Contacts of the helix formed by residues 111 - 128 (chain A) in PDB entry 1HUW
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 TYR 111 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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87A LEU* 3.3 39.4 - - + +
88A GLU* 4.6 8.2 + - - -
90A VAL* 4.0 12.9 - - + +
91A GLN* 3.4 24.2 - - - +
109A ASN* 3.1 10.4 + - - +
110A VAL* 1.3 78.1 - - - +
112A ASP* 1.3 72.2 + - - +
114A LEU* 3.4 5.6 + - - +
115A LYS* 3.1 56.5 + - + +
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Residues in contact with ASP 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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109A ASN* 3.0 38.8 + - + +
111A TYR* 1.3 92.0 - - - +
113A LEU* 1.3 65.9 + - + +
115A LYS* 3.8 6.4 - - - +
116A ASP* 3.0 35.6 + - - +
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Residues in contact with LEU 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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16A ARG* 5.4 2.6 - - - +
19A ARG* 3.8 34.3 - - - +
20A LEU* 4.0 31.0 - - + +
23A LEU* 4.4 10.5 - - + -
108A SER* 4.0 21.8 - - - +
109A ASN 3.3 16.4 + - - +
110A VAL* 3.3 16.2 + - - +
112A ASP* 1.3 78.1 - - + +
114A LEU* 1.3 60.5 + - - +
116A ASP* 3.6 10.8 + - - +
117A LEU* 3.3 20.6 + - - +
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Residues in contact with LEU 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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20A LEU* 3.9 19.3 - - + -
83A ILE* 3.5 39.6 - - + +
86A TRP* 4.1 21.1 - - + +
87A LEU* 4.0 12.8 - - + -
90A VAL* 3.8 35.2 - - + -
110A VAL* 3.3 15.3 + - + +
111A TYR 3.7 6.7 - - - +
112A ASP 3.2 0.2 - - - -
113A LEU* 1.3 75.9 - - - +
115A LYS* 1.3 59.2 + - - +
117A LEU* 3.2 4.1 + - - +
118A GLU* 2.9 25.3 + - - +
166A PHE* 4.4 6.5 - - + -
170A MET* 4.0 15.5 - - + -
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Residues in contact with LYS 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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87A LEU* 3.5 27.8 - - + +
111A TYR* 3.1 51.9 + - + +
112A ASP* 3.3 8.5 + - - +
114A LEU* 1.3 74.4 - - - +
116A ASP* 1.3 64.3 + - - +
118A GLU* 3.0 28.9 + - - +
119A GLU* 3.1 24.3 + - - +
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Residues in contact with ASP 116 (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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16A ARG* 4.4 25.9 + - - +
112A ASP* 3.0 26.3 + - - +
113A LEU* 3.7 12.5 - - + +
115A LYS* 1.3 79.2 - - - +
117A LEU* 1.3 56.5 + - - +
119A GLU* 3.5 18.2 + - - +
120A GLY* 3.0 23.6 + - - -
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Residues in contact with LEU 117 (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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13A ALA* 3.4 33.4 - - + +
16A ARG* 3.9 16.8 - - + +
17A ALA* 4.0 19.3 - - + +
20A LEU* 3.9 19.1 - - + -
83A ILE* 3.8 25.8 - - + -
113A LEU 3.3 10.7 + - - +
114A LEU* 3.2 9.0 + - - +
116A ASP* 1.3 74.6 - - - +
118A GLU* 1.3 66.6 + - - +
120A GLY* 3.0 2.9 + - - -
121A ILE* 2.9 38.2 + - + +
170A MET* 5.5 0.9 - - - -
173A VAL* 4.4 4.9 - - + -
177A LEU* 4.0 10.8 - - + -
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Residues in contact with GLU 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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80A LEU* 3.6 20.3 - - + +
83A ILE* 3.8 14.9 - - + +
84A GLN* 2.8 33.2 - - + +
87A LEU* 4.2 7.8 - - + +
114A LEU 2.9 16.6 + - - +
115A LYS* 3.0 41.1 + - + +
117A LEU* 1.3 77.3 - - - +
119A GLU* 1.3 58.8 + - - +
121A ILE* 3.4 5.1 + - - +
122A GLN* 3.1 36.0 + - - +
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Residues in contact with GLU 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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115A LYS 3.1 17.4 + - - +
116A ASP* 3.8 15.8 - - - +
118A GLU* 1.3 73.7 - - - +
120A GLY* 1.3 63.0 + - - +
122A GLN* 3.3 12.2 + - - +
123A THR* 2.9 37.1 + - - +
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Residues in contact with GLY 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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9A LEU* 5.5 3.8 - - - +
