Contacts of the helix formed by residues 93 - 109 (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 VAL 93 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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91A ARG 3.9 0.4 + - - -
92A ARG* 1.3 74.1 - - - +
94A ASN* 1.3 57.3 + - - +
96A PHE* 3.2 8.3 + - - +
97A LEU* 2.9 48.6 + - + +
25B LEU 3.4 26.9 - - - +
26B ILE* 4.2 5.6 - - - +
28B ASN* 3.7 24.4 + - + +
31B LEU* 3.7 33.2 + - + +
33B ILE* 4.6 9.4 - - + -
55B LEU* 4.2 13.5 - - + -
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Residues in contact with ASN 94 (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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92A ARG* 4.0 28.3 + - - +
93A VAL* 1.3 74.7 + - - +
95A GLN* 1.3 75.6 + - - +
97A LEU* 3.3 2.3 + - - -
98A ASP* 3.0 35.6 + - - +
22B ARG* 3.5 23.6 + - - +
26B ILE* 3.9 22.8 - - + +
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Residues in contact with GLN 95 (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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91A ARG* 3.2 52.8 + - + +
92A ARG* 3.0 37.1 + - - +
94A ASN* 1.3 89.2 - - - +
96A PHE* 1.3 65.7 + - - +
98A ASP* 3.1 22.0 + - - +
99A TYR* 3.4 8.7 + - - +
35B VAL* 4.3 6.4 - - + +
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Residues in contact with PHE 96 (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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92A ARG 2.9 11.7 + - - +
93A VAL* 3.2 9.4 + - + +
95A GLN* 1.3 72.5 - - - +
97A LEU* 1.3 72.7 + - + +
99A TYR* 3.1 20.4 + + + +
100A LEU* 3.3 34.4 + - + +
33B ILE* 3.4 40.6 - - + -
34B PRO 4.0 15.5 - - - -
35B VAL* 3.6 17.0 - - + +
36B PRO* 6.0 0.7 - - + -
48B ILE* 3.8 37.5 - - + -
51B GLY* 3.9 6.5 - - - -
52B ILE* 3.8 24.2 - - + -
55B LEU* 4.8 8.3 - - + -
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Residues in contact with LEU 97 (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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93A VAL* 2.9 54.0 + - + +
94A ASN* 3.7 6.3 - - - +
95A GLN 3.2 0.4 + - - -
96A PHE* 1.3 75.3 - - + +
98A ASP* 1.3 62.5 + - - +
100A LEU* 3.1 16.7 + - + +
101A GLN* 3.1 24.6 + - - +
18B LEU* 3.8 31.9 - - + +
22B ARG* 3.7 29.4 - - + +
25B LEU* 4.0 26.7 - - + -
26B ILE* 4.7 3.1 - - + -
55B LEU* 4.5 13.5 - - + -
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Residues in contact with ASP 98 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94A ASN* 3.0 26.5 + - - +
95A GLN* 3.1 14.2 + - - +
97A LEU* 1.3 77.7 - - - +
99A TYR* 1.4 61.5 + - - +
101A GLN* 3.7 21.4 + - - +
102A GLU* 3.4 25.9 + - - +
22B ARG* 3.8 12.8 + - - -
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Residues in contact with TYR 99 (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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95A GLN 3.4 2.6 + - - -
96A PHE* 3.1 15.0 + + + +
98A ASP* 1.4 75.8 - - - +
100A LEU* 1.3 60.0 + - - +
102A GLU* 3.1 21.7 + - - +
103A PHE* 2.9 25.6 + + + +
35B VAL* 4.0 19.5 - - + -
36B PRO* 3.3 52.9 - - + +
38B HIS 2.6 25.2 + - - -
39B LYS* 5.2 1.3 - - + -
41B HIS* 3.2 37.6 - + + -
44B CYS* 4.5 3.3 - - - -
48B ILE* 3.7 28.9 - - + -
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Residues in contact with LEU 100 (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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96A PHE* 3.3 38.1 + - + +
97A LEU* 3.1 17.1 + - + +
99A TYR* 1.3 75.6 - - - +
101A GLN* 1.3 66.0 + - - +
103A PHE* 3.3 14.6 + - + +
104A LEU* 3.0 45.9 + - + +
18B LEU* 4.2 21.5 - - + -
48B ILE* 5.1 6.7 - - + -
49B PHE* 6.3 0.7 - - + -
52B ILE* 4.1 20.4 - - + -
55B LEU* 5.7 2.2 - - + -
72B LEU* 4.4 15.0 - - + -
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Residues in contact with GLN 101 (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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97A LEU 3.1 16.4 + - - +
98A ASP* 3.7 16.4 + - - +
