Contacts of the helix formed by residues 45 - 58 (chain B) in PDB entry 1HUL
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 45 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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43A LEU* 4.0 19.1 - - + -
103A PHE* 4.1 19.7 - - + -
111A TRP* 5.8 1.1 - - + -
41B HIS 4.0 1.2 + - - -
42B GLN* 3.8 21.6 + - + +
43B LEU 3.5 2.4 + - - -
44B CYS* 1.3 73.4 - - - +
46B GLU* 1.3 74.6 + - - +
48B ILE* 3.5 10.2 - - - +
49B PHE* 2.7 39.9 + - - -
79B ILE* 4.0 19.1 - - + -
83B LYS* 3.7 11.6 + - - +
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Residues in contact with GLU 46 (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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43B LEU 5.2 0.4 + - - -
44B CYS 2.9 1.2 + - - -
45B THR* 1.3 85.8 + - - +
47B GLU* 1.3 65.1 + - - +
49B PHE* 3.6 23.4 - - - +
50B GLN* 3.5 18.2 + - - +
76B LYS* 3.1 27.3 + - - +
79B ILE* 4.1 4.5 - - - +
80B ASP* 3.0 21.9 - - - +
83B LYS* 3.1 28.6 + - - +
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Residues in contact with GLU 47 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A LYS* 5.0 3.9 - - - +
86A CYS* 3.6 45.9 - - + +
87A GLY* 4.4 7.0 - - - -
34B PRO* 4.6 23.0 - - + +
36B PRO* 5.6 0.9 - - + -
43B LEU 4.3 3.1 - - - +
44B CYS* 3.1 16.4 + - + +
46B GLU* 1.3 76.7 + - - +
48B ILE* 1.4 68.7 + - + +
50B GLN* 3.6 5.6 + - - +
51B GLY* 3.2 14.9 + - - -
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Residues in contact with ILE 48 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96A PHE* 3.8 19.5 - - + -
99A TYR* 3.7 30.7 - - + -
100A LEU* 5.1 7.6 - - + -
103A PHE* 3.5 42.4 - - + -
34B PRO 6.0 0.2 - - - +
36B PRO* 4.9 5.2 - - + -
41B HIS 4.5 1.3 - - - +
44B CYS* 3.1 27.0 + - + +
45B THR 3.5 5.4 - - - +
47B GLU* 1.4 73.5 - - - +
49B PHE* 1.3 77.3 + - + +
51B GLY* 2.8 21.8 + - - -
52B ILE* 3.2 18.4 + - + +
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Residues in contact with PHE 49 (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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100A LEU* 6.3 0.4 - - + -
103A PHE* 4.4 10.3 - + - -
104A LEU* 6.4 0.4 - - + -
45B THR* 2.7 37.1 + - - +
46B GLU* 3.6 21.3 - - - +
47B GLU 3.5 0.2 - - - -
48B ILE* 1.3 83.8 - - + +
50B GLN* 1.3 58.2 + - - +
51B GLY 3.2 0.6 + - - -
52B ILE* 3.7 29.1 + - + +
53B GLY* 3.4 14.2 + - - -
72B LEU* 3.9 23.1 - - + -
75B ILE* 4.3 11.7 - - + -
76B LYS* 3.8 40.4 - - + -
79B ILE* 3.7 32.3 - - + -
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Residues in contact with GLN 50 (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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46B GLU 3.5 17.3 + - - +
47B GLU* 3.6 5.1 + - - +
48B ILE 3.4 1.2 - - - -
49B PHE* 1.3 72.1 - - - +
51B GLY* 1.3 60.9 + - - +
53B GLY* 3.6 16.1 - - - -
54B THR* 3.0 34.1 + - - +
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Residues in contact with GLY 51 (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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96A PHE* 3.9 16.2 - - - -
33B ILE* 4.0 21.1 - - - +
34B PRO* 5.9 2.2 - - - -
47B GLU 3.2 8.9 + - - -
48B ILE 2.8 10.1 + - - -
50B GLN* 1.3 74.8 - - - +
52B ILE* 1.3 64.1 + - - -
53B GLY 3.0 2.0 + - - -
