Contacts of the helix formed by residues 58 - 74 (chain D) in PDB entry 1Y9D
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 HIS 58 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58B HIS* 4.9 0.9 - + - -
60B GLU* 2.7 23.7 + - - -
452B MET* 3.5 29.8 - - + -
2705B NA 4.0 8.1 - - - -
32D ILE* 3.8 5.6 - - - -
56D VAL* 3.2 11.5 - - - +
57D ARG* 1.3 80.2 - - - +
59D GLU* 1.3 69.1 + - - +
60D GLU* 3.2 49.2 + - + +
61D VAL* 3.1 16.5 + - + +
89D HIS* 3.3 40.3 + + - -
455D GLN* 3.4 22.2 - - - +
456D ASP* 3.3 2.8 + - - -
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Residues in contact with GLU 59 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
452B MET* 3.7 4.4 - - - +
2702B TPP 2.5 37.5 + - - +
31D GLY* 5.8 0.4 - - - -
32D ILE* 3.7 30.6 - - + +
56D VAL* 4.1 7.2 - - - -
58D HIS* 1.3 73.5 + - - +
60D GLU* 1.3 61.3 + - - +
62D GLY* 3.0 11.0 + - - -
63D ALA 3.0 10.2 + - - -
80D PHE 4.3 11.7 - - - +
81D GLY* 4.5 1.8 - - - -
82D SER* 4.4 0.2 + - - -
86D GLY* 3.3 31.1 - - - +
89D HIS* 2.8 33.9 + - + -
90D LEU* 3.5 16.8 - - + +
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Residues in contact with GLU 60 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58B HIS* 2.7 29.2 + - - -
89B HIS* 2.6 30.4 + - + -
58D HIS* 3.1 28.4 + - + +
59D GLU* 1.3 76.0 - - - +
61D VAL* 1.3 62.5 + - + +
63D ALA* 3.2 3.5 + - - +
64D MET* 2.8 53.6 + - + +
89D HIS 3.1 23.5 + - - +
90D LEU* 4.5 3.6 - - - +
92D ASN* 3.9 7.5 - - + +
93D GLY 5.3 0.7 - - - +
452D MET 4.1 2.9 - - - +
453D THR* 4.3 17.9 - - + -
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Residues in contact with VAL 61 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56D VAL* 4.2 9.0 - - + -
58D HIS* 3.1 11.0 + - + +
60D GLU* 1.3 77.8 - - + +
62D GLY* 1.3 57.2 + - - +
65D ALA* 2.8 30.1 + - + +
427D PRO* 3.6 26.9 - - + +
430D ILE* 4.4 7.4 - - + -
453D THR* 3.8 26.2 - - + -
455D GLN* 3.6 13.7 - - - +
456D ASP* 3.2 44.4 - - + +
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Residues in contact with GLY 62 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30D TYR* 3.5 32.3 - - - -
31D GLY* 5.7 0.2 - - - -
56D VAL* 3.9 10.4 - - - +
58D HIS 3.6 2.4 + - - -
59D GLU* 3.0 10.2 + - - -
61D VAL* 1.3 78.3 - - - +
63D ALA* 1.3 58.3 + - - +
65D ALA 3.4 0.3 + - - -
66D ALA* 3.0 29.3 + - - +
79D CYS* 3.7 8.8 - - - +
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Residues in contact with ALA 63 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59D GLU 3.0 11.6 + - - +
60D GLU 3.7 6.3 - - - +
62D GLY* 1.3 76.0 - - - +
64D MET* 1.4 62.9 + - - +
66D ALA* 3.5 2.9 + - - +
67D ALA* 3.1 21.1 + - - +
79D CYS* 3.7 19.0 - - - +
90D LEU* 3.3 39.9 - - + +
93D GLY* 3.7 11.0 - - - +
94D LEU* 4.1 5.2 - - + +
104D VAL* 5.1 2.6 - - - +
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Residues in contact with MET 64 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60D GLU* 2.8 47.7 + - + +
63D ALA* 1.4 70.3 - - - +
65D ALA* 1.3 58.6 + - - +
67D ALA* 3.3 5.6 + - - +
68D ALA* 3.0 27.4 + - - +
92D ASN* 4.0 7.9 - - + +
93D GLY* 3.8 15.5 - - - -
96D ASP* 5.0 2.4 - - - +
421D THR* 3.7 20.0 - - + +
422D MET 3.5 24.9 - - - +
423D GLY* 3.9 8.5 - - - +
424D VAL* 3.8 22.8 - - + +
427D PRO* 3.7 28.9 - - + +
428D GLY 5.2 0.2 + - - -
453D THR* 4.4 5.8 - - - -
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Residues in contact with ALA 65 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30D TYR* 3.4 34.3 - - + +
61D VAL* 2.8 23.0 + - + +
62D GLY 3.9 1.1 - - - +
64D MET* 1.3 72.1 - - - +
66D ALA* 1.3 52.4 + - - +
68D ALA* 3.2 1.7 + - - -
69D ASP* 2.7 32.9 + - - -
427D PRO* 3.7 25.7 - - + +
430D ILE* 4.9 2.9 - - + -
431D ALA* 3.4 8.9 - - + +
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Residues in contact with ALA 66 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30D TYR* 3.6 7.9 - - + -
