Contacts of the helix formed by residues 59 - 80 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38A ASP* 3.3 25.4 - - - -
55A GLU* 3.7 2.9 - - - +
58A GLU* 1.3 82.5 - - - +
60A TRP* 1.3 66.7 + - - +
61A ARG* 3.8 4.3 + - - +
62A GLU* 3.1 34.1 + - - +
63A MSE 3.1 18.7 + - - +
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Residues in contact with TRP 60 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38A ASP* 3.6 36.6 + - + +
39A GLN* 4.6 7.6 - - - +
41A TRP* 3.8 2.4 - - - +
42A LYS* 3.6 48.0 - - + +
45A CYS* 3.5 37.8 - - + -
53A ARG 4.4 12.3 - - - -
54A PRO* 4.9 5.6 - - + -
55A GLU* 3.4 37.6 - - + +
59A SER* 1.3 73.9 - - - +
61A ARG* 1.3 57.2 + - - +
63A MSE 3.4 2.7 + - - +
64A TYR* 3.1 24.4 + - - +
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Residues in contact with ARG 61 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A TYR* 3.3 31.4 + - - -
27A GLU* 3.0 48.4 + - - +
28A GLU* 5.1 1.2 - - - +
38A ASP* 3.3 12.9 + - - +
41A TRP* 3.5 38.9 - - + +
59A SER* 3.9 4.9 - - - +
60A TRP* 1.3 76.4 - - - +
62A GLU* 1.3 69.9 + - + +
64A TYR* 3.4 1.9 + - - +
65A LEU* 3.3 42.5 + - + +
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Residues in contact with GLU 62 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58A GLU* 3.1 33.8 - - + +
59A SER* 3.1 20.3 + - - +
61A ARG* 1.3 81.3 - - + +
63A MSE 1.3 69.4 + - - +
65A LEU* 3.5 9.8 + - + +
66A ARG* 3.2 21.0 + - - +
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Residues in contact with MSE 63 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45A CYS* 4.8 12.3 - - - -
53A ARG* 3.6 37.2 - - + +
54A PRO* 2.9 43.3 - - + +
55A GLU* 3.7 10.8 - - + -
56A GLU* 5.8 0.7 - - + -
58A GLU* 3.6 15.1 - - + +
59A SER 3.1 14.4 + - - +
60A TRP* 3.6 11.0 - - - +
61A ARG 3.3 0.2 - - - -
62A GLU* 1.3 75.2 - - - +
64A TYR* 1.3 64.3 + - - +
66A ARG* 3.1 30.5 + - - +
67A LEU* 3.0 40.2 + - + +
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Residues in contact with TYR 64 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20A PRO* 3.6 29.3 - - + +
41A TRP* 3.7 24.0 - + + -
44A HIS* 3.5 37.5 + - + +
45A CYS* 3.9 19.0 - - - -
60A TRP 3.1 14.2 + - - +
61A ARG 3.7 8.1 - - - +
63A MSE 1.3 76.4 - - - +
65A LEU* 1.3 56.7 + - + +
67A LEU* 3.3 6.3 + - + +
68A GLN* 2.7 79.2 + - + +
71A ARG* 5.3 2.1 + - - -
19D THR* 3.8 12.0 - - - +
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Residues in contact with LEU 65 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A TYR* 3.7 33.9 - - + +
41A TRP* 4.1 28.9 - - + -
61A ARG* 3.3 37.7 + - + +
62A GLU* 3.9 8.5 - - + +
63A MSE 3.3 0.2 - - - -
64A TYR* 1.3 82.6 - - + +
66A ARG* 1.3 58.2 + - - +
68A GLN* 4.0 4.8 - - - +
69A ASP* 3.3 26.3 + - - +
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Residues in contact with ARG 66 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56A GLU* 4.1 21.1 + - - +
58A GLU* 3.0 37.6 + - - -
62A GLU 3.2 11.4 + - - +
63A MSE 3.1 35.0 + - - +
65A LEU* 1.3 77.4 - - - +
67A LEU* 1.3 74.8 + - + +
69A ASP* 3.4 6.0 + - - +
70A ALA* 3.1 27.1 + - + +
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Residues in contact with LEU 67 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45A CYS* 6.2 1.3 - - - -
50A LYS 5.7 3.8 - - - +
53A ARG* 3.7 41.1 - - + +
63A MSE 3.0 51.6 + - + +
64A TYR* 3.9 5.8 - - + +
66A ARG* 1.3 95.6 - - - +
68A GLN* 1.3 59.7 + - - +
70A ALA* 3.8 9.3 - - + +
71A ARG* 3.1 28.7 + - - +
74A ARG* 5.4 0.9 + - - -
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Residues in contact with GLN 68 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20A PRO* 4.9 3.4 - - + +
64A TYR* 2.7 59.6 + - + +
65A LEU* 4.3 4.3 - - - +
67A LEU* 1.3 71.5 - - - +
69A ASP* 1.3 61.0 + - - +
71A ARG* 3.5 16.1 + - - -
72A GLU* 2.8 30.2 + - - +
19D THR* 3.7 13.5 + - - +
21D ASP* 4.8 4.6 + - - -
22D GLN* 3.0 44.5 + - - +
25D ARG* 4.3 11.0 - - - +
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Residues in contact with ASP 69 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65A LEU 3.3 19.1 + - - +
66A ARG* 3.5 7.4 - - - +
68A GLN* 1.3 76.7 - - - +
70A ALA* 1.3 55.5 + - - +
72A GLU* 3.0 14.6 + - - +
73A GLN* 2.8 57.2 + - - +
