Contacts of the helix formed by residues 64 - 80 (chain A) in PDB entry 4HRE
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 64 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21A PRO* 6.5 0.4 - - - -
27A VAL* 4.1 5.6 - - - -
28A LYS* 4.2 5.7 + - - -
29A PRO* 3.7 28.2 - - - +
63A ARG* 1.3 76.0 - - - +
65A ASN* 1.3 66.1 - - - +
66A VAL* 3.8 9.9 + - - +
67A GLN* 2.9 40.5 + - - +
68A ARG* 3.0 11.0 + - - +
297A GLU* 3.7 16.8 - - - -
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Residues in contact with ASN 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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64A SER* 1.3 71.6 - - - +
66A VAL* 1.3 63.5 + - + +
68A ARG* 3.3 15.8 + - - +
69A GLN* 3.3 28.6 + - - +
101A GLY 5.2 0.2 + - - -
102A LEU 3.4 14.1 + - - -
104A LYS 2.9 25.7 + - - -
105A THR* 3.3 21.6 - - - +
106A PRO* 3.4 19.2 - - + +
293A VAL* 6.4 0.2 - - - +
297A GLU* 2.6 26.4 + - - +
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Residues in contact with VAL 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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14A GLU* 5.0 11.0 - - + +
15A GLY 5.7 0.2 - - - +
17A HIS* 4.3 35.9 - - + +
64A SER* 3.1 9.8 - - - +
65A ASN* 1.3 80.5 - - + +
67A GLN* 1.3 65.2 + - + +
69A GLN* 3.5 7.5 + - - +
70A ASP* 3.2 29.6 + - - +
297A GLU* 6.1 0.7 - - - +
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Residues in contact with GLN 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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29A PRO* 3.4 6.2 - - + +
30A TYR* 2.7 53.0 + - - +
33A PHE* 3.2 43.6 - - + +
63A ARG* 3.2 11.7 - - + -
64A SER* 2.9 36.0 + - - +
66A VAL* 1.3 77.8 - - + +
68A ARG* 1.3 62.2 + - - +
70A ASP* 4.1 1.3 - - - -
71A ILE* 2.9 34.1 + - - +
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Residues in contact with ARG 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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27A VAL* 4.1 16.2 - - - +
60A LEU* 3.0 26.9 + - + +
61A THR* 4.9 0.8 - - - +
63A ARG* 3.0 34.0 + - + -
64A SER 3.0 8.7 + - - +
65A ASN* 3.5 27.3 - - - +
66A VAL 3.3 0.2 - - - -
67A GLN* 1.3 77.1 - - - +
69A GLN* 1.3 57.6 + - - +
71A ILE* 3.2 10.3 + - - +
72A ALA* 2.7 36.9 + - - +
102A LEU* 2.8 72.4 + - - +
103A LEU* 4.3 15.6 - - + +
293A VAL* 5.6 1.6 + - - +
296A SER* 4.8 4.0 + - - -
297A GLU* 4.2 5.9 + - - -
334A LEU* 4.2 8.5 - - - +
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Residues in contact with GLN 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 ASN* 3.3 26.3 + - - +
66A VAL* 3.7 10.3 - - - +
68A ARG* 1.3 78.8 - - - +
70A ASP* 1.3 65.0 + - - +
72A ALA* 4.0 9.0 - - + +
73A PHE* 3.2 21.3 + - - +
103A LEU 3.0 28.9 + - - +
105A THR* 3.5 24.9 - - + +
108A GLN* 3.9 7.4 - - - +
6G PHE* 5.1 17.0 - - + -
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Residues in contact with ASP 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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14A GLU* 2.7 40.3 - - - +
33A PHE* 3.6 15.9 - - + -
35A ALA* 3.8 17.6 - - + +
66A VAL* 3.2 19.5 + - - +
67A GLN* 3.3 9.8 - - - +
68A ARG 3.2 0.2 - - - -
69A GLN* 1.3 75.8 - - - +
71A ILE* 1.3 67.0 + - - +
73A PHE* 2.9 17.6 + - - +
74A ALA* 3.0 14.9 + - - +
5G GLU* 3.8 16.1 - - - +
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Residues in contact with ILE 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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33A PHE* 3.8 10.1 - - + -
35A ALA* 4.1 9.6 - - - -
38A ASP* 3.5 33.7 - - + +
39A ALA* 4.0 13.5 - - - +
42A ILE* 3.6 27.6 - - + -
59A ILE* 4.1 7.2 - - + -
60A LEU* 4.4 8.7 - - + -
63A ARG* 3.6 27.1 - - + -
67A GLN 2.9 17.6 + - - +
68A ARG* 3.4 7.2 - - - +
