Contacts of the helix formed by residues 46 - 65 (chain A) in PDB entry 1HZ4
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 TRP 46 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6A ARG* 4.3 13.2 - - + -
9A THR* 3.2 35.7 + - + +
10A MET* 4.0 36.1 - - + -
13A GLU* 3.3 38.8 - - + +
42A LEU* 4.2 11.9 - - + -
43A PRO* 3.2 27.2 + - + +
44A PRO 4.0 6.3 - - - -
45A GLY* 1.3 75.7 - - - +
47A PHE* 1.3 62.6 + - - +
48A TYR 3.4 2.7 - - - -
49A SER* 3.3 13.6 + - - -
50A ARG* 3.5 14.7 - - - +
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Residues in contact with PHE 47 (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 GLY* 3.0 22.6 + - - +
46A TRP* 1.3 74.3 - - - +
48A TYR* 1.3 92.8 + + + +
50A ARG* 3.3 9.7 + - - +
51A ILE* 3.0 29.5 + - + +
80A MET* 5.6 0.2 - - - +
84A HIS* 3.4 65.3 - + + +
86A VAL* 4.2 11.2 - - + -
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Residues in contact with TYR 48 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A GLU* 4.8 5.2 - - - +
17A LEU* 5.0 14.3 - - + +
46A TRP 3.4 1.2 - - - -
47A PHE* 1.3 94.8 - + + +
49A SER* 1.3 65.5 + - - +
51A ILE* 3.1 8.9 + - + +
52A VAL* 3.0 36.2 + - + +
86A VAL* 3.6 38.4 - - + -
88A HIS* 2.9 25.5 + + - -
89A TYR* 3.4 17.4 - + - -
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Residues in contact with SER 49 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A GLU* 2.6 49.4 + - - -
16A ALA* 3.5 10.7 - - - +
17A LEU* 4.8 3.1 - - - -
42A LEU* 3.2 27.8 - - - +
46A TRP 3.3 4.0 + - - -
48A TYR* 1.3 80.7 - - - +
50A ARG* 1.3 58.3 + - - +
52A VAL* 3.3 5.6 + - - -
53A ALA* 2.9 31.0 + - - +
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Residues in contact with ARG 50 (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 LEU* 3.1 48.5 + - + +
42A LEU* 2.8 50.3 + - + +
43A PRO 4.2 8.1 - - - -
44A PRO* 5.3 3.4 - - - -
46A TRP 3.5 15.7 + - - +
47A PHE* 3.3 11.1 + - - +
48A TYR 3.2 1.0 - - - -
49A SER* 1.3 75.9 + - - +
51A ILE* 1.3 64.2 + - - +
53A ALA 4.0 0.2 - - - -
54A THR* 2.8 32.5 + - - -
80A MET* 4.8 13.8 - - - -
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Residues in contact with ILE 51 (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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47A PHE* 3.0 30.8 + - + +
48A TYR* 3.1 9.2 + - + +
50A ARG* 1.3 77.7 - - - +
52A VAL* 1.3 63.6 + - - +
54A THR* 3.8 1.2 - - - -
55A SER* 2.9 22.9 + - - -
77A THR* 4.0 11.0 - - + +
80A MET* 3.7 47.3 - - + +
81A ALA* 3.8 12.1 - - + -
84A HIS* 4.4 3.1 - - + -
86A VAL* 3.8 22.2 - - + -
89A TYR* 3.7 37.5 - - + -
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Residues in contact with VAL 52 (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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16A ALA* 3.6 24.9 - - + +
17A LEU* 4.1 14.8 - - + -
20A GLN* 3.8 16.2 - - + +
48A TYR* 3.0 39.2 + - + +
49A SER 3.7 7.4 - - - +
50A ARG 3.3 0.2 - - - -
51A ILE* 1.3 76.4 - - - +
53A ALA* 1.3 59.2 + - - +
55A SER* 3.1 3.5 + - - -
56A VAL* 2.8 32.3 + - + +
89A TYR* 3.6 37.5 - - + +
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Residues in contact with ALA 53 (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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16A ALA* 4.0 15.9 - - + +
35A ALA* 3.8 19.9 - - + +
38A ALA* 4.4 2.9 - - + -
39A LEU* 3.6 29.4 - - + -
42A LEU* 5.1 0.2 - - + -
49A SER 2.9 20.1 + - - +
52A VAL* 1.3 73.9 - - - +
54A THR* 1.3 63.1 + - - +
56A VAL* 3.3 5.3 + - - +
57A LEU* 3.0 28.2 + - - +
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Residues in contact with THR 54 (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 LEU* 4.0 15.9 - - - +
50A ARG* 2.8 23.1 + - - +
51A ILE 3.8 2.2 - - - -
53A ALA* 1.3 76.5 - - - +
55A SER* 1.3 63.4 + - - +
57A LEU* 3.2 8.5 + - + +
58A GLY* 3.0 18.5 + - - -
73A LEU* 4.0 20.9 - - + +
76A GLN* 4.3 15.9 - - + +
77A THR* 3.4 16.8 + - - +
80A MET* 3.6 23.8 - - + +
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Residues in contact with SER 55 (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 GLN* 4.8 1.2 + - - -
51A ILE 2.9 18.8 + - - -
52A VAL 3.4 4.5 - - - -
54A THR* 1.3 77.8 - - - +
56A VAL* 1.3 61.9 + - - +
58A GLY* 3.0 4.7 + - - +
59A GLU* 3.0 24.0 + - - +
74A MET* 6.2 0.7 - - - +
77A THR* 3.3 24.0 + - - +
89A TYR* 3.5 27.6 + - - -
92A TRP* 3.9 14.2 + - - -
93A SER* 5.9 0.2 - - - -
96A GLN* 4.1 8.3 + - - +
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Residues in contact with VAL 56 (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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16A ALA 4.4 2.2 - - - +
