Contacts of the helix formed by residues 57 - 75 (chain D) in PDB entry 4H7Y
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 ASN 57 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13D PRO* 3.6 21.2 - - - +
14D GLU* 3.0 23.3 + - - +
54D TYR* 3.0 31.9 + - + +
55D GLY 3.4 0.2 - - - -
56D GLN* 1.3 76.0 - - - +
58D GLU* 1.3 64.3 + - - +
59D SER* 2.9 13.5 + - - -
60D PHE* 2.9 22.5 + - + +
61D ALA* 3.1 17.0 + - - +
93D PHE* 3.8 4.8 - - - -
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Residues in contact with GLU 58 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56D GLN 3.6 3.6 + - - -
57D ASN* 1.3 74.2 + - - +
59D SER* 1.3 58.9 + - - +
61D ALA* 3.2 2.8 + - - +
62D ARG* 2.9 40.8 + - + +
93D PHE* 3.6 33.0 - - + -
95D PHE* 4.3 15.7 - - + -
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Residues in contact with SER 59 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13D PRO* 3.9 23.1 - - - -
14D GLU* 3.6 20.0 + - - +
17D LEU* 3.6 27.1 - - - +
57D ASN* 2.9 8.3 + - - -
58D GLU* 1.3 76.1 - - - +
60D PHE* 1.3 66.4 + - - +
62D ARG* 3.1 5.5 + - - +
63D ILE* 3.0 26.6 + - - +
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Residues in contact with PHE 60 (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 PRO* 3.6 9.3 - - + +
46D ILE* 5.5 4.3 - - + -
49D LEU* 3.8 41.7 - - + -
51D PRO* 3.8 28.0 - - + -
54D TYR* 3.3 39.0 - + + -
57D ASN* 2.9 18.6 + - + +
59D SER* 1.3 76.1 - - - +
61D ALA* 1.3 62.5 + - - +
63D ILE* 3.0 10.2 + - + +
64D GLN* 2.9 58.9 + - + +
89D ASN* 4.1 11.0 - - + -
90D CYS* 3.7 17.5 - - - -
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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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57D ASN 3.1 5.6 + - - +
58D GLU 3.2 9.2 + - - +
60D PHE* 1.3 78.7 - - - +
62D ARG* 1.3 58.2 + - - +
64D GLN* 3.3 1.0 + - - +
65D VAL* 2.9 35.0 + - - +
90D CYS* 3.7 25.4 - - + -
93D PHE* 3.6 26.9 - - + -
95D PHE* 3.5 17.0 - - + -
96D VAL* 4.0 2.5 - - + -
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Residues in contact with ARG 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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17D LEU* 3.8 35.0 - - + +
21D LEU* 4.1 27.0 - - - +
58D GLU* 2.9 31.6 + - + +
59D SER* 3.1 9.1 + - - +
61D ALA* 1.3 75.9 - - - +
63D ILE* 1.3 57.7 + - - +
65D VAL* 4.1 1.0 - - - +
66D ARG* 3.0 32.6 + - - +
95D PHE* 3.8 23.1 - - + -
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Residues in contact with ILE 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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13D PRO* 3.6 26.9 - - + +
16D TRP* 3.9 11.9 - - + -
17D LEU* 4.0 15.9 - - + +
20D LEU* 4.2 6.7 - - + -
42D TYR* 3.6 22.1 - - + -
45D ALA* 4.2 11.4 - - + -
46D ILE* 4.0 20.6 - - + +
49D LEU* 3.8 24.9 - - + -
59D SER 3.0 17.0 + - - +
60D PHE* 3.0 9.2 + - + +
62D ARG* 1.3 74.6 - - - +
64D GLN* 1.3 66.8 + - + +
67D PHE* 3.0 24.1 + - - +
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Residues in contact with GLN 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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43A SER* 5.5 0.4 + - - -
47A GLU* 3.7 18.5 + - - +
46D ILE* 4.0 23.8 + - + +
51D PRO* 4.9 2.8 - - - +
60D PHE* 2.9 57.5 + - + +
61D ALA 3.8 3.6 - - - +
63D ILE* 1.3 75.9 - - + +
65D VAL* 1.3 62.0 + - - +
67D PHE* 3.7 8.3 - - - +
68D ALA* 3.3 20.3 + - - +
82D TYR 4.6 1.2 - - - +
85D MET 3.5 1.2 - - - +
86D ALA* 3.5 34.3 + - + +
89D ASN* 3.1 26.5 + - - +
90D CYS* 3.9 5.8 - - - -
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Residues in contact with VAL 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 20.0 + - - +
62D ARG 4.1 1.8 - - - +
64D GLN* 1.3 77.9 - - - +
66D ARG* 1.3 58.0 + - - +
68D ALA* 3.1 7.0 + - - +
69D GLU* 2.9 38.0 + - - +
83D PHE* 5.6 1.1 - - + -
86D ALA* 4.4 7.0 - - + -
95D PHE* 3.6 17.7 - - + -
96D VAL* 3.6 40.6 - - + +
99D SER* 3.4 28.4 + - - +
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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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17D LEU* 6.3 0.4 - - + -
21D LEU* 6.1 1.8 - - + -
