Contacts of the helix formed by residues 62 - 74 (chain D) in PDB entry 5E6J
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 62 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61D SER* 1.3 85.9 + - - +
63D ASP* 1.3 64.1 + - - +
64D THR* 2.7 27.8 + - + +
65D LEU* 2.8 34.3 + - - +
66D ARG* 3.2 36.2 + - - +
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Residues in contact with ASP 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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64C GLU* 5.7 4.3 - - - +
62D ASP* 1.3 74.9 - - - +
64D THR* 1.3 63.9 + - + +
66D ARG* 3.3 22.0 + - - +
67D SER* 2.8 29.5 + - - -
46F ALA* 3.9 16.6 - - + +
48F LYS* 3.3 22.8 + - - +
59F TYR 5.6 1.4 - - - +
60F ASN* 4.8 12.1 + - - -
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Residues in contact with THR 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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4C PHE* 3.7 33.4 - - + -
64C GLU* 3.9 24.5 - - - +
18D HIS* 5.0 3.0 - - - -
62D ASP* 2.7 22.4 + - - -
63D ASP* 1.3 77.6 - - + +
65D LEU* 1.3 65.9 + - - +
67D SER* 3.0 9.2 + - - -
68D GLU* 2.9 43.0 + - - +
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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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10D THR* 5.6 3.4 - - - +
11D THR* 5.8 1.3 - - - -
12D VAL* 3.6 17.4 - - + +
18D HIS* 3.9 31.9 - - + +
58D VAL* 3.8 27.8 - - + -
60D PRO* 3.8 16.6 - - + -
61D SER* 3.9 25.8 - - - +
62D ASP* 2.8 35.2 + - - +
64D THR* 1.3 79.3 + - - +
66D ARG* 1.3 57.8 + - - +
68D GLU* 3.5 5.6 + - - -
69D ALA* 2.8 30.5 + - - +
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Residues in contact with ARG 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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60D PRO* 3.5 34.9 + - + +
61D SER* 3.1 26.1 + - - +
62D ASP* 3.2 18.6 + - - +
63D ASP* 3.4 22.1 + - - +
64D THR 3.2 0.2 - - - -
65D LEU* 1.3 77.3 - - - +
67D SER* 1.3 59.5 + - - +
69D ALA* 3.3 3.4 + - - +
70D PHE* 2.9 32.7 + - - +
78D GLU* 3.4 28.4 + - + +
46F ALA 3.3 17.7 - - - +
47F GLY* 3.8 14.5 - - - +
48F LYS* 3.1 28.6 - - - +
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Residues in contact with SER 67 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63D ASP 2.8 17.2 + - - -
64D THR* 3.0 12.1 + - - -
66D ARG* 1.3 74.0 - - - +
68D GLU* 1.3 59.2 + - - +
70D PHE* 3.5 2.9 + - - +
71D GLU* 2.9 41.3 + - - +
45F PHE* 6.1 0.7 - - - -
46F ALA* 3.9 16.1 + - - +
47F GLY* 4.0 10.1 - - - +
68F HIS* 5.7 2.3 - - - -
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Residues in contact with GLU 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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12D VAL* 3.9 14.4 - - + +
13D ASP* 3.5 16.6 - - - +
16D ASN* 3.3 33.9 + - - +
18D HIS* 3.2 35.5 + - - -
64D THR* 2.9 25.4 + - - +
65D LEU* 3.8 4.9 - - - +
67D SER* 1.3 72.4 - - - +
69D ALA* 1.3 56.4 + - - +
71D GLU* 3.2 6.8 + - - +
72D TYR* 2.8 39.0 + - - +
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Residues in contact with ALA 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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12D VAL* 3.7 16.7 - - + +
60D PRO* 4.3 16.2 - - + -
65D LEU 2.8 17.8 + - - +
66D ARG* 3.5 8.5 - - - +
68D GLU* 1.3 76.5 - - - +
70D PHE* 1.3 58.4 + - - +
72D TYR* 4.6 0.7 - - - -
73D TYR* 2.8 50.0 + - + +
75D THR 4.9 1.3 - - - +
81D LEU* 6.4 0.2 - - + -
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Residues in contact with PHE 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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66D ARG 2.9 19.6 + - - +
67D SER 3.9 2.7 - - - +
69D ALA* 1.3 71.2 - - - +
71D GLU* 1.3 64.6 + - - +
74D HIS* 2.6 47.1 + + + +
75D THR* 3.4 41.0 + - - +
76D LEU* 3.7 13.2 - - + -
8F LEU* 5.0 8.7 - - + -
44F ILE* 3.4 40.6 - - + -
47F GLY* 4.1 13.2 - - - +
68F HIS* 3.4 45.1 - + + -
70F VAL* 4.9 5.6 - - + -
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Residues in contact with GLU 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 SER* 2.9 28.0 + - - +
68D GLU* 3.7 5.7 - - - +
70D PHE* 1.3 83.8 - - - +
72D TYR* 1.3 59.4 + - - +
74D HIS* 4.0 8.3 + - - -
131D PRO* 3.7 18.2 - - - +
6F LYS* 3.6 21.4 + - - +
66F THR* 5.9 0.9 - - - +
68F HIS* 3.8 27.2 + - + +
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Residues in contact with TYR 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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13D ASP* 3.3 47.9 + - + +
14D ASN* 5.2 2.6 - - + +
15D THR* 4.5 7.4 - - - -
68D GLU 2.8 16.7 + - - +
69D ALA* 3.8 2.7 - - - +
71D GLU* 1.3 80.2 - - - +
73D TYR* 1.3 91.4 + + + +
74D HIS 3.6 0.4 - - - -
84D TYR* 6.2 0.7 - + - -
130D ALA 4.3 0.7 - - - -
131D PRO* 3.4 32.5 - - + +
132D ALA* 3.4 42.9 + - + +
135D GLU* 3.3 24.6 + - - +
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Residues in contact with TYR 73 (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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12D VAL* 2.7 31.7 + - + -
57D PHE* 4.1 4.5 - - - -
69D ALA* 2.8 39.7 + - + +
72D TYR* 1.3 100.2 - + - +
74D HIS* 1.3 70.8 + - - +
75D THR* 3.3 19.4 + - + -
80D PHE* 3.8 30.1 - + + -
81D LEU* 3.8 25.3 - - + +
84D TYR* 3.9 13.6 - + - -
130D ALA* 4.2 1.6 - - - +
132D ALA* 3.9 12.8 - - + -
151D LEU* 4.4 9.0 - - + -
155D TYR* 3.0 29.9 + - - +
176D HIS* 4.1 0.2 - - - -
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Residues in contact with HIS 74 (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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70D PHE* 2.6 43.9 + + - -
71D GLU* 4.0 13.8 + - - -
73D TYR* 1.3 74.8 - - - +
75D THR* 1.3 58.1 + - - +
129D ASN* 3.1 29.1 + - - +
130D ALA* 3.8 12.4 + - + +
131D PRO* 4.0 9.0 - - + +
176D HIS* 3.3 26.2 + - - +
8F LEU* 3.3 59.4 + - + +
68F HIS* 5.8 4.7 - + - -
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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