Contacts of the helix formed by residues 59 - 72 (chain D) in PDB entry 3PJV
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 59 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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56D ASN* 2.9 16.1 + - + +
57D ILE 3.4 0.2 - - - -
58D ASP* 1.3 77.6 - - - +
60D PRO* 1.3 67.7 - - - +
61D ALA* 3.3 18.1 + - - +
62D MSE 3.3 29.4 + - + +
63D VAL* 3.0 24.0 + - - +
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Residues in contact with PRO 60 (chain D).
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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57D ILE 5.2 0.6 - - - +
58D ASP 3.3 11.4 - - - +
59D ASP* 1.3 85.8 - - - +
61D ALA* 1.3 64.0 + - - +
63D VAL* 3.2 9.9 + - + +
64D GLU* 3.0 23.8 + - - +
90D ILE* 6.2 3.4 - - + -
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Residues in contact with ALA 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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59D ASP* 3.3 9.4 + - - +
60D PRO* 1.3 80.0 - - - +
62D MSE 1.3 58.9 + - + +
64D GLU* 3.2 9.0 + - - +
65D LEU* 2.9 32.9 + - + +
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Residues in contact with MSE 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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56D ASN* 3.6 33.9 - - + +
59D ASP* 3.1 34.1 + - + +
61D ALA* 1.3 76.6 - - + +
63D VAL* 1.3 62.0 + - - +
65D LEU* 3.2 20.8 + - + -
66D LEU* 2.9 44.3 + - + +
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Residues in contact with VAL 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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53D LEU* 3.9 26.9 - - + +
56D ASN* 3.4 17.0 - - + +
57D ILE* 3.9 23.1 - - + +
59D ASP 3.0 19.2 + - - +
60D PRO* 3.2 11.2 + - + +
62D MSE 1.3 77.3 - - - +
64D GLU* 1.3 62.4 + - - +
66D LEU* 3.3 1.7 + - - +
67D VAL* 3.0 25.5 + - + +
81D VAL* 5.1 3.8 - - + -
90D ILE* 4.3 17.0 - - + -
91D VAL* 4.2 21.5 - - + -
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Residues in contact with GLU 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 PRO 3.0 12.9 + - - +
61D ALA* 3.6 10.4 - - - +
63D VAL* 1.3 78.4 - - - +
65D LEU* 1.3 56.4 + - + +
67D VAL* 3.8 1.4 - - - +
68D SER* 2.9 35.8 + - - +
91D VAL* 4.2 21.8 - - + -
93D ARG* 2.9 31.7 + - - +
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Residues in contact with LEU 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 ALA* 2.9 19.8 + - + +
62D MSE 3.2 25.8 + - + +
64D GLU* 1.3 78.8 - - + +
66D LEU* 1.3 57.9 + - + +
68D SER* 3.4 8.4 + - - -
69D SER* 3.0 29.8 + - - -
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Residues in contact with LEU 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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49D LEU* 3.8 9.2 - - + +
52D SER* 3.6 25.4 - - - +
53D LEU* 3.9 20.0 - - + -
56D ASN* 3.5 26.9 - - + +
62D MSE 2.9 36.8 + - + +
63D VAL 3.8 2.5 - - - +
65D LEU* 1.3 76.3 - - + +
67D VAL* 1.3 63.1 + - - +
69D SER* 3.5 18.6 - - - -
70D ILE* 3.6 14.9 + - - +
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Residues in contact with VAL 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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49D LEU* 4.2 17.9 - - + -
53D LEU* 4.6 2.5 - - + -
63D VAL* 3.0 20.3 + - + +
64D GLU* 3.9 2.9 - - - +
66D LEU* 1.3 75.2 - - - +
68D SER* 1.3 65.8 + - - +
70D ILE* 3.3 4.3 + - - +
71D PHE* 3.0 19.9 + - - +
79D ILE* 3.9 30.3 - - + +
81D VAL* 3.9 15.3 - - + -
91D VAL* 3.7 32.5 - - + -
93D ARG* 4.4 17.5 - - + -
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Residues in contact with SER 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 GLU* 2.9 20.5 + - - +
65D LEU* 3.7 10.5 - - - -
67D VAL* 1.3 75.2 - - - +
69D SER* 1.3 59.4 + - - +
71D PHE* 4.4 4.0 - - - -
72D ASP* 2.8 54.3 + - - -
93D ARG* 3.2 30.1 + - - +
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Residues in contact with SER 69 (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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65D LEU 3.0 17.7 + - - -
66D LEU* 3.5 14.4 - - - -
68D SER* 1.3 78.1 - - - +
70D ILE* 1.3 71.6 + - - +
72D ASP* 3.6 12.2 + - - +
73D SER* 4.3 3.5 + - - -
37F GLN* 5.9 1.6 - - - +
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Residues in contact with ILE 70 (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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45D ALA* 4.8 10.8 - - + +
48D ALA* 6.4 2.5 - - + -
49D LEU* 4.4 21.5 - - + -
66D LEU 3.6 14.1 - - - +
67D VAL 3.3 5.9 + - - +
68D SER 3.3 0.4 - - - -
69D SER* 1.3 85.6 - - - +
71D PHE* 1.3 63.5 + - - +
72D ASP 3.4 0.2 + - - -
73D SER* 3.1 19.9 + - - -
76D TYR* 3.6 28.3 - - + +
79D ILE* 4.0 13.7 - - + -
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Residues in contact with PHE 71 (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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67D VAL* 3.0 17.9 + - + +
68D SER* 3.9 3.1 - - - +
70D ILE* 1.3 78.4 - - - +
72D ASP* 1.3 68.3 + - - +
73D SER 3.0 6.4 + - - -
74D GLY* 3.0 17.7 + - - -
75D TYR 4.7 0.3 + - - -
76D TYR* 3.3 29.7 - - + -
77D SER 4.2 1.8 - - - -
78D SER* 4.3 1.3 - - - -
79D ILE* 4.0 24.2 - - + +
93D ARG* 3.7 48.0 - - + -
94D ASN 3.6 29.8 - - - -
95D GLY* 3.7 8.1 - - - -
143D LYS* 4.9 0.7 + - - -
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Residues in contact with ASP 72 (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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68D SER* 2.8 36.7 + - - +
69D SER* 3.6 6.8 + - - +
70D ILE 3.3 0.8 - - - -
71D PHE* 1.3 87.7 - - - +
73D SER* 1.3 57.9 + - - +
74D GLY 3.2 0.4 - - - -
93D ARG* 5.7 1.6 + - - -
143D LYS* 2.8 26.2 + - - +
33F GLN* 3.9 25.0 + - - +
34F TYR* 5.0 2.6 - - - -
37F GLN* 4.5 11.8 + - + +
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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