Contacts of the helix formed by residues 102 - 120 (chain A) in PDB entry 1HMU
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 ASP 102 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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92A TYR* 3.4 8.5 - - - -
98A HIS 5.4 1.3 - - - +
99A TYR* 2.8 32.4 + - - +
100A TYR 2.9 3.8 + - - +
101A GLY* 1.3 69.2 - - - +
103A ASP* 1.3 59.3 + - - +
104A LYS* 3.0 16.6 + - - +
105A VAL* 2.8 39.7 + - + +
106A PHE 3.0 23.2 + - - -
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Residues in contact with ASP 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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92A TYR* 5.6 0.2 + - - -
101A GLY 3.2 10.7 + - - +
102A ASP* 1.3 74.2 + - - +
104A LYS* 1.3 62.3 + - - +
106A PHE* 3.3 9.8 + - - +
107A ASP* 3.2 28.2 + - - +
148A LYS* 5.7 1.6 - - - +
149A LYS* 4.5 16.6 - - + +
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Residues in contact with LYS 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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102A ASP* 3.0 16.8 + - - +
103A ASP* 1.3 75.7 - - - +
105A VAL* 1.3 64.7 + - - +
107A ASP* 3.2 14.2 + - + +
108A GLN* 3.1 57.5 + - + +
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Residues in contact with VAL 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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54A LEU* 3.6 27.1 - - + -
88A ILE* 3.8 18.4 - - + +
92A TYR* 4.0 16.2 - - + -
99A TYR* 3.7 22.2 - - + +
102A ASP* 2.8 33.1 + - + +
104A LYS* 1.3 69.7 - - + +
106A PHE* 1.3 66.2 + - - +
108A GLN* 3.1 11.7 + - - +
109A ILE* 2.8 40.3 + - + +
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Residues in contact with PHE 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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92A TYR* 3.4 24.2 - + - +
102A ASP 3.0 13.4 + - - +
103A ASP* 3.4 12.1 - - - +
105A VAL* 1.3 76.1 - - - +
107A ASP* 1.3 71.8 + - - +
109A ILE* 3.0 8.0 + - - +
110A SER* 2.8 49.4 + - - -
144A MET* 4.2 7.4 - - + -
149A LYS* 3.2 62.4 - - + -
150A PRO 3.5 21.8 - - - -
151A LEU* 3.8 20.0 - - + -
152A ASP 4.7 1.3 - - - -
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Residues in contact with ASP 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 ASP* 3.2 14.0 + - - +
104A LYS* 3.2 14.8 + - + +
106A PHE* 1.3 96.0 - - - +
108A GLN* 1.3 59.3 + - + +
110A SER* 3.3 6.5 + - - -
111A LYS* 2.8 29.0 + - - +
149A LYS* 5.3 1.2 - - - -
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Residues in contact with GLN 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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54A LEU* 3.5 40.0 - - + +
57A LEU* 3.5 28.6 - - + +
88A ILE* 6.2 0.2 - - - -
104A LYS* 3.1 53.6 + - - +
105A VAL* 3.1 17.5 + - - +
107A ASP* 1.3 73.7 - - + +
109A ILE* 1.3 61.6 + - + +
111A LYS* 3.3 7.1 + - - +
112A ALA* 2.8 30.3 + - - +
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Residues in contact with ILE 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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85A LEU* 4.1 15.7 - - + -
88A ILE* 3.9 18.8 - - + -
89A ILE* 4.1 18.8 - - + -
92A TYR* 3.7 35.4 - - + -
105A VAL* 2.8 22.8 + - + +
106A PHE* 3.0 7.6 + - - +
108A GLN* 1.3 75.5 - - - +
110A SER* 1.3 64.0 + - - +
112A ALA* 3.2 2.6 + - - +
113A PHE* 3.0 48.9 + - + -
144A MET* 4.1 22.2 - - + -
151A LEU* 4.4 0.9 - - + -
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Residues in contact with SER 110 (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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106A PHE* 2.8 36.0 + - - -
107A ASP* 3.5 11.2 - - - -
109A ILE* 1.3 78.7 - - - +
111A LYS* 1.3 55.7 + - - +
113A PHE* 3.4 3.7 + - - +
114A LYS* 3.0 27.6 + - - +
151A LEU* 3.6 20.7 - - - +
152A ASP 5.4 1.2 + - - -
155A LEU* 4.0 14.8 - - - +
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Residues in contact with LYS 111 (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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57A LEU* 5.8 0.4 - - + -
58A GLN 5.8 0.2 - - - +
59A PRO 4.7 9.4 - - - +
60A ASP 4.2 3.5 - - - +
61A GLY* 3.8 16.9 - - - -
107A ASP 2.8 17.5 + - - +
108A GLN* 3.6 8.3 - - - +
110A SER* 1.3 74.5 - - - +
112A ALA* 1.3 58.8 + - - +
114A LYS* 3.2 7.8 + - - +
115A TYR* 2.9 28.9 + - - +
