41.7 - - + -
160A ILE 4.1 4.3 - - - -
161A GLY* 3.5 33.0 - - - -
162A VAL* 4.9 0.7 - - + -
187A GLY 3.6 12.6 - - - -
188A ASN* 4.4 0.9 - - - -
189A THR* 4.0 14.8 - - + +
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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