70A ASP* 1.3 77.9 - - - +
72A ALA* 1.3 57.9 - - - +
73A PHE 3.0 0.3 + - - -
74A ALA* 3.3 1.7 + - - +
75A TYR* 2.8 30.7 + - - +
83A LEU* 4.3 6.7 - - + -
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Residues in contact with ALA 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 ARG 2.7 21.6 + - - +
69A GLN* 4.0 11.9 - - + +
71A ILE* 1.3 72.0 - - - +
73A PHE* 1.3 58.5 + - - +
75A TYR* 3.8 2.8 - - - +
76A GLN* 3.5 17.2 + - - +
82A GLU* 5.5 0.7 - - - +
83A LEU* 3.5 36.0 + - + +
84A PRO* 5.0 6.0 - - + +
103A LEU* 4.7 8.1 - - + +
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Residues in contact with PHE 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 GLN 3.2 13.5 + - - +
70A ASP* 2.9 13.2 + - - +
72A ALA* 1.3 73.9 - - - +
74A ALA* 1.3 60.5 + - - +
75A TYR 3.0 1.3 - - - -
76A GLN* 2.8 32.6 + - + +
77A ARG* 3.2 58.2 + - + +
3G ARG* 6.1 1.8 - - + -
4G PHE 4.0 4.9 - - - -
5G GLU* 3.6 48.2 - - + -
6G PHE 4.7 4.9 - - - -
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Residues in contact with ALA 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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35A ALA* 3.9 28.7 - - + +
36A GLU* 4.2 8.7 - - + +
39A ALA* 4.0 6.5 - - + -
70A ASP 3.0 8.2 + - - +
71A ILE 3.8 6.1 - - - +
73A PHE* 1.3 81.8 - - + +
75A TYR* 1.3 63.3 + - - +
77A ARG* 3.5 13.4 + - - +
78A ARG* 3.0 27.4 + - - +
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Residues in contact with TYR 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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39A ALA* 3.7 24.8 - - + +
42A ILE* 4.5 3.4 - - + -
43A GLU* 3.6 36.6 - - + -
46A VAL* 5.0 5.4 - - + +
47A LYS* 4.1 16.5 + - - -
71A ILE 2.8 18.7 + - - +
72A ALA* 3.8 10.8 - - - +
74A ALA* 1.3 78.0 - - - +
76A GLN* 1.3 55.5 + - - +
78A ARG* 4.7 1.6 - - - -
79A THR* 2.9 58.5 + - + +
81A LYS* 3.7 11.1 - - + +
83A LEU* 3.6 48.5 - - + -
86A ALA* 3.8 20.5 - - + +
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Residues in contact with GLN 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 ALA 3.5 10.0 + - - +
73A PHE* 2.8 24.1 + - + +
75A TYR* 1.3 73.4 - - - +
77A ARG* 1.3 65.9 + - - +
80A LYS* 2.5 65.2 + - - +
81A LYS 3.4 13.4 + - - +
82A GLU* 3.1 28.1 - - - +
88E VAL* 6.0 3.7 - - - +
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Residues in contact with ARG 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 PHE* 3.2 48.3 + - + +
74A ALA* 3.6 15.0 - - + +
76A GLN* 1.3 87.6 - - - +
78A ARG* 1.3 65.1 + - + +
80A LYS* 3.6 20.3 - - - +
81E ALA* 5.9 3.8 - - - +
84E ASP* 3.9 22.4 + - - +
3G ARG* 4.3 23.8 - - - +
4G PHE 4.7 8.7 + - - +
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Residues in contact with ARG 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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36A GLU* 5.0 9.5 + - - +
39A ALA* 5.4 3.8 - - - -
40A LEU* 3.2 41.1 - - - +
43A GLU* 4.0 14.7 + - - +
74A ALA 3.0 19.7 + - - +
75A TYR* 4.1 3.4 - - - +
77A ARG* 1.3 82.5 - - + +
79A THR* 1.3 73.6 + - + +
80A LYS* 3.8 3.3 + - - +
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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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43A GLU* 3.5 33.0 - - + +
47A LYS* 6.2 1.3 - - - +
75A TYR* 2.9 48.8 + - + +
78A ARG* 1.3 83.4 - - + +
80A LYS* 1.3 66.5 + - - +
81A LYS* 3.0 34.6 + - - +
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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 GLN* 2.5 47.0 + - - +
77A ARG* 3.6 22.7 - - - +
78A ARG 4.7 2.9 - - - +
79A THR* 1.3 73.7 - - - +
81A LYS* 1.3 58.2 + - - +
82A GLU 4.4 0.3 + - - -
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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