Contacts of the helix formed by residues 44 - 64 (chain E) in PDB entry 1H4O
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 THR 44 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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41E GLY* 2.8 28.5 + - - +
42E ALA 3.7 8.3 - - - +
43E PHE* 1.3 78.2 - - - +
45E PRO* 1.3 70.2 - - + +
47E CYS* 3.1 19.2 - - - -
48E SER* 2.6 35.8 + - - -
120E PHE* 3.9 28.7 - - + -
124E ARG* 5.2 0.9 - - - +
1162E BEZ 3.3 13.2 + - + -
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Residues in contact with PRO 45 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43E PHE 4.5 1.8 - - - +
44E THR* 1.3 86.6 - - - +
46E GLY* 1.3 57.7 + - - +
48E SER* 3.2 1.7 + - - -
49E LYS* 2.8 62.8 + - + +
1162E BEZ 3.2 19.1 - - + +
64F ALA 5.2 5.8 - - - +
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Residues in contact with GLY 46 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45E PRO* 1.3 73.7 - - - +
47E CYS* 1.3 60.6 + - - +
49E LYS* 5.1 0.9 - - - -
50E THR* 3.0 13.8 + - - -
51E HIS 3.0 19.1 + - - -
127E ARG* 4.3 0.9 - - - -
149E LEU* 3.9 29.1 - - - +
1162E BEZ 2.8 23.8 + - - -
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Residues in contact with CYS 47 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39E VAL* 3.6 7.6 - - + -
40E PRO* 3.5 22.0 - - - -
41E GLY 3.5 16.6 - - - +
44E THR* 3.1 26.2 - - - +
45E PRO 3.3 0.4 - - - -
46E GLY* 1.3 75.5 - - - +
48E SER* 1.3 60.4 + - - +
51E HIS* 3.5 2.9 + - - -
52E LEU* 2.9 34.3 + - - +
84E TRP* 3.7 15.7 - - + -
127E ARG* 3.3 23.3 - - - +
1162E BEZ 3.1 15.1 + - - -
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Residues in contact with SER 48 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43E PHE* 3.3 12.6 - - - -
44E THR 2.6 23.8 + - - -
45E PRO* 3.9 2.7 - - - -
47E CYS* 1.3 77.7 - - - +
49E LYS* 1.3 63.1 + - - +
50E THR 3.4 0.2 - - - -
53E PRO* 3.0 12.4 - - - +
84E TRP* 3.0 22.9 + - - -
88E HIS* 2.9 41.3 - - - -
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Residues in contact with LYS 49 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45E PRO* 2.8 44.1 + - + +
46E GLY* 5.1 0.7 - - - -
48E SER* 1.3 80.6 - - - +
50E THR* 1.3 66.1 + - - +
53E PRO* 3.8 10.6 - - - +
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Residues in contact with THR 50 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46E GLY* 3.0 10.6 + - - -
48E SER 3.4 0.6 - - - -
49E LYS* 1.3 88.2 + - - +
51E HIS* 1.3 69.5 + - - +
52E LEU 3.6 0.9 - - - -
53E PRO* 3.7 2.8 - - - +
54E GLY* 3.1 20.8 + - - -
149E LEU* 4.0 29.5 - - + +
153E LEU* 4.2 22.9 - - + +
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Residues in contact with HIS 51 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37E PHE* 3.6 18.8 - + - +
38E GLY 3.6 12.3 - - - -
39E VAL* 3.4 10.8 - - + +
46E GLY 3.0 5.7 + - - +
47E CYS* 3.8 6.5 - - - +
50E THR* 1.3 81.9 - - - +
52E LEU* 1.3 65.0 + - - +
54E GLY* 3.3 6.4 + - - -
55E PHE* 3.5 20.8 + + - -
127E ARG* 3.0 56.2 + - + +
128E PHE 4.0 4.9 - - - -
149E LEU* 4.3 3.4 - - + -
152E SER* 2.9 29.1 + - - -
153E LEU* 3.7 18.4 - - + -
154E ALA 5.5 0.5 + - - -
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Residues in contact with LEU 52 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37E PHE* 4.0 17.2 - - + -
39E VAL* 5.3 0.2 - - - +
47E CYS 2.9 17.7 + - - +
48E SER* 5.1 0.2 - - - -
51E HIS* 1.3 72.4 - - - +
53E PRO* 1.3 68.5 - - + +
55E PHE* 3.1 5.0 + - - +
56E VAL* 3.1 29.3 + - + +
72E CYS* 4.6 0.9 - - + -
84E TRP* 3.7 46.0 - - + +
85E GLY* 4.8 3.1 - - - -
88E HIS* 3.9 22.7 - - + -
90E ALA* 4.8 0.9 - - + -
94E VAL* 3.7 33.7 - - + -
96E LEU* 4.3 15.7 - - + -
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Residues in contact with PRO 53 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47E CYS 3.6 3.1 - - - +
48E SER 3.0 27.1 - - - +
49E LYS* 3.8 15.0 - - - +
50E THR 3.6 6.3 - - - +
51E HIS 3.6 2.7 - - - -
52E LEU* 1.3 96.7 - - + +
54E GLY* 1.3 56.0 + - - +
56E VAL* 3.6 9.1 - - + +
57E GLU* 2.8 51.1 + - - +
88E HIS* 4.1 13.9 - - + +
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Residues in contact with GLY 54 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50E THR 3.1 18.7 + - - -
51E HIS 3.9 1.6 - - - -
52E LEU 3.2 0.4 - - - -
