Contacts of the helix formed by residues 59 - 79 (chain B) in PDB entry 4HFX
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 59 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58B GLU* 1.3 78.8 - - - +
60B TRP* 1.3 66.3 + - - +
61B ARG* 3.6 8.6 + - - +
62B GLU* 3.0 41.1 + - - +
63B MSE 2.9 22.4 + - - +
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Residues in contact with TRP 60 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B GLN* 5.7 7.2 - - - +
41B TRP* 4.1 5.6 - - + -
42B LYS* 3.9 39.1 - - + +
45B CYS* 3.5 44.5 - - + -
50B LYS 5.2 9.0 - - - -
58B GLU 4.1 0.6 + - - -
59B SER* 1.3 71.1 - - - +
61B ARG* 1.3 62.2 + - - +
63B MSE 3.3 20.2 + - - +
64B TYR* 3.1 18.5 + - - +
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Residues in contact with ARG 61 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B TYR* 3.7 23.0 + - - -
27B GLU* 3.2 48.4 + - - +
28B GLU* 4.6 4.9 + - - -
34B ILE* 4.2 22.9 - - - +
41B TRP* 3.5 39.2 - - + +
59B SER* 3.1 8.0 + - - +
60B TRP* 1.3 78.9 - - - +
62B GLU* 1.3 65.9 + - + +
64B TYR* 3.2 12.7 + - - +
65B LEU* 3.3 37.4 + - + +
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Residues in contact with GLU 62 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58B GLU* 2.7 31.8 + - - +
59B SER* 3.0 32.1 + - - +
61B ARG* 1.3 77.4 - - + +
63B MSE 1.3 60.5 + - - +
65B LEU* 3.7 10.2 + - + +
66B ARG* 3.3 24.5 + - - +
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Residues in contact with MSE 63 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45B CYS* 4.5 17.3 - - - -
48B ASP 5.5 0.7 - - - +
49B PHE 5.1 1.8 - - - +
50B LYS* 3.5 37.0 - - - +
58B GLU* 4.8 5.5 - - - +
59B SER 2.9 12.2 + - - +
60B TRP* 3.4 23.3 - - - +
61B ARG 3.2 0.2 - - - -
62B GLU* 1.3 76.7 - - - +
64B TYR* 1.3 62.4 + - - +
66B ARG* 3.4 27.9 + - - +
67B LEU* 3.2 44.3 + - + +
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Residues in contact with TYR 64 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B PRO* 3.3 35.1 - - + +
41B TRP* 3.7 24.7 - + + -
44B HIS* 3.6 35.9 + - + +
45B CYS* 4.1 18.1 - - - -
47B ARG 5.3 1.7 + - - -
48B ASP* 4.0 18.9 + - + +
60B TRP 3.1 12.5 + - - +
61B ARG 3.2 8.2 + - - +
63B MSE 1.3 75.0 - - - +
65B LEU* 1.3 65.4 + - + +
67B LEU* 3.9 4.4 - - - +
68B GLN* 2.9 67.9 + - + +
19C THR* 4.3 6.0 - - + +
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Residues in contact with LEU 65 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B TYR* 4.4 27.4 - - + -
41B TRP* 4.4 13.9 - - + -
61B ARG* 3.3 47.8 + - + +
62B GLU* 4.2 7.6 - - + +
64B TYR* 1.3 92.9 - - + +
66B ARG* 1.3 53.6 + - - +
68B GLN* 3.2 7.9 + - + +
69B ASP* 2.6 38.4 + - - +
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Residues in contact with ARG 66 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62B GLU 3.3 15.2 + - - +
63B MSE 3.4 37.5 + - - +
64B TYR 3.3 0.2 - - - -
65B LEU* 1.3 78.3 - - - +
67B LEU* 1.3 84.0 + - - +
69B ASP* 3.5 9.8 + - + +
70B ALA* 3.0 25.9 + - + +
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Residues in contact with LEU 67 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48B ASP* 3.8 36.8 - - - +
49B PHE* 6.1 0.9 - - + -
50B LYS* 5.6 2.0 - - - -
63B MSE 3.2 41.2 + - + +
64B TYR* 4.1 3.8 - - - +
66B ARG* 1.3 109.9 - - + +
68B GLN* 1.3 58.8 + - - +
70B ALA* 3.4 9.2 + - + +
71B ARG* 3.0 27.3 + - - +
74B ARG* 4.8 1.9 + - - -
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Residues in contact with GLN 68 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48B ASP* 4.0 7.8 + - - +
64B TYR* 2.9 60.1 + - + +
65B LEU* 3.4 8.1 - - + +
67B LEU* 1.3 73.3 - - - +
69B ASP* 1.3 59.7 + - - +
71B ARG* 3.1 30.8 + - - +
72B GLU* 2.8 38.8 + - - +
19C THR* 4.1 13.8 - - - +
22C GLN* 2.5 33.7 + - - +
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Residues in contact with ASP 69 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65B LEU 2.6 20.9 + - - +
66B ARG* 3.7 9.8 - - - +
67B LEU 3.4 0.2 - - - -
68B GLN* 1.3 70.0 - - - +
70B ALA* 1.3 64.4 + - - +