13A ALA* 5.1 10.0 - - - +
16A ARG* 4.5 14.6 - - - -
116A ASP 3.0 11.8 + - - -
117A LEU* 3.0 8.9 + - - -
119A GLU* 1.3 77.1 - - - +
121A ILE* 1.3 62.2 + - - +
123A THR* 3.5 6.2 + - - -
124A LEU* 3.2 23.0 + - - +
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Residues in contact with ILE 121 (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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13A ALA* 5.1 2.7 - - + -
76A LEU* 3.4 35.0 - - + +
79A SER* 4.0 28.0 - - - -
80A LEU* 3.8 16.6 - - + +
83A ILE* 4.3 10.5 - - + -
117A LEU* 2.9 36.9 + - + +
118A GLU* 3.7 5.4 - - - +
119A GLU 3.3 0.2 - - - -
120A GLY* 1.3 77.4 - - - +
122A GLN* 1.3 56.8 + - - +
124A LEU* 3.3 8.7 + - - +
125A MET* 3.0 29.6 + - - +
173A VAL* 4.8 0.4 - - + -
177A LEU* 4.3 18.4 - - + -
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Residues in contact with GLN 122 (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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80A LEU* 4.1 23.6 - - + +
84A GLN* 4.0 14.2 - - - +
118A GLU* 3.1 32.1 + - - +
119A GLU* 3.8 11.3 - - - +
121A ILE* 1.3 71.7 - - - +
123A THR* 1.3 64.6 + - - +
125A MET* 3.4 9.3 + - - +
126A GLY* 3.1 20.8 + - - -
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Residues in contact with THR 123 (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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9A LEU* 4.0 28.7 - - + -
119A GLU* 2.9 24.6 + - - +
120A GLY* 3.7 6.5 - - - -
122A GLN* 1.3 77.1 - - - +
124A LEU* 1.4 60.6 - - - +
126A GLY* 3.4 3.4 + - - -
127A ARG* 3.4 29.2 + - - +
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Residues in contact with LEU 124 (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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6A LEU* 3.9 28.3 - - + +
9A LEU* 4.2 23.6 - - + +
10A ALA* 4.0 27.8 - - + +
13A ALA* 4.2 13.9 - - + -
76A LEU* 3.9 31.4 - - + -
120A GLY 3.2 13.5 + - - +
121A ILE* 3.3 8.9 + - - +
123A THR* 1.4 72.9 - - - +
125A MET* 1.3 64.5 + - - +
127A ARG* 3.4 7.3 + - - +
128A LEU* 3.3 29.6 + - + +
177A LEU* 5.3 2.2 - - + -
180A VAL* 5.0 7.9 - - + -
184A SER* 5.7 1.6 - - - +
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Residues in contact with MET 125 (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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73A LEU* 3.8 17.7 - - + -
76A LEU* 3.7 31.6 - - + +
77A ARG* 3.7 36.3 - - + +
80A LEU* 4.0 26.9 - - + -
121A ILE* 3.0 17.1 + - - +
122A GLN* 3.6 10.8 - - - +
123A THR 3.4 0.2 - - - -
124A LEU* 1.3 75.1 - - - +
126A GLY* 1.3 57.7 + - - +
128A LEU 3.0 2.6 + - - -
129A GLU* 2.9 50.4 + - - +
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Residues in contact with GLY 126 (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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122A GLN 3.1 11.7 + - - -
123A THR* 3.4 4.9 + - - -
124A LEU 3.3 0.6 - - - -
125A MET* 1.3 78.1 - - - +
127A ARG* 1.3 59.7 + - - +
128A LEU 3.6 0.2 + - - -
129A GLU* 3.9 18.3 + - - +
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Residues in contact with ARG 127 (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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2A PRO* 3.5 39.1 + - - +
4A ILE* 2.8 35.9 + - - +
5A PRO* 4.3 1.2 - - - +
6A LEU* 3.6 43.4 - - + +
9A LEU* 3.6 24.4 - - + +
123A THR* 3.4 20.8 + - - +
124A LEU 3.4 3.8 + - - +
125A MET 3.2 0.8 - - - -
126A GLY* 1.3 75.6 - - - +
128A LEU* 1.3 62.3 + - - +
129A GLU 3.4 2.4 + - - -
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Residues in contact with LEU 128 (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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6A LEU* 4.4 24.0 - - + -
72A ASN* 4.2 23.3 - - + +
73A LEU* 3.6 25.9 - - + +
76A LEU* 3.6 29.4 - - + -
124A LEU* 3.3 16.1 + - + +
125A MET 3.0 6.0 + - - +
127A ARG* 1.3 79.3 - - - +
129A GLU* 1.3 60.6 + - - +
180A VAL* 5.3 2.9 - - + -
184A SER* 5.4 3.6 - - - +
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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