Contacts of the helix formed by residues 57 - 73 (chain D) in PDB entry 4HXD
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 SER 57 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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46D ALA* 3.7 19.5 - - - -
50D PHE* 3.8 14.2 - - - -
52D VAL 3.9 3.6 + - - -
53D LYS* 3.4 9.2 - - - -
54D THR* 2.6 45.6 + - - -
55D PRO 3.4 2.4 - - - -
56D SER* 1.3 72.9 - - - +
58D PHE* 1.3 53.4 + - - +
59D ARG 2.8 6.0 + - - -
60D LYS* 2.7 34.7 + - - +
61D VAL 3.6 2.6 + - - -
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Residues in contact with PHE 58 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37D ASP* 5.9 0.2 - - - -
39D ASN* 3.7 37.0 - - + -
42D TYR* 3.6 29.2 - - + -
43D HIS* 3.3 35.3 + + - +
46D ALA* 3.9 2.0 - - - +
55D PRO 3.5 15.0 - - - -
56D SER* 4.0 1.8 - - - -
57D SER* 1.3 77.4 - - - +
59D ARG* 1.3 101.9 + - + +
60D LYS 3.3 0.4 - - - -
61D VAL* 3.1 15.8 - - - +
62D LYS* 3.0 40.4 + - + +
96D ASP* 4.6 8.7 - - - -
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Residues in contact with ARG 59 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56D SER* 3.2 42.8 + - - +
57D SER 2.8 1.8 + - - -
58D PHE* 1.3 107.4 - - + +
60D LYS* 1.3 59.8 + - - +
62D LYS* 3.4 7.2 + - + +
63D GLU* 2.8 28.1 + - - +
96D ASP* 3.5 21.8 + - - -
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Residues in contact with LYS 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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137B ARG* 6.0 2.4 - - - +
50D PHE* 3.8 30.4 - - + -
56D SER 4.3 0.6 + - - -
57D SER* 2.7 20.1 + - - +
59D ARG* 1.3 73.9 - - - +
61D VAL* 1.3 55.5 + - - +
63D GLU* 3.2 24.2 - - - +
64D HIS* 2.9 48.5 + - + -
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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
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42D TYR* 3.5 26.7 - - + +
45D ILE* 3.8 24.5 - - + -
46D ALA* 4.3 9.0 - - + +
49D PHE* 6.1 2.5 - - + -
50D PHE* 4.5 8.7 - - + -
57D SER 3.6 2.6 + - - +
58D PHE* 3.1 32.1 - - - +
60D LYS* 1.3 74.9 - - - +
62D LYS* 1.3 58.4 + - - +
64D HIS* 3.1 11.6 + - + +
65D LEU* 2.9 25.8 + - - +
108D LEU* 3.8 25.0 - - + +
112D LEU* 5.4 3.8 - - + -
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Residues in contact with LYS 62 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39D ASN* 4.5 7.2 - - - +
42D TYR* 3.6 43.7 - - + -
58D PHE* 3.0 36.8 + - + +
59D ARG* 3.8 8.1 - - + +
61D VAL* 1.3 72.1 - - - +
63D GLU* 1.3 64.7 + - - +
65D LEU* 3.2 7.6 + - - +
66D GLN 3.1 18.9 + - - -
93D ALA 3.0 28.4 + - - -
94D MET* 3.4 42.9 + - + +
95D LYS 3.1 19.4 + - - -
96D ASP* 4.4 4.8 - - - +
98D GLU* 4.6 2.4 - - - +
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Residues in contact with GLU 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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59D ARG 2.8 15.3 + - - +
60D LYS* 3.2 28.0 - - - +
62D LYS* 1.3 75.7 - - - +
64D HIS* 1.3 68.8 + - - +
66D GLN* 3.5 9.4 + - + +
67D LEU* 3.3 41.0 + - + +
94D MET* 4.5 3.5 - - - +
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Residues in contact with HIS 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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135B PRO* 5.9 1.4 - - - +
137B ARG* 5.9 2.6 + - - -
49D PHE* 4.7 14.1 - + - -
50D PHE* 5.3 1.5 - + - -
60D LYS* 2.9 48.9 + - + -
61D VAL* 3.1 12.4 + - - +
63D GLU* 1.3 81.7 + - - +
65D LEU* 1.3 52.8 + - - +
67D LEU* 3.4 10.7 + - + +
68D ALA* 2.7 36.0 + - - +
108D LEU* 3.8 13.9 - - + -
111D HIS* 2.7 37.6 - + + +
112D LEU* 3.4 19.3 - - + +
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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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42D TYR* 3.5 26.7 - - + +
61D VAL 2.9 12.0 + - - +
62D LYS* 3.4 11.4 - - - +
63D GLU 3.2 0.4 - - - -
64D HIS* 1.3 74.6 - - - +