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Residues in contact with ALA 112 (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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57A LEU* 4.5 10.8 - - + -
61A GLY* 3.4 17.9 - - - +
63A TRP* 4.7 1.8 - - + -
81A HIS* 3.0 27.1 + - + +
85A LEU* 3.6 27.8 - - + -
108A GLN 2.8 16.8 + - - +
109A ILE 3.5 4.9 - - - +
111A LYS* 1.3 72.9 - - - +
113A PHE* 1.3 66.8 + - - +
115A TYR* 3.3 1.2 + - - +
116A TRP* 3.1 10.9 + - - +
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Residues in contact with PHE 113 (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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82A LEU* 5.5 1.3 - - + -
85A LEU* 3.8 15.9 - - + -
89A ILE* 3.8 23.1 - - + -
109A ILE* 3.0 41.3 + - + -
110A SER 3.6 7.0 - - - +
112A ALA* 1.3 76.6 - - - +
114A LYS* 1.3 63.6 + - - +
116A TRP* 3.1 10.3 + + + +
117A TYR* 2.9 23.3 + - - +
137A LEU* 5.2 11.7 - - + -
140A MET* 4.0 22.2 - - + -
141A LEU* 4.0 17.9 - - + -
144A MET* 4.3 0.7 - - + -
151A LEU* 3.9 26.7 - - + -
155A LEU* 4.1 8.1 - - + -
159A LEU* 3.7 29.4 - - + +
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Residues in contact with LYS 114 (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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110A SER 3.0 14.5 + - - +
111A LYS* 3.4 12.8 - - - +
113A PHE* 1.3 77.1 - - - +
115A TYR* 1.3 57.9 + - - +
117A TYR* 3.3 4.9 + - + +
118A ASP* 2.4 81.1 + - - +
155A LEU* 4.5 17.9 - - + +
158A LYS* 3.8 23.8 - - - +
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Residues in contact with TYR 115 (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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60A ASP* 3.9 28.8 + - - +
61A GLY 3.5 18.6 - - - +
62A SER* 3.4 34.6 + - - -
68A TYR* 3.4 49.5 - + - +
81A HIS* 4.2 1.8 - + - -
111A LYS 2.9 10.0 + - - +
112A ALA 3.7 2.2 - - - +
113A PHE 3.2 0.2 - - - -
114A LYS* 1.3 74.4 - - - +
116A TRP* 1.3 62.3 + - - +
118A ASP* 3.2 8.2 + - + +
119A SER* 2.8 46.5 + - - -
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Residues in contact with TRP 116 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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68A TYR* 4.5 3.6 - + - -
76A TRP* 3.8 26.9 - + - -
78A PRO* 3.1 28.9 - - + -
79A ASN 4.4 0.2 - - - -
81A HIS* 3.5 31.4 - + + +
82A LEU* 3.5 31.6 - - + -
85A LEU* 6.1 0.2 - - + -
112A ALA 3.1 12.0 + - - +
113A PHE* 3.1 13.5 + + + +
115A TYR* 1.3 77.9 - - - +
117A TYR* 1.3 60.3 + - - +
119A SER* 4.7 1.8 - - - -
120A ASP* 2.9 29.8 + - - +
121A PRO* 3.6 31.5 - - + +
133A THR* 3.9 19.0 - - + +
137A LEU* 3.8 32.3 - - + +
159A LEU* 5.1 4.9 - - + -
162A ARG* 5.9 4.5 - - + +
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Residues in contact with TYR 117 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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113A PHE 2.9 12.9 + - - +
114A LYS* 3.6 11.7 - - + +
116A TRP* 1.3 81.3 - - - +
118A ASP* 1.3 77.3 + - - +
120A ASP* 3.4 3.8 + - - +
155A LEU* 5.3 3.4 - - + -
158A LYS* 3.3 68.2 + - + +
159A LEU* 4.1 20.0 - - + -
162A ARG* 2.9 64.2 + - + +
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Residues in contact with ASP 118 (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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114A LYS* 2.4 55.4 + - - +
115A TYR* 3.7 9.6 - - + +
117A TYR* 1.3 91.8 - - - +
119A SER* 1.3 60.6 + - - +
120A ASP* 4.4 2.6 - - - +
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Residues in contact with SER 119 (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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68A TYR* 3.6 18.8 + - - +
69A LYS* 5.6 7.1 + - - +
115A TYR* 2.8 41.2 + - - -
116A TRP 4.2 0.4 - - - -
118A ASP* 1.3 74.2 - - - +
120A ASP* 1.3 69.6 + - - +
121A PRO* 3.2 21.2 - - - +
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Residues in contact with ASP 120 (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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116A TRP* 2.9 16.1 + - - +
117A TYR 3.7 3.6 - - - +
118A ASP 3.3 3.3 - - - +
119A SER* 1.3 79.0 - - - +
121A PRO* 1.3 67.5 - - - +
122A LYS* 3.3 18.5 + - - +
162A ARG* 3.5 26.6 + - - +
165A ARG* 2.9 43.7 + - - -
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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