Contacts of the helix formed by residues 93 - 109 (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 VAL 93 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25A LEU* 3.3 33.0 - - + +
26A ILE* 4.0 8.3 - - + +
28A ASN* 4.4 7.8 + - + +
31A LEU* 3.9 29.6 + - + +
33A ILE* 4.0 8.5 - - + -
55A LEU* 3.7 30.7 - - + -
92B ARG* 1.3 71.8 - - - +
94B ASN* 1.3 62.5 + - - +
96B PHE* 3.1 7.8 + - + +
97B LEU* 3.0 39.8 + - + +
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Residues in contact with ASN 94 (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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22A ARG* 3.2 25.8 - - - +
26A ILE* 3.9 19.0 - - + +
92B ARG* 3.5 19.8 - - - +
93B VAL* 1.3 71.7 - - - +
95B GLN* 1.3 84.4 + - - +
97B LEU* 3.2 4.7 + - - +
98B ASP* 2.9 32.1 + - - +
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Residues in contact with GLN 95 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A VAL* 4.4 7.0 - - + +
91B ARG* 2.7 58.9 - - + +
92B ARG* 3.1 21.5 + - - +
94B ASN* 1.3 107.4 + - - +
96B PHE* 1.3 62.8 + - - +
98B ASP* 3.7 7.1 + - - +
99B TYR* 3.2 21.1 + - - +
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Residues in contact with PHE 96 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A ILE* 4.0 27.6 - - + -
34A PRO 4.3 7.4 - - - -
35A VAL* 3.7 25.0 - - + +
36A PRO* 6.1 0.9 - - + -
47A GLU 5.1 0.2 - - - -
48A ILE* 3.9 26.7 - - + -
51A GLY* 3.7 38.1 - - - -
52A ILE* 3.8 10.8 - - + -
55A LEU* 4.2 17.7 - - + -
92B ARG 3.1 4.9 + - - +
93B VAL* 3.1 8.3 + - - +
95B GLN* 1.3 77.7 - - - +
97B LEU* 1.3 67.1 + - + +
99B TYR* 3.4 10.8 + + + +
100B LEU* 2.9 44.4 + - + +
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Residues in contact with LEU 97 (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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18A LEU* 4.7 17.9 - - + +
22A ARG* 3.9 24.7 - - + +
25A LEU* 4.0 28.3 - - + -
26A ILE* 4.2 13.5 - - + -
55A LEU* 3.9 27.1 - - + -
93B VAL* 3.0 33.3 + - + +
94B ASN 3.5 4.0 - - - +
96B PHE* 1.3 80.7 - - + +
98B ASP* 1.3 60.7 + - - +
100B LEU* 3.2 6.8 + - + +
101B GLN* 2.9 36.1 + - + +
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Residues in contact with ASP 98 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A ARG* 3.7 21.4 + - - +
94B ASN* 2.9 28.2 + - - +
95B GLN* 4.1 6.3 + - - +
97B LEU* 1.3 73.3 - - - +
99B TYR* 1.3 62.4 + - - +
101B GLN* 3.4 14.0 + - - +
102B GLU* 3.0 25.4 + - - +
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Residues in contact with TYR 99 (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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35A VAL* 4.1 16.6 - - + -
36A PRO* 3.2 47.4 - - + +
38A HIS 2.8 28.7 + - - -
39A LYS* 5.1 0.2 - - - -
40A ASN 4.7 0.2 - - - -
41A HIS* 3.5 42.9 + + - -
44A CYS* 4.5 1.6 - - - -
48A ILE* 4.0 24.7 - - + -
95B GLN 3.2 12.5 + - - +
96B PHE* 3.4 13.7 - + + +
97B LEU 3.2 0.8 - - - -
98B ASP* 1.3 77.3 - - - +
100B LEU* 1.3 58.0 + - - +
102B GLU* 3.1 14.2 + - - +
103B PHE* 2.9 23.6 + - + +
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Residues in contact with LEU 100 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A LEU* 4.3 27.4 - - + -
48A ILE* 3.7 27.4 - - + -
49A PHE* 5.9 0.7 - - + -
52A ILE* 4.0 29.4 - - + -
55A LEU* 6.1 0.4 - - + -
72A LEU* 4.6 10.8 - - + -
96B PHE* 2.9 34.2 + - + +
97B LEU* 3.2 9.4 + - + +
99B TYR* 1.3 76.0 - - - +
101B GLN* 1.3 55.0 + - - +
103B PHE* 3.2 17.5 + - + +
104B LEU* 2.9 34.1 + - + +
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Residues in contact with GLN 101 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A LEU* 3.6 17.7 - - + +
18A LEU* 4.0 22.5 - - + +
19A SER* 3.6 26.1 + - - -
22A ARG* 4.5 16.0 + - - +
97B LEU* 2.9 21.4 + - + +