72B GLU* 4.2 12.1 + - - +
73B GLN* 3.2 43.0 + - - +
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Residues in contact with ALA 70 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66B ARG* 3.0 14.9 + - + +
67B LEU* 3.5 15.0 - - + +
68B GLN 3.2 0.2 - - - -
69B ASP* 1.3 75.8 + - - +
71B ARG* 1.3 63.1 + - - +
73B GLN* 3.3 12.9 + - - +
74B ARG* 3.2 42.7 + - - +
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Residues in contact with ARG 71 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48B ASP* 4.3 22.9 + - - +
67B LEU 3.0 14.7 + - - +
68B GLN* 3.4 35.8 - - - +
70B ALA* 1.3 76.5 - - - +
72B GLU* 1.3 56.7 + - - +
74B ARG* 3.4 18.8 + - - +
75B LEU* 3.0 34.7 + - + +
101B SO4 3.3 37.5 + - - +
14C VAL 6.0 0.4 - - - -
17C ARG* 3.0 37.5 + - - +
18C CYS* 4.9 2.4 - - - +
19C THR* 5.8 0.4 - - - +
22C GLN* 3.7 15.5 + - - +
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Residues in contact with GLU 72 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68B GLN* 2.8 23.9 + - - +
69B ASP* 4.2 12.4 + - - +
71B ARG* 1.3 70.8 - - - +
73B GLN* 1.3 66.1 + - - +
74B ARG 3.2 0.2 - - - -
75B LEU* 3.1 17.9 + - + +
76B ARG* 3.1 35.7 + - - +
21C ASP* 4.5 6.6 - - - +
22C GLN* 2.8 46.2 + - + +
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Residues in contact with GLN 73 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69B ASP* 3.2 41.8 + - - +
70B ALA* 3.5 12.7 - - - +
72B GLU* 1.3 76.5 - - - +
74B ARG* 1.3 63.6 + - + +
76B ARG* 3.6 10.0 + - - +
77B VAL* 3.5 24.2 + - - +
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Residues in contact with ARG 74 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67B LEU 4.8 1.8 + - - -
70B ALA* 3.2 28.5 + - - +
71B ARG* 3.4 26.8 - - - +
72B GLU 3.2 0.4 - - - -
73B GLN* 1.3 75.5 - - + +
75B LEU* 1.3 59.6 + - - +
77B VAL* 3.4 7.4 + - - +
78B LEU* 2.9 44.1 + - + +
101B SO4 2.7 46.3 + - - +
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Residues in contact with LEU 75 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71B ARG* 3.0 24.7 + - + +
72B GLU* 3.1 13.2 + - + +
74B ARG* 1.3 78.6 - - - +
76B ARG* 1.3 49.9 - - + +
78B LEU* 3.2 5.2 + - + -
79B THR* 2.5 47.1 + - + +
101B SO4 4.3 10.1 - - - +
14C VAL* 3.4 32.8 - - + +
15C LEU* 5.3 0.7 - - + -
18C CYS* 3.5 28.3 - - - -
22C GLN* 3.8 21.1 - - + +
26C ILE* 3.9 23.3 - - + -
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Residues in contact with ARG 76 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72B GLU* 3.1 34.9 + - - +
73B GLN* 3.8 11.2 - - - +
74B ARG 3.4 0.2 - - - -
75B LEU* 1.3 76.8 - - + +
77B VAL* 1.3 64.2 + - + +
79B THR* 3.2 10.1 + - - +
80B LYS* 3.2 19.9 + - - +
24D TYR* 5.6 5.5 + - - -
28D GLU* 4.6 18.3 + - - +
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Residues in contact with VAL 77 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73B GLN 3.5 15.9 + - - +
74B ARG* 3.4 8.7 + - - +
75B LEU 3.3 0.2 - - - -
76B ARG* 1.3 74.7 - - + +
78B LEU* 1.3 70.9 + - + +
80B LYS* 3.2 21.1 + - - +
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Residues in contact with LEU 78 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74B ARG* 2.9 31.4 + - + +
75B LEU* 3.5 7.9 - - + +
77B VAL* 1.3 83.9 - - + +
79B THR* 1.3 57.2 + - + +
80B LYS 3.3 3.3 + - - -
81B ASN* 4.0 9.4 + - - +
101B SO4 5.5 2.2 - - - +
11C LEU* 3.9 28.7 - - + +
14C VAL* 4.0 33.7 - - + -
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Residues in contact with THR 79 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75B LEU* 2.5 32.3 + - + +
76B ARG* 3.3 14.6 + - - +
77B VAL 3.2 0.4 - - - -
78B LEU* 1.3 74.0 - - + +
80B LYS* 1.3 61.5 + - - +
81B ASN* 3.3 6.4 - - - +
11C LEU* 4.2 21.1 - - + -
14C VAL* 6.6 0.2 - - + -
15C LEU* 4.9 3.6 - - + -
26C ILE* 3.9 39.7 - - + +
31D HIS* 4.5 4.2 - - - -
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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
------------------------------------------------------------
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