Contacts of the helix formed by residues 41 - 58 (chain A) 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 HIS 41 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39A LYS* 2.7 36.2 + - + -
40A ASN* 1.4 70.5 - - - +
42A GLN* 1.3 59.4 + - + +
44A CYS* 3.2 26.2 + - - +
45A THR* 4.0 1.0 + - - +
48A ILE* 4.0 8.0 - - - +
112A ILE* 3.4 21.8 - - + +
99B TYR* 3.5 42.3 - + + -
102B GLU* 3.1 45.7 + - + +
103B PHE* 4.2 33.2 - - + -
106B VAL* 4.3 7.6 - - + +
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Residues in contact with GLN 42 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A ASN 3.0 1.4 + - - -
41A HIS* 1.3 77.5 - - + +
43A LEU* 1.4 63.8 + - - +
44A CYS 3.3 0.2 - - - -
45A THR* 3.6 22.1 + - + +
112A ILE* 3.9 20.8 - - + +
40B ASN* 4.2 13.8 - - - +
42B GLN* 3.3 36.2 + - + +
43B LEU* 3.8 19.8 - - + +
103B PHE* 5.1 3.8 - - + -
106B VAL* 4.2 5.6 - - + +
110B GLU* 3.6 19.6 + - - -
111B TRP* 3.5 42.0 + - + +
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Residues in contact with LEU 43 (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 HIS* 4.1 2.9 - - + -
40A ASN* 3.1 32.0 + - + +
42A GLN* 1.4 78.0 - - - +
44A CYS* 1.3 59.2 + - - +
45A THR* 3.3 5.2 + - - -
46A GLU 4.8 1.4 + - - -
47A GLU* 3.9 4.7 - - - +
111A TRP* 4.7 8.3 - - + -
42B GLN* 3.8 31.6 - - + +
45B THR* 4.0 19.5 - - + -
79B ILE* 4.7 7.6 - - + +
82B GLN* 3.8 31.6 - - + +
83B LYS* 4.3 30.8 - - + +
86B CYS* 3.9 8.5 - - - -
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Residues in contact with CYS 44 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A PRO* 3.5 28.9 - - + -
38A HIS* 3.5 25.1 - - - -
40A ASN 4.2 2.5 - - - -
41A HIS 3.2 12.1 + - - +
43A LEU* 1.3 74.6 - - - +
45A THR* 1.3 62.6 + - - -
46A GLU 3.3 2.5 - - - -
47A GLU* 3.1 18.4 + - + +
48A ILE* 3.1 15.0 + - + +
86B CYS* 2.0 47.6 - - + -
99B TYR* 4.5 1.6 - - - -
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Residues in contact with THR 45 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A HIS 4.0 0.4 + - - +
42A GLN* 3.6 27.7 + - - +
43A LEU 3.3 4.7 + - - -
44A CYS* 1.3 75.4 - - - +
46A GLU* 1.3 81.6 + - - +
48A ILE* 3.2 9.2 + - - +
49A PHE* 3.0 32.2 + - - -
79A ILE* 4.4 10.9 - - + +
83A LYS* 3.8 10.9 + - - -
43B LEU* 4.1 15.5 - - + +
103B PHE* 4.0 23.6 - - + -
111B TRP* 5.5 0.9 - - + -
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Residues in contact with GLU 46 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A LEU 4.8 1.2 + - - -
44A CYS 3.3 0.4 - - - -
45A THR* 1.3 112.5 + - - +
47A GLU* 1.3 66.5 + - - +
49A PHE* 3.5 17.9 - - + +
50A GLN* 3.3 31.8 + - - +
76A LYS* 4.2 12.6 - - - +
79A ILE* 4.2 6.3 - - - +
80A ASP* 2.9 25.8 - - - +
83A LYS* 3.1 26.1 + - - +
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Residues in contact with GLU 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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34A PRO* 4.8 19.1 - - + +
36A PRO* 5.6 2.7 - - + -
43A LEU 3.9 3.3 - - - +
44A CYS* 3.1 32.3 + - + +
46A GLU* 1.3 79.0 + - - +
48A ILE* 1.4 60.6 + - + +
50A GLN* 3.7 15.1 - - - +
51A GLY* 3.2 19.9 + - - -
83B LYS 5.0 3.9 - - - +
86B CYS* 3.6 27.7 - - + +
87B GLY* 4.3 15.0 - - - +
96B PHE* 5.1 0.2 - - - -
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Residues in contact with ILE 48 (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 PRO* 5.1 4.7 - - + -
41A HIS 4.0 17.3 - - - +
44A CYS* 3.1 18.4 + - + +
45A THR* 3.4 10.8 - - - +
47A GLU* 1.4 74.7 - - - +
49A PHE* 1.3 68.3 + - + +
51A GLY* 2.9 13.0 + - - +
52A ILE* 3.1 18.3 + - + +
96B PHE* 3.9 15.7 - - + -
99B TYR* 4.0 29.6 - - + -
100B LEU* 3.7 29.4 - - + -
103B PHE* 4.2 28.0 - - + -
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Residues in contact with PHE 49 (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 THR* 3.0 26.7 + - - +
46A GLU* 3.5 20.4 + - + +
47A GLU 3.5 0.2 - - - -
48A ILE* 1.3 77.7 - - + +