98B ASP* 3.5 16.2 + - - +
99B TYR 3.3 0.2 - - - -
100B LEU* 1.3 72.7 - - - +
102B GLU* 1.3 57.9 + - - +
104B LEU* 3.2 1.5 + - - +
105B GLY* 2.8 32.4 + - - -
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Residues in contact with GLU 102 (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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39A LYS* 5.1 6.9 - - - +
41A HIS* 3.1 33.5 + - + +
98B ASP 3.0 10.2 + - - +
99B TYR* 3.1 20.9 - - - +
101B GLN* 1.3 79.6 - - - +
103B PHE* 1.3 59.6 + - - -
105B GLY* 3.6 2.0 + - - +
106B VAL* 3.3 25.1 + - + +
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Residues in contact with PHE 103 (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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41A HIS* 4.2 29.1 - - + -
42A GLN* 5.1 4.0 - - + -
45A THR* 4.0 20.4 - - + -
48A ILE* 4.2 24.7 - - + -
49A PHE* 4.1 22.9 - + - -
75A ILE* 5.7 0.9 - - + -
79A ILE* 4.0 22.9 - - + -
99B TYR 2.9 12.3 + - - +
100B LEU* 3.2 27.8 + - + +
102B GLU* 1.3 76.6 - - - +
104B LEU* 1.3 65.8 + - + +
106B VAL* 3.6 6.4 + - + +
107B MET* 3.3 37.0 + - + +
111B TRP* 4.5 10.8 - + - -
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Residues in contact with LEU 104 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A VAL* 3.7 14.8 - - + +
14A THR* 3.8 21.3 - - + -
15A LEU* 3.7 22.4 - - + +
18A LEU* 3.6 30.7 - - + -
72A LEU* 4.7 7.0 - - + -
75A ILE* 3.9 29.6 - - + -
100B LEU* 2.9 28.9 + - + +
103B PHE* 1.3 77.0 - - + +
105B GLY* 1.3 66.3 + - - +
107B MET* 3.2 16.3 + - - +
108B ASN* 3.0 23.2 + - - +
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Residues in contact with GLY 105 (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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15A LEU* 3.8 10.9 - - - +
101B GLN 2.8 19.7 + - - -
102B GLU* 3.9 2.9 - - - -
103B PHE 3.3 0.2 - - - -
104B LEU* 1.3 70.7 - - - +
106B VAL* 1.3 54.6 + - - +
108B ASN* 3.0 11.1 + - - +
109B THR* 2.8 33.4 + - - -
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Residues in contact with VAL 106 (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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41A HIS* 4.3 9.4 - - + +
42A GLN* 4.2 11.2 - - + +
112A ILE* 4.1 22.0 - - + -
102B GLU* 3.3 15.6 + - + +
103B PHE* 3.7 15.7 - - + +
105B GLY* 1.3 69.0 - - - +
107B MET* 1.3 61.6 + - - +
109B THR* 4.5 3.6 - - + -
110B GLU* 2.7 61.3 + - + +
111B TRP* 3.4 17.9 + - + +
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Residues in contact with MET 107 (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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7A THR* 5.4 1.3 - - + -
11A VAL* 4.3 23.8 - - + -
75A ILE* 4.1 25.1 - - + -
78A TYR* 4.1 20.4 - - + -
79A ILE* 4.5 3.4 - - + -
103B PHE* 3.3 33.3 + - + +
104B LEU* 3.2 16.4 + - - +
106B VAL* 1.3 79.2 - - - +
108B ASN* 1.3 60.2 + - - +
111B TRP* 3.5 71.1 + - + +
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Residues in contact with ASN 108 (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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8A SER* 4.5 2.4 - - - +
11A VAL* 3.8 13.4 - - + +
12A LYS* 3.3 42.9 + - - +
15A LEU* 4.4 14.6 - - + +
104B LEU 3.0 10.4 + - - +
105B GLY* 3.0 9.2 + - - +
107B MET* 1.3 79.6 - - - +
109B THR* 1.3 62.3 + - - +
111B TRP 5.1 1.5 - - - +
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Residues in contact with THR 109 (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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105B GLY* 2.8 17.0 + - - -
106B VAL* 4.3 3.4 - - + -
108B ASN* 1.3 81.4 + - - +
110B GLU* 1.3 72.6 + - + +
111B TRP 5.3 0.2 - - - -
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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