66D GLN* 1.3 66.1 + - - +
68D ALA* 3.0 1.7 + - - -
69D ALA* 2.7 28.5 + - - +
89D TYR* 3.6 21.1 - - + +
90D ILE* 6.0 0.7 - - + -
93D ALA* 4.7 5.8 - - + -
94D MET* 4.5 15.3 - - - -
104D GLU* 3.8 23.3 - - + +
107D MET* 3.7 29.6 - - + -
108D LEU* 3.8 20.1 - - + +
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Residues in contact with GLN 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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62D LYS 3.1 9.5 + - - +
63D GLU* 3.5 12.3 - - + +
65D LEU* 1.3 78.6 - - - +
67D LEU* 1.3 73.6 + - + +
69D ALA* 3.5 4.0 + - - +
70D GLU* 3.5 28.1 + - - +
90D ILE* 3.9 37.5 - - - +
94D MET* 3.6 31.6 - - + +
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Residues in contact with LEU 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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63D GLU* 3.3 37.3 + - + +
64D HIS* 3.5 13.2 - - + +
65D LEU 3.2 0.2 - - - -
66D GLN* 1.3 87.7 - - + +
68D ALA* 1.3 62.2 - - - +
70D GLU* 3.1 23.4 + - - +
71D VAL* 4.0 7.1 - - - +
111D HIS* 4.1 18.4 - - + +
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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 HIS 2.7 22.2 + - - +
65D LEU* 3.5 8.3 - - - +
67D LEU* 1.3 73.1 - - - +
69D ALA* 1.3 60.2 + - - +
70D GLU 3.2 0.7 + - - -
71D VAL* 3.3 4.1 + - - +
72D TYR* 3.1 30.4 + - + +
107D MET* 3.7 22.0 - - + +
108D LEU* 4.6 2.5 - - + +
111D HIS* 3.5 32.5 - - + -
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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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65D LEU 2.7 18.7 + - - +
66D GLN 3.7 5.4 - - - +
67D LEU 3.3 0.2 - - - -
68D ALA* 1.3 72.4 - - - +
70D GLU* 1.3 64.0 + - - +
72D TYR 4.0 0.2 - - - -
73D TYR* 3.1 30.6 + - + +
74D ASP 4.9 0.3 + - - -
86D LYS* 4.9 6.7 - - + +
89D TYR* 4.4 7.9 - - + -
90D ILE* 4.4 18.8 - - + -
107D MET* 3.8 29.5 - - + -
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Residues in contact with GLU 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 GLN* 3.5 18.8 + - - +
67D LEU* 3.1 16.8 + - - +
69D ALA* 1.3 79.6 - - - +
71D VAL* 1.3 60.5 + - + +
86D LYS* 6.1 2.0 - - - +
90D ILE* 6.0 2.3 - - - +
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Residues in contact with VAL 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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11B ARG* 3.5 46.0 - - - +
15B GLU* 5.6 0.7 - - - +
17B TYR* 6.0 0.7 - - - +
67D LEU 4.0 9.9 - - - +
68D ALA* 3.8 11.9 - - - +
70D GLU* 1.3 79.4 - - + +
72D TYR* 1.3 86.1 + - + +
73D TYR 3.7 0.7 - - - -
74D ASP* 5.0 3.9 + - - +
75D THR* 4.9 6.8 + - - +
111D HIS* 6.0 2.0 - - + -
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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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11B ARG* 4.1 7.3 + - - -
14B ASP* 4.1 10.1 - - - -
15B GLU* 2.9 40.5 + - - -
68D ALA* 3.1 24.4 + - - +
71D VAL* 1.3 102.4 - - + +
73D TYR* 1.3 65.5 + - - +
74D ASP 3.4 2.5 - - - -
75D THR* 3.2 23.3 + - - -
76D GLU* 3.1 28.9 - - - +
107D MET* 4.2 13.2 - - + -
110D LYS* 3.6 47.3 + - + +
111D HIS* 3.8 8.7 - + + -
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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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69D ALA* 3.1 23.7 + - + +
72D TYR* 1.3 75.9 - - - +
74D ASP* 1.3 66.8 - - - +
75D THR 3.0 5.9 + - - -
76D GLU* 3.1 20.6 + - - +
79D ALA* 3.6 33.7 - - + +
80D VAL* 5.1 0.9 + - - -
82D THR* 4.0 3.1 + - - -
84D ILE* 2.5 45.8 + - - +
85D SER* 3.9 5.6 - - - -
86D LYS* 3.5 31.2 - - + -
89D TYR* 3.5 41.4 - + + +
103D LEU* 4.4 4.1 - - + +
107D MET* 4.1 16.5 - - + -
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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
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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