19A ALA* 3.8 17.7 - - + +
20A GLN* 3.5 45.5 - - + +
23A ILE* 4.2 5.4 - - + -
31A ALA* 3.9 28.7 - - + +
35A ALA* 4.1 5.2 - - + -
52A VAL* 2.8 23.8 + - + +
53A ALA* 3.6 5.6 - - - +
54A THR 3.2 0.4 - - - -
55A SER* 1.3 76.6 - - - +
57A LEU* 1.3 57.2 + - - +
59A GLU* 3.0 9.8 + - - +
60A VAL* 2.9 27.0 + - + +
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Residues in contact with LEU 57 (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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32A GLU* 4.1 33.0 - - + +
35A ALA* 3.7 19.3 - - + -
36A LYS* 4.4 16.6 - - + -
39A LEU* 3.6 29.6 - - + -
53A ALA 3.0 15.3 + - - +
54A THR* 3.2 9.8 + - - +
56A VAL* 1.3 75.9 - - - +
58A GLY* 1.3 61.8 + - - +
60A VAL* 3.2 5.3 + - + +
61A LEU* 3.0 31.1 + - + +
73A LEU* 3.7 18.6 - - + -
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Residues in contact with GLY 58 (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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54A THR 3.0 11.8 + - - -
55A SER* 3.0 6.2 + - - -
57A LEU* 1.3 78.0 - - - +
59A GLU* 1.3 60.0 + - - +
61A LEU 3.4 0.3 + - - -
62A HIS* 3.0 8.3 + - - +
70A SER* 2.7 31.8 + - - -
73A LEU* 3.8 22.8 - - - +
74A MET* 4.3 8.2 - - - +
96A GLN* 4.7 4.5 - - - -
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Residues in contact with GLU 59 (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 GLN* 3.3 21.8 + - - +
23A ILE* 3.8 28.7 - - + +
24A ASN* 4.3 6.2 - - - +
55A SER* 3.0 16.6 + - - +
56A VAL* 3.0 8.9 + - - +
58A GLY* 1.3 75.2 - - - +
60A VAL* 1.3 64.4 + - - +
62A HIS* 3.3 9.2 + - - +
63A CYS* 3.0 28.3 + - - -
92A TRP* 3.2 36.5 + - - +
96A GLN* 3.3 19.7 + - - +
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Residues in contact with VAL 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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23A ILE* 4.2 9.4 - - + -
28A PRO* 3.7 24.7 - - + +
31A ALA* 4.0 11.0 - - + -
32A GLU* 3.9 33.4 - - + +
56A VAL* 2.9 19.2 + - + +
57A LEU* 3.2 11.2 + - + +
59A GLU* 1.3 76.2 - - - +
61A LEU* 1.3 66.9 + - + +
63A CYS* 3.1 9.0 + - - +
64A LYS* 3.0 45.9 + - + +
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Residues in contact with LEU 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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32A GLU* 5.2 6.1 - - - +
57A LEU* 3.0 20.3 + - + +
60A VAL* 1.3 81.6 - - + +
62A HIS* 1.3 62.6 + - - +
64A LYS* 3.2 14.2 + - + +
65A GLY 3.1 3.8 + - - -
66A GLU* 2.9 51.0 + - + +
69A ARG* 3.6 31.9 - - + -
70A SER* 3.7 15.9 - - - -
73A LEU* 3.5 24.9 - - + -
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Residues in contact with HIS 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 GLY 3.0 8.5 + - - +
59A GLU* 3.4 13.1 - - - +
61A LEU* 1.3 77.6 - - - +
63A CYS* 1.3 63.4 + - - +
65A GLY* 3.0 5.4 + - - -
67A LEU* 3.8 20.1 - - + +
70A SER* 3.3 18.3 + - - +
74A MET* 3.9 10.4 - - + +
96A GLN* 4.7 4.7 + - - +
99A GLU* 4.0 29.4 + - + -
100A ILE* 3.6 24.4 - - + +
248A HIS* 3.0 25.7 + - - -
249A PHE* 3.6 27.8 - + + -
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Residues in contact with CYS 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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23A ILE* 3.9 22.7 - - - -
28A PRO* 4.5 15.3 - - + -
59A GLU* 3.0 17.7 + - - -
60A VAL* 3.1 10.3 + - - +
62A HIS* 1.3 78.4 - - - +
64A LYS* 1.3 61.6 + - + +
65A GLY 3.2 1.4 + - - -
247A ASN* 4.6 9.4 - - - +
248A HIS* 3.6 10.6 + - - -
249A PHE* 3.6 31.9 - - + -
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Residues in contact with LYS 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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28A PRO* 5.8 4.2 - - + +
29A ASP* 4.0 18.2 + - - -
32A GLU* 3.5 27.6 + - - -
60A VAL* 3.0 29.6 + - + +
61A LEU* 3.7 17.3 - - + +
62A HIS 3.2 0.2 - - - -
63A CYS* 1.3 75.6 - - + +
65A GLY* 1.3 60.2 + - - +
66A GLU* 4.1 26.5 - - + +
248A HIS* 4.9 0.2 - - - -
284A LEU* 5.6 0.9 - - - +
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Residues in contact with GLY 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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62A HIS 3.0 15.5 + - - -
63A CYS 3.1 2.0 + - - -
64A LYS* 1.3 78.4 - - - +
66A GLU* 1.3 57.4 + - - +
67A LEU* 3.1 19.4 + - - +
248A HIS* 3.7 17.3 - - - -
284A LEU* 3.4 31.5 - - - +
782A SO4 4.3 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
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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