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Residues in contact with ALA 70 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66A ARG* 3.1 13.6 + - + +
67A LEU* 3.8 11.7 - - + +
68A GLN 3.4 0.2 - - - -
69A ASP* 1.3 79.1 - - - +
71A ARG* 1.3 63.0 + - - +
73A GLN* 3.4 10.7 + - - +
74A ARG* 3.1 44.5 + - - +
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Residues in contact with ARG 71 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50A LYS 4.8 13.7 - - - +
53A ARG* 6.0 1.4 - - - +
64A TYR* 5.3 2.2 + - - -
67A LEU* 3.1 19.3 + - - +
68A GLN* 3.7 14.8 + - - +
69A ASP 3.3 0.2 - - - -
70A ALA* 1.3 78.4 - - - +
72A GLU* 1.3 56.5 + - - +
74A ARG* 3.2 22.6 + - - +
75A LEU* 3.0 48.0 + - + +
14D VAL* 6.4 0.4 - - - -
17D ARG* 3.4 33.9 + - - +
18D CYS* 4.6 5.6 - - - +
19D THR* 5.1 4.9 - - - +
22D GLN* 3.4 31.2 + - - +
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Residues in contact with GLU 72 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68A GLN 2.8 18.8 + - - +
69A ASP* 3.0 13.7 + - - +
71A ARG* 1.3 73.6 - - - +
73A GLN* 1.3 65.2 + - - +
75A LEU* 3.9 7.5 - - - +
76A ARG* 3.0 38.4 + - - +
22D GLN* 4.4 7.2 - - + +
25D ARG* 2.7 43.1 + - + +
26D ILE* 4.6 12.0 - - + +
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Residues in contact with GLN 73 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69A ASP* 2.8 48.1 + - - +
70A ALA* 3.7 9.0 - - - +
72A GLU* 1.3 72.1 - - - +
74A ARG* 1.3 59.8 + - + +
76A ARG* 3.0 31.4 + - - +
77A VAL* 3.2 15.7 + - + +
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Residues in contact with ARG 74 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67A LEU 5.4 0.8 + - - -
70A ALA* 3.1 42.2 + - - +
71A ARG* 3.6 24.0 - - - +
72A GLU 3.2 0.4 - - - -
73A GLN* 1.3 73.7 - - + +
75A LEU* 1.3 69.3 - - + +
77A VAL* 3.5 7.8 + - - +
78A LEU* 3.3 29.9 + - + +
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Residues in contact with LEU 75 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71A ARG* 3.0 39.8 + - + +
72A GLU* 3.9 2.5 - - - +
74A ARG* 1.3 77.2 - - + +
76A ARG* 1.3 58.4 - - - +
78A LEU* 3.2 10.6 + - + -
79A THR* 2.6 40.6 + - + +
14D VAL* 3.6 29.4 - - + -
15D LEU* 5.2 7.9 - - + -
18D CYS* 3.5 29.4 - - - -
22D GLN* 4.6 7.2 - - + -
26D ILE* 3.4 30.7 - - + -
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Residues in contact with ARG 76 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72A GLU* 3.0 33.1 + - - +
73A GLN* 3.0 22.8 + - - +
75A LEU* 1.3 77.2 - - - +
77A VAL* 1.3 60.1 + - + +
79A THR* 3.4 6.3 + - - -
80A LYS* 3.5 6.6 + - - +
27C GLU 4.4 19.0 + - - -
26D ILE* 4.5 3.1 - - + +
29D TYR* 3.3 67.8 + - + +
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Residues in contact with VAL 77 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73A GLN* 3.2 15.3 + - + +
74A ARG* 4.0 8.3 - - - +
75A LEU 3.2 0.4 - - - -
76A ARG* 1.3 77.3 - - + +
78A LEU* 1.3 69.1 + - + +
79A THR 3.4 0.2 + - - -
80A LYS* 3.9 11.0 + - - +
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Residues in contact with LEU 78 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74A ARG* 3.3 20.3 + - + +
75A LEU* 3.2 19.6 + - + +
77A VAL* 1.3 82.3 - - + +
79A THR* 1.3 61.0 + - + +
80A LYS 3.6 1.6 + - - +
81A ASN 4.2 10.7 - - - +
10D VAL* 6.3 3.1 - - + -
11D LEU* 3.7 30.3 - - + +
14D VAL* 4.9 15.0 - - + -
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Residues in contact with THR 79 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75A LEU* 2.6 28.6 + - + +
76A ARG 3.4 6.6 + - - -
77A VAL 3.2 0.2 - - - -
78A LEU* 1.3 78.5 - - + +
80A LYS* 1.3 49.8 + - - +
81A ASN* 2.6 9.2 + - - -
11D LEU* 4.1 23.8 - - + -
15D LEU* 4.8 7.2 - - + -
26D ILE* 4.0 26.1 - - + +
29D TYR* 3.5 17.8 - - - -
30D ASN* 2.5 35.9 + - - -
33D LEU* 4.4 14.1 - - + +
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Residues in contact with LYS 80 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76A ARG 3.5 8.3 + - - +
77A VAL* 4.4 7.9 - - - +
78A LEU 3.5 2.8 - - - +
79A THR* 1.3 73.8 - - - +
81A ASN* 1.3 83.0 + - + +
29D TYR* 3.5 51.1 + - + +
30D ASN* 4.3 13.7 + - - +
31D HIS* 5.6 3.6 - - - -
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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