100A LEU* 1.3 74.6 - - - +
102A GLU* 1.4 58.3 + - - +
104A LEU* 3.5 3.0 + - - -
105A GLY* 2.8 26.3 + - - -
15B LEU* 4.0 22.4 - - + +
18B LEU* 3.9 21.2 - - + +
19B SER* 5.7 5.9 + - - +
22B ARG* 3.4 21.9 + - - -
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Residues in contact with GLU 102 (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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98A ASP* 3.4 18.9 + - - +
99A TYR* 3.1 22.7 + - - +
101A GLN* 1.4 76.5 - - - +
103A PHE* 1.3 54.1 + - - +
105A GLY* 3.0 3.7 + - - -
106A VAL* 2.8 35.3 + - - +
39B LYS* 4.2 16.8 - - - +
41B HIS* 3.1 31.5 + - + +
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Residues in contact with PHE 103 (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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99A TYR* 2.9 14.8 + - + +
100A LEU* 3.4 19.5 - - + +
102A GLU* 1.3 76.4 - - - +
104A LEU* 1.3 72.6 + - + +
106A VAL* 3.4 5.5 + - + +
107A MET* 3.1 52.1 + - + +
111A TRP* 5.2 5.4 - + - -
41B HIS* 3.8 35.1 + - + -
42B GLN* 4.8 1.8 - - + -
45B THR* 4.1 25.6 - - + -
48B ILE* 3.5 34.5 - - + -
49B PHE* 4.4 21.8 - + - -
75B ILE* 5.4 0.2 - - + -
79B ILE* 4.3 7.4 - - + -
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Residues in contact with LEU 104 (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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100A LEU* 3.0 39.7 + - + +
101A GLN 4.0 2.9 - - - +
103A PHE* 1.3 83.7 - - + +
105A GLY* 1.3 64.6 + - - +
107A MET* 3.3 11.3 + - - +
108A ASN* 3.3 9.4 + - - +
11B VAL* 3.2 29.4 - - + +
14B THR* 4.1 24.2 - - + +
15B LEU* 4.0 20.2 - - + -
18B LEU* 4.7 14.8 - - + -
49B PHE* 6.4 0.7 - - + -
72B LEU* 4.6 7.2 - - + -
75B ILE* 4.0 28.0 - - + -
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Residues in contact with GLY 105 (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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101A GLN 2.8 15.9 + - - -
102A GLU* 3.0 4.0 + - - -
104A LEU* 1.3 73.1 - - - +
106A VAL* 1.3 56.7 + - - +
108A ASN* 3.1 1.8 + - - -
109A THR* 2.6 47.9 + - - -
110A GLU* 5.4 1.8 - - - -
15B LEU* 4.4 11.6 - - - +
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Residues in contact with VAL 106 (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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102A GLU 2.8 13.8 + - - +
103A PHE* 3.6 11.0 - - + +
105A GLY* 1.3 69.7 - - - +
107A MET* 1.4 57.2 + - + +
110A GLU* 2.8 49.9 + - + +
111A TRP* 2.9 40.6 + - + +
112A ILE* 5.7 2.5 - - + -
41B HIS* 3.5 38.4 - - + +
42B GLN* 5.9 0.4 - - + +
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Residues in contact with MET 107 (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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103A PHE* 3.1 43.6 + - + +
104A LEU* 3.5 15.7 - - - +
105A GLY 3.2 0.2 - - - -
106A VAL* 1.4 75.8 - - + +
108A ASN* 1.3 63.0 + - - +
111A TRP* 3.2 59.5 - - + +
11B VAL* 4.5 20.1 - - + +
75B ILE* 4.1 25.1 - - + -
78B TYR* 4.7 11.9 - - + -
79B ILE* 4.3 7.4 - - + -
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Residues in contact with ASN 108 (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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104A LEU 3.3 4.0 + - - +
105A GLY* 3.1 2.5 + - - +
107A MET* 1.3 84.5 - - - +
109A THR* 1.3 70.9 + - - +
110A GLU 3.1 8.5 + - - -
111A TRP* 3.7 4.7 + - - +
8B SER* 3.0 35.6 + - - +
11B VAL* 3.5 25.9 - - + +
12B LYS* 3.3 31.4 - - - +
15B LEU* 5.3 4.3 - - + +
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Residues in contact with THR 109 (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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105A GLY* 2.6 34.8 + - - -
108A ASN* 1.3 81.8 + - - +
110A GLU* 1.3 77.8 + - - +
12B LYS* 5.8 2.9 - - - -
15B LEU* 5.8 1.2 - - - +
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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