50A GLN* 1.3 58.4 + - - +
52A ILE* 3.6 27.9 + - + +
53A GLY* 3.4 18.5 + - - -
72A LEU* 3.6 17.7 - - + -
75A ILE* 4.4 12.8 - - + -
76A LYS* 3.5 52.0 - - + -
79A ILE* 3.9 20.4 - - + -
100B LEU* 5.9 0.9 - - + -
103B PHE* 4.1 18.6 - + - -
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Residues in contact with GLN 50 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A PRO* 6.3 2.0 - - + -
46A GLU* 3.3 22.5 + - - +
47A GLU* 3.7 14.9 - - - +
48A ILE 3.2 0.8 - - - -
49A PHE* 1.3 74.3 - - - +
51A GLY* 1.3 63.2 + - - +
52A ILE 3.4 0.3 + - - -
53A GLY* 3.5 1.8 + - - -
54A THR* 3.3 22.3 + - - -
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Residues in contact with GLY 51 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A ILE* 3.6 27.9 - - - +
34A PRO* 5.7 2.3 - - - +
47A GLU 3.2 11.4 + - - -
48A ILE 2.9 9.2 + - - -
50A GLN* 1.3 75.0 - - - +
52A ILE* 1.3 59.9 + - - +
54A THR* 3.4 6.0 + - - -
55A LEU* 3.2 19.1 + - - +
96B PHE* 3.7 14.5 - - - -
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Residues in contact with ILE 52 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A ILE* 3.1 12.9 + - + +
49A PHE* 3.6 41.3 - - + +
50A GLN 3.4 0.2 - - - -
51A GLY* 1.3 72.2 - - - +
53A GLY* 1.3 59.5 + - - +
55A LEU* 2.9 11.5 + - + +
56A GLU* 2.8 29.8 + - - +
69A PHE* 4.3 14.8 - - + +
72A LEU* 3.7 36.6 - - + -
96B PHE* 4.1 6.1 - - + -
100B LEU* 4.0 33.2 - - + -
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Residues in contact with GLY 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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49A PHE 3.4 11.7 + - - -
50A GLN* 3.5 2.7 + - - -
52A ILE* 1.3 77.0 - - - +
54A THR* 1.3 60.3 + - - +
56A GLU* 3.4 16.9 + - - +
57A SER* 2.9 22.2 + - - -
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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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31A LEU* 3.9 28.7 - - + -
32A ARG 5.6 1.6 - - - +
33A ILE* 4.0 16.6 - - + -
50A GLN 3.3 12.5 + - - -
51A GLY* 3.6 10.5 - - - -
52A ILE 3.1 1.4 + - - -
53A GLY* 1.3 70.7 - - - +
55A LEU* 1.3 64.1 + - - +
57A SER* 2.8 23.7 + - - -
58A GLN* 3.3 15.3 + - + +
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Residues in contact with LEU 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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25A LEU* 4.4 20.4 - - + +
28A ASN* 4.1 12.3 - - - +
31A LEU* 3.8 12.8 - - + -
33A ILE* 4.1 4.0 - - + -
51A GLY 3.2 7.2 + - - +
52A ILE* 2.9 12.4 + - + +
54A THR* 1.3 78.3 - - - +
56A GLU* 1.3 61.9 + - - +
58A GLN* 3.2 9.4 + - - +
59A THR* 3.1 24.1 + - - -
69A PHE* 4.3 9.2 - - + -
93B VAL* 3.7 32.5 - - + -
96B PHE* 4.2 17.9 - - + -
97B LEU* 3.9 28.0 - - + -
100B LEU* 6.1 1.1 - - + -
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Residues in contact with GLU 56 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A ILE* 2.8 15.3 + - - +
53A GLY* 3.5 19.9 + - - +
55A LEU* 1.3 77.4 - - - +
57A SER* 1.3 57.9 + - - +
59A THR* 3.9 12.6 + - - +
61A GLN* 4.4 19.2 + - + +
69A PHE* 4.0 49.1 - - + +
73A SER* 6.2 0.5 - - - -
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Residues in contact with SER 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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53A GLY 2.9 11.5 + - - -
54A THR* 2.8 17.3 + - - -
56A GLU* 1.3 77.6 - - - +
58A GLN* 1.3 72.7 + - - +
59A THR 3.5 2.5 - - - -
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Residues in contact with GLN 58 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A ASN* 2.7 38.9 - - - +
31A LEU* 3.5 35.9 - - + +
54A THR* 3.4 15.8 + - - +
55A LEU 3.2 6.3 + - - +
57A SER* 1.3 99.2 + - - +
59A THR* 1.3 59.3 + - - +
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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
------------------------------------------------------------
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