Contacts of the helix formed by residues 59 - 71 (chain A) in PDB entry 3DCY
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 59 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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24A GLY 3.8 19.7 - - - +
25A GLN* 4.7 7.0 - - + -
28A ASP* 3.6 26.5 - - + +
57A SER* 3.2 11.9 - - - +
58A ASP* 1.3 84.3 - - - +
60A MSE 1.3 63.8 + - - +
61A ARG* 3.3 11.2 - - - +
62A THR* 2.9 18.8 + - - +
63A LYS* 3.0 14.3 + - - +
88A ARG* 3.6 43.1 - - + +
89A GLU 4.3 2.2 - - - +
198A HIS* 3.6 29.4 - - + +
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Residues in contact with MSE 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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28A ASP* 2.8 43.0 + - - +
29A GLU 4.2 7.6 - - - +
30A PRO* 4.1 19.1 - - + -
59A LEU* 1.3 71.1 - - - +
61A ARG* 1.3 59.2 + - - +
63A LYS* 3.2 8.0 + - + -
64A GLN* 2.8 64.5 + - + +
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Residues in contact with ARG 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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11A HIS* 3.4 24.5 - - + +
14A THR* 3.7 17.5 - - + -
23A GLN* 3.3 39.1 + - - +
24A GLY 2.8 26.5 + - - -
27A VAL 4.2 11.7 + - - -
28A ASP* 4.6 3.0 + - - +
29A GLU 3.5 19.9 + - - +
31A LEU* 3.6 12.3 - - + +
59A LEU* 3.9 18.8 - - + +
60A MSE 1.3 77.8 - - - +
62A THR* 1.3 58.4 + - - +
64A GLN* 4.4 3.4 - - - -
65A THR* 2.7 34.0 + - - -
89A GLU* 3.8 1.2 - - - +
198A HIS* 3.4 19.9 + - + -
271A PO4 2.9 29.9 + - - -
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Residues in contact with THR 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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11A HIS* 3.8 7.4 - - + -
56A SER* 3.4 17.4 + - - -
57A SER* 3.1 20.5 + - - -
59A LEU* 2.9 19.2 + - - +
61A ARG* 1.3 75.0 - - - +
63A LYS* 1.3 61.1 + - - -
65A THR* 3.1 3.1 + - - -
66A MSE 2.9 21.3 + - - +
196A VAL* 3.6 12.3 - - + +
197A SER* 3.4 33.4 - - - +
198A HIS* 3.3 28.3 - - + +
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Residues in contact with LYS 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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56A SER* 3.6 7.7 + - - -
58A ASP* 5.9 0.9 - - - -
59A LEU 3.0 19.1 + - - +
60A MSE 3.7 9.0 - - + +
62A THR* 1.3 77.6 + - - +
64A GLN* 1.3 60.3 + - + +
66A MSE 3.3 3.7 + - - +
67A HIS* 2.9 28.6 + - + +
83A TYR* 3.5 45.9 + - + +
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Residues in contact with GLN 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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30A PRO* 3.3 12.2 - - - +
31A LEU* 2.8 48.6 + - + +
36A PHE* 3.6 29.1 - - + -
39A ALA* 4.6 0.5 - - - +
60A MSE 2.8 47.9 + - + +
63A LYS* 1.3 75.3 - - + +
65A THR* 1.3 57.5 + - - +
67A HIS* 3.3 8.7 + - - +
68A GLY* 2.9 26.0 + - - -
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Residues in contact with THR 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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9A VAL* 4.9 0.7 - - + -
10A ARG 4.2 2.5 - - - +
11A HIS* 3.4 11.8 - - - -
12A GLY* 2.9 28.9 + - - +
31A LEU* 3.6 6.6 - - - +
39A ALA* 4.0 17.0 - - + +
61A ARG 2.7 21.4 + - - -
62A THR 3.1 5.8 + - - -
64A GLN* 1.3 76.3 - - - +
66A MSE 1.3 60.9 + - - +
68A GLY* 3.2 1.9 + - - -
69A ILE* 2.9 45.9 + - + +
196A VAL* 4.0 8.5 - - + -
233A THR* 4.2 10.1 - - + -
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Residues in contact with MSE 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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54A ALA* 3.9 8.5 - - + -
55A PHE 3.1 43.5 - - - +
56A SER* 4.1 6.5 - - - -
62A THR 2.9 13.2 + - - +
63A LYS* 3.5 9.2 - - - +
65A THR* 1.3 75.7 - - - +
67A HIS* 1.3 58.3 + - - +
69A ILE* 3.2 3.5 + - - +
70A LEU* 2.9 43.0 + - + +
81A VAL* 3.7 29.2 - - + -
83A TYR* 5.2 0.9 - - - +
194A LEU* 3.6 31.4 - - + +
196A VAL* 3.5 27.3 - - + +
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Residues in contact with HIS 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 LYS* 2.9 16.5 + - + +
64A GLN* 3.5 12.3 - - - +
65A THR 3.2 0.4 - - - -
66A MSE 1.3 78.3 - - - +
68A GLY* 1.3 54.9 + - - +
70A LEU* 3.3 3.7 + - - +
71A GLU* 2.8 71.6 + - + +
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Residues in contact with GLY 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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36A PHE* 6.6 0.2 - - - -
39A ALA* 3.8 17.8 - - - +
64A GLN 2.9 13.7 + - - -
65A THR 3.2 4.4 + - - -
67A HIS* 1.3 76.7 - - - +
69A ILE* 1.3 62.9 + - - +
71A GLU* 3.7 7.2 - - - +
72A ARG* 2.8 40.0 + - - -
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Residues in contact with ILE 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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9A VAL* 4.4 11.4 - - + -
39A ALA 4.0 12.3 - - - +
42A ALA* 4.0 13.0 - - + -
43A GLY* 3.7 22.8 - - - +
46A LEU* 3.9 25.6 - - + -
51A PHE* 5.1 2.0 - - + -
65A THR* 2.9 35.4 + - + +
66A MSE 3.7 4.5 - - - +
68A GLY* 1.3 78.0 - - - +
70A LEU* 1.3 67.9 + - + +
72A ARG 3.3 9.9 + - - -
73A SER* 3.7 9.0 + - - -
194A LEU* 3.9 24.5 - - + -
196A VAL* 4.2 18.4 - - + -
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Residues in contact with LEU 70 (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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51A PHE* 5.3 4.5 - - + -
54A ALA* 4.5 7.9 - - + -
66A MSE 2.9 31.0 + - + +
67A HIS* 4.2 3.8 - - - +
69A ILE* 1.3 73.5 - - + +
71A GLU* 1.3 65.1 - - - +
72A ARG 3.0 4.5 + - - -
73A SER* 3.0 15.0 + - - -
76A CYS* 3.8 34.8 - - + +
77A LYS* 3.4 23.5 - - - +
79A MSE 4.2 16.6 - - + +
81A VAL* 3.5 31.9 - - + -
194A LEU* 4.4 18.2 - - + -
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Residues in contact with GLU 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 HIS* 2.8 57.1 + - + +
68A GLY* 3.7 4.4 - - - +
70A LEU* 1.3 73.1 - - - +
72A ARG* 1.3 99.8 + - + +
77A LYS* 3.3 32.7 - - - +
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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