24D GLU* 2.8 36.8 + - - +
30D LEU* 5.4 1.2 - - - +
42D TYR* 3.3 31.2 - - + +
62D ARG 3.0 20.0 + - - +
65D VAL* 1.3 74.5 - - - +
67D PHE* 1.3 60.6 + - - +
69D GLU* 2.8 35.4 + - - +
70D LEU* 2.9 57.0 + - + +
73D ILE* 4.5 12.3 - - - +
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Residues in contact with PHE 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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47A GLU* 3.6 35.9 - - + -
39D ILE* 3.8 9.4 - - + -
42D TYR* 3.7 28.5 - - + -
43D SER* 3.3 25.6 - - - -
46D ILE* 3.4 24.7 - - + -
63D ILE 3.0 18.6 + - - +
64D GLN 3.7 4.0 - - - +
66D ARG* 1.3 76.6 - - - +
68D ALA* 1.3 58.0 + - - +
70D LEU* 3.4 4.4 + - - +
71D LYS* 3.0 60.6 + - + +
82D TYR* 3.7 29.6 - + + -
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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
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64D GLN 3.3 8.1 + - - +
65D VAL* 3.1 10.8 + - - +
67D PHE* 1.3 81.0 - - - +
69D GLU* 1.3 57.2 + - - +
71D LYS* 3.3 3.7 + - - +
72D ALA* 2.9 28.9 + - - +
79D ALA* 4.3 0.3 - - - +
82D TYR* 3.7 42.0 - - + +
83D PHE* 3.6 26.4 - - + +
86D ALA* 5.3 0.2 - - + -
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Residues in contact with GLU 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 VAL* 2.9 27.8 + - - +
66D ARG* 2.8 40.2 + - - +
68D ALA* 1.3 75.0 - - - +
70D LEU* 1.3 63.7 + - - +
72D ALA* 3.1 6.2 + - - +
73D ILE* 3.1 27.5 + - + +
83D PHE* 4.0 9.2 - - + -
99D SER* 2.9 32.5 + - - +
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Residues in contact with LEU 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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24D GLU* 4.1 1.1 - - - +
30D LEU* 4.4 4.7 - - + -
35D LEU* 4.1 15.3 - - + +
38D LEU* 3.7 36.1 - - + -
39D ILE* 3.7 23.8 - - + +
42D TYR* 3.7 29.6 - - + -
66D ARG* 2.9 56.3 + - + +
67D PHE* 3.8 4.0 - - - +
69D GLU* 1.3 72.9 - - - +
71D LYS* 1.3 65.5 + - - +
73D ILE* 3.2 11.9 + - + +
74D GLN* 3.1 22.2 + - - +
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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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47A GLU 5.3 0.8 + - - -
50A PRO* 4.8 11.1 - - - +
39D ILE* 3.7 22.9 - - + +
43D SER* 5.2 1.5 + - - -
67D PHE* 3.0 48.0 + - + +
68D ALA 3.3 3.1 + - - +
70D LEU* 1.3 76.0 - - - +
72D ALA* 1.3 57.9 + - - +
74D GLN* 3.2 18.1 + - - +
75D GLU* 2.8 33.6 + - - +
79D ALA* 3.9 3.6 - - + -
82D TYR* 3.5 47.6 + - + -
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Residues in contact with ALA 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 ALA 2.9 13.8 + - - +
69D GLU* 3.1 9.8 + - - +
71D LYS* 1.3 76.9 - - - +
73D ILE* 1.3 61.5 + - + +
76D PRO* 3.2 28.9 - - + +
79D ALA* 3.6 18.1 - - + +
83D PHE* 4.0 5.6 - - + -
103D PHE* 3.9 23.8 - - + -
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Residues in contact with ILE 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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30D LEU* 5.3 7.0 - - + -
35D LEU* 4.0 19.7 - - + -
66D ARG* 4.5 12.6 - - - +
69D GLU* 3.1 20.1 + - + +
70D LEU* 3.4 25.6 - - + +
71D LYS 3.2 0.2 - - - -
72D ALA* 1.3 78.1 - - - +
74D GLN* 1.3 62.9 - - - +
76D PRO* 4.4 3.8 - - - +
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Residues in contact with GLN 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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32D ASP 4.9 1.6 + - - -
35D LEU* 3.7 18.6 - - + +
36D ASN* 2.7 43.8 + - - +
39D ILE* 3.4 18.2 - - + +
70D LEU 3.1 15.7 + - - +
71D LYS* 3.7 21.1 + - - +
73D ILE* 1.3 80.1 - - - +
75D GLU* 1.3 68.4 + - + +
76D PRO* 4.2 1.3 - - - +
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Residues in contact with GLU 75 (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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71D LYS 2.8 18.2 + - - +
73D ILE 3.5 0.2 - - - -
74D GLN* 1.3 84.5 - - + +
76D PRO* 1.3 72.4 - - - +
77D ASP* 3.5 30.0 + - - +
78D ASP* 3.2 41.2 + - + +
79D ALA* 3.6 6.1 + - - +
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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