53E PRO* 1.3 77.5 - - - +
55E PHE* 1.3 56.4 + - - +
57E GLU* 3.7 10.6 + - - +
58E GLN* 2.9 37.3 + - - +
154E ALA* 3.8 12.1 - - - -
155E PRO* 5.9 2.5 - - - -
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Residues in contact with PHE 55 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35E VAL* 3.8 21.8 - - + -
37E PHE* 3.3 52.5 - + + -
51E HIS* 3.5 26.5 + + - -
52E LEU 3.1 3.7 + - - +
54E GLY* 1.3 71.4 - - - +
56E VAL* 1.3 64.2 + - - +
58E GLN* 3.6 2.2 + - - -
59E ALA* 3.4 19.6 + - - +
62E LEU* 3.9 20.4 - - + +
70E VAL* 4.0 6.2 - - + +
93E LYS 4.8 0.9 - - - +
94E VAL* 3.8 12.4 - - + +
129E SER* 4.4 5.4 - - - -
152E SER 3.6 22.0 - - - -
153E LEU 4.1 0.9 - - - -
154E ALA* 3.6 36.3 - - + -
157E ILE* 4.2 11.9 - - + -
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Residues in contact with VAL 56 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52E LEU* 3.1 29.3 + - + +
53E PRO* 3.6 10.8 - - + +
55E PHE* 1.3 75.9 - - - +
57E GLU* 1.3 67.1 + - + +
59E ALA* 3.2 19.1 + - - +
60E GLU* 4.8 0.5 - - - +
88E HIS 3.9 17.9 - - - +
89E LYS* 3.9 19.3 - - + +
90E ALA* 4.1 11.7 - - + -
93E LYS* 3.5 24.2 + - + +
94E VAL* 3.8 19.5 - - + -
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Residues in contact with GLU 57 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53E PRO* 2.8 40.2 + - + +
54E GLY* 3.7 8.4 - - - +
56E VAL* 1.3 76.9 - - + +
58E GLN* 1.3 67.1 + - + +
59E ALA 3.3 3.0 + - - -
60E GLU* 3.6 11.6 - - - +
93E LYS* 6.0 0.4 - - - +
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Residues in contact with GLN 58 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54E GLY* 2.9 26.2 + - - +
55E PHE 3.8 3.8 - - - +
56E VAL 3.2 0.2 - - - -
57E GLU* 1.3 82.5 + - - +
59E ALA* 1.3 64.6 + - - +
60E GLU 3.2 2.9 - - - -
61E ALA* 3.1 17.6 + - - +
62E LEU* 2.9 26.2 + - + +
154E ALA* 3.7 20.6 - - + -
155E PRO* 5.0 11.7 - - + +
158E ILE* 3.2 27.7 - - + +
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Residues in contact with ALA 59 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55E PHE 3.4 8.0 + - - +
56E VAL 3.2 17.3 + - - +
57E GLU 3.3 1.4 - - - -
58E GLN* 1.3 75.3 - - - +
60E GLU* 1.3 64.3 + - - +
62E LEU* 3.2 9.1 + - - +
63E LYS* 2.9 41.9 + - - +
70E VAL* 5.9 2.0 - - - +
93E LYS* 3.8 35.7 - - + +
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Residues in contact with GLU 60 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56E VAL 4.8 0.5 - - - +
57E GLU 3.6 17.2 - - - +
59E ALA* 1.3 79.0 + - - +
61E ALA* 1.3 61.6 + - - +
63E LYS* 3.5 13.4 - - + +
64E ALA* 2.9 30.1 + - - +
93E LYS* 4.3 18.2 + - - -
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Residues in contact with ALA 61 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58E GLN* 3.1 30.7 + - - +
60E GLU* 1.3 81.7 - - - +
62E LEU* 1.3 59.9 + - - +
64E ALA* 3.5 17.1 - - - +
65E LYS* 3.6 13.7 + - - +
158E ILE* 4.4 14.3 - - + +
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Residues in contact with LEU 62 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35E VAL* 4.4 8.3 - - + -
55E PHE* 3.9 31.0 - - + +
58E GLN* 2.9 27.5 + - + +
59E ALA* 3.6 6.3 - - - +
61E ALA* 1.3 73.1 - - - +
63E LYS* 1.3 66.5 + - + +
65E LYS* 2.9 13.7 + - - +
67E VAL* 3.1 33.8 + - + +
70E VAL* 4.0 18.6 - - + -
154E ALA* 5.3 0.2 - - + -
157E ILE* 3.7 29.4 - - + -
158E ILE* 3.8 17.3 - - + -
161E LEU* 3.9 13.0 - - + -
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Residues in contact with LYS 63 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59E ALA* 2.9 26.4 + - - +
60E GLU* 3.5 16.6 - - + +
62E LEU* 1.3 75.8 - - + +
64E ALA* 1.3 55.7 + - - +
65E LYS 2.9 0.2 - - - -
66E GLY* 2.7 24.4 + - - -
67E VAL 3.5 20.0 + - - +
68E GLN* 5.2 8.1 + - - +
92E GLY 4.9 13.8 + - - -
93E LYS* 6.1 0.4 - - - +
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Residues in contact with ALA 64 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60E GLU 2.9 16.2 + - - +
61E ALA* 3.5 11.4 - - - +
62E LEU 3.1 0.2 - - - -
63E LYS* 1.3 77.2 - - - +
65E LYS* 1.3 61.5 + - + +
66E GLY 3.3 1.3 + - - -
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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
------------------------------------------------------------
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