62D GLY 3.0 17.0 + - - +
63D ALA 3.6 5.6 - - - +
65D ALA* 1.3 74.5 - - - +
67D ALA* 1.3 64.9 + - - +
69D ASP* 3.3 8.2 + - - +
70D ALA 3.1 16.8 + - - -
77D GLY* 3.4 10.9 - - - -
78D VAL 3.6 34.5 - - - +
79D CYS* 4.3 2.0 - - + -
104D VAL* 3.9 14.1 - - + +
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Residues in contact with ALA 67 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63D ALA 3.1 13.9 + - - +
64D MET* 3.3 7.4 + - - +
66D ALA* 1.3 75.4 - - - +
68D ALA* 1.3 58.7 + - - +
70D ALA* 3.1 2.6 + - - -
71D LYS* 2.8 36.8 + - - +
93D GLY 4.0 3.6 - - - +
96D ASP* 3.5 24.9 - - - +
97D ALA* 3.9 21.1 - - + -
102D VAL* 3.7 3.8 - - + +
104D VAL* 3.7 12.6 - - - +
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Residues in contact with ALA 68 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64D MET 3.0 16.3 + - - +
65D ALA 3.5 4.7 - - - +
67D ALA* 1.3 75.9 - - - +
69D ASP* 1.3 66.1 + - - +
71D LYS* 3.3 14.2 + - + +
72D LEU* 2.9 31.4 + - - +
414D ILE* 3.8 22.6 - - + +
428D GLY* 3.8 16.6 - - - -
431D ALA* 3.9 6.1 - - + -
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Residues in contact with ASP 69 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28D HIS* 2.8 32.6 + - - +
30D TYR* 2.9 36.6 + - - -
65D ALA 2.7 13.8 + - - -
66D ALA* 3.3 11.7 - - - +
68D ALA* 1.3 73.2 - - - +
70D ALA* 1.3 56.5 + - - +
72D LEU* 3.3 2.1 + - - +
73D THR* 3.0 35.3 + - - +
75D LYS 4.2 2.2 - - - +
76D ILE 5.2 0.4 - - - +
77D GLY* 4.2 12.0 - - - -
78D VAL 4.9 0.3 + - - -
431D ALA* 3.4 5.1 - - - +
435D ASN* 2.8 25.4 + - - +
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Residues in contact with ALA 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 ALA 3.1 6.1 + - - +
67D ALA 3.1 8.4 + - - +
69D ASP* 1.3 76.8 - - - +
71D LYS* 1.3 62.0 + - - +
74D GLY* 2.9 28.3 + - - +
75D LYS 3.2 19.5 - - - +
77D GLY 4.0 0.2 - - - +
102D VAL* 3.8 19.1 - - + +
103D PRO* 3.2 33.9 - - + +
104D VAL* 4.7 0.2 - - + -
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Residues in contact with LYS 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 ALA* 2.8 25.4 + - - +
68D ALA* 3.6 12.9 - - + +
70D ALA* 1.3 77.3 - - - +
72D LEU* 1.3 58.8 + - - +
74D GLY 4.7 0.7 + - - -
96D ASP* 2.8 32.7 + - - -
100D ASP* 3.2 23.4 + - + +
102D VAL* 3.8 21.9 - - + +
412D ARG* 3.1 17.6 + - - -
414D ILE* 3.9 23.4 - - + +
415D THR 2.7 33.3 + - - +
416D SER* 3.7 0.4 - - - +
417D ASN* 5.7 1.3 - - - +
424D VAL* 5.6 1.8 - - - +
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Residues in contact with LEU 72 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68D ALA 2.9 21.0 + - - +
69D ASP 3.3 3.1 + - - +
71D LYS* 1.3 78.1 - - - +
73D THR* 1.3 68.8 + - + +
389D ILE* 4.1 22.0 - - + -
412D ARG* 2.9 44.8 + - + +
414D ILE* 4.1 27.8 - - + -
431D ALA 4.2 3.8 - - - -
432D ALA* 3.6 37.0 - - + +
435D ASN* 4.2 7.0 - - - +
436D TYR* 3.8 19.0 + - + -
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Residues in contact with THR 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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69D ASP* 3.0 14.9 + - - +
72D LEU* 1.3 80.3 - - + +
74D GLY* 1.3 57.9 + - - +
75D LYS* 3.1 29.8 + - - +
435D ASN* 3.5 36.9 + - + +
436D TYR* 3.9 15.9 - - + +
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Residues in contact with GLY 74 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70D ALA* 2.9 18.2 + - - -
71D LYS 4.6 0.8 + - - -
72D LEU 3.6 1.2 - - - -
73D THR* 1.3 76.3 - - - +
75D LYS* 1.3 59.7 + - - +
103D PRO* 4.2 8.8 - - - +
158D TYR* 3.7 16.1 - - - -
161D GLN* 5.7 0.5 + - - -
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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
------------------------------------------------------------
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