54B THR* 3.3 6.3 + - - -
55B LEU* 3.2 19.1 + - - +
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Residues in contact with ILE 52 (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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96A PHE* 3.8 5.5 - - + -
100A LEU* 4.1 26.2 - - + -
48B ILE* 3.2 12.4 + - + +
49B PHE* 3.7 41.3 + - + +
51B GLY* 1.3 71.5 - - - +
53B GLY* 1.3 55.1 + - - +
55B LEU* 3.3 11.0 - - + +
56B GLU* 3.0 31.9 + - - +
69B PHE* 4.3 14.3 - - + +
72B LEU* 3.7 44.6 - - + -
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Residues in contact with GLY 53 (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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49B PHE 3.4 10.1 + - - -
50B GLN* 3.6 16.6 + - - -
51B GLY 3.0 2.0 - - - -
52B ILE* 1.3 72.7 - - - +
54B THR* 1.3 60.1 + - - +
55B LEU 3.1 1.1 - - - -
56B GLU* 3.4 9.6 + - - +
57B SER* 3.0 28.9 + - - -
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Residues in contact with THR 54 (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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31B LEU* 3.8 24.7 - - + +
32B ARG 5.9 1.6 - - - +
33B ILE* 4.5 11.2 - - + -
50B GLN* 3.0 27.2 + - - +
51B GLY* 3.3 7.2 + - - -
53B GLY* 1.3 71.6 - - - +
55B LEU* 1.3 66.0 + - - +
57B SER* 3.3 18.0 + - - +
58B GLN* 3.4 12.4 + - + +
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Residues in contact with LEU 55 (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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93A VAL* 4.2 20.9 - - + -
96A PHE* 4.8 10.3 - - + -
97A LEU* 4.5 23.3 - - + -
100A LEU* 5.7 1.6 - - + -
25B LEU* 3.9 29.8 - - + +
28B ASN* 6.3 1.3 - - + -
31B LEU* 4.6 13.2 - - + -
33B ILE* 4.4 12.7 - - + +
51B GLY 3.2 9.2 + - - +
52B ILE* 3.3 14.4 - - + +
53B GLY 3.1 0.6 - - - -
54B THR* 1.3 74.2 - - - +
56B GLU* 1.3 55.3 + - - +
58B GLN* 2.8 25.4 + - + +
59B THR* 2.8 29.7 + - - +
68B LEU* 6.3 0.4 - - + -
69B PHE* 4.5 11.0 - - + -
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Residues in contact with GLU 56 (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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52B ILE* 3.0 18.8 + - - +
53B GLY* 3.6 9.2 - - - +
55B LEU* 1.3 80.9 - - - +
57B SER* 1.3 59.6 + - - +
59B THR* 3.7 15.6 + - - +
61B GLN* 4.6 5.7 + - - +
66B GLU* 4.4 11.9 - - - +
69B PHE* 3.8 49.6 - - + +
73B SER* 5.5 2.6 + - - -
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Residues in contact with SER 57 (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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53B GLY 3.0 14.0 + - - -
54B THR* 3.3 13.9 + - - +
55B LEU 3.2 0.2 - - - -
56B GLU* 1.3 76.8 - - - +
58B GLN* 1.4 89.8 + - - +
59B THR 4.5 3.0 - - - +
61B GLN* 4.6 7.1 + - - +
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Residues in contact with GLN 58 (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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28B ASN* 4.0 22.7 + - + +
31B LEU* 3.7 30.2 - - + +
54B THR* 3.6 14.1 - - + +
55B LEU* 2.8 13.5 + - + +
57B SER* 1.4 101.3 + - - +
59B THR* 1.3 60.5 + - - +
60B VAL* 3.9 1.6 + - - +
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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