Contacts of the helix formed by residues 110 - 127 (chain A) in PDB entry 2HR9
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 ARG 110 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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103A LEU* 3.3 19.1 - - + +
107A ARG* 2.6 41.6 + - + +
109A GLU* 1.3 84.3 + - + +
111A VAL* 1.3 60.0 + - - +
112A LYS 3.2 2.7 - - - -
113A PRO* 3.3 23.3 - - - +
114A PHE* 3.4 11.6 + - - +
164A LYS* 3.3 38.1 - - - +
165A ASP* 3.9 7.7 + - - +
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Residues in contact with VAL 111 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100A LYS* 3.5 20.8 - - + +
103A LEU* 3.6 13.7 - - + -
104A GLU* 3.4 48.9 - - + +
108A PRO* 2.7 32.3 - - + +
110A ARG* 1.3 76.8 - - - +
112A LYS* 1.3 72.6 + - + +
114A PHE* 3.7 4.6 + - - +
115A MET* 3.1 28.5 + - - +
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Residues in contact with LYS 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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108A PRO 4.4 2.0 + - - +
109A GLU* 4.9 3.8 - - - +
111A VAL* 1.3 86.9 - - + +
113A PRO* 1.3 73.8 - - + +
115A MET* 3.0 17.8 + - - +
116A THR* 3.2 14.9 + - - -
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Residues in contact with PRO 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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27A LEU* 3.5 12.8 - - + +
109A GLU 3.9 6.5 - - - +
110A ARG* 3.3 32.5 - - - +
112A LYS* 1.3 95.9 - - + +
114A PHE* 1.3 49.9 + - - +
116A THR* 3.3 6.2 + - - -
117A GLY* 2.7 34.3 + - - -
165A ASP* 5.7 0.9 - - - +
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Residues in contact with PHE 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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27A LEU* 3.8 17.7 - - + +
95A TYR* 4.1 8.7 - + - -
96A MET* 3.3 41.7 - - + -
99A ILE* 3.7 33.7 - - + -
100A LYS* 4.4 15.0 - - + -
103A LEU* 4.7 1.8 - - + -
110A ARG 3.4 14.3 + - - +
111A VAL* 3.8 5.4 - - - +
112A LYS 3.2 0.6 - - - -
113A PRO* 1.3 80.0 - - - +
115A MET* 1.3 57.8 + - + +
118A ALA* 2.6 48.1 + - + +
163A PHE* 4.6 11.9 - + + -
165A ASP* 3.0 44.2 + - + +
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Residues in contact with MET 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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96A MET* 4.7 24.9 - - - +
100A LYS* 4.6 31.9 - - + +
111A VAL* 3.1 18.9 + - + +
112A LYS* 3.0 13.9 + - + +
114A PHE* 1.3 80.1 - - + +
116A THR* 1.3 62.1 + - - +
118A ALA* 4.0 3.9 - - - +
119A ALA* 3.5 20.6 + - - +
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Residues in contact with THR 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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112A LYS 3.2 10.2 + - - -
113A PRO* 3.8 7.6 - - - -
115A MET* 1.3 75.7 - - - +
117A GLY* 1.3 62.8 + - - +
119A ALA* 3.6 4.5 + - - +
120A GLU* 3.0 40.5 + - + +
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Residues in contact with GLY 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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24A ALA* 5.8 2.4 - - - +
27A LEU* 3.8 22.6 - - - +
113A PRO 2.7 20.5 + - - -
116A THR* 1.3 70.8 - - - +
118A ALA* 1.3 57.7 + - - +
120A GLU* 3.5 5.8 - - - +
121A GLN* 2.8 37.9 + - - +
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Residues in contact with ALA 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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27A LEU* 4.4 5.6 - - - +
92A ILE* 4.2 20.4 - - + +
95A TYR* 4.9 4.3 + - - +
96A MET* 4.3 12.3 - - + -
114A PHE* 2.6 44.4 + - + +
115A MET 4.0 3.1 - - - +
117A GLY* 1.3 72.3 - - - +
119A ALA* 1.3 56.6 + - - +
121A GLN* 4.2 2.1 - - - +
122A ILE* 3.0 33.7 + - - +
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Residues in contact with ALA 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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92A ILE* 5.2 3.1 - - - -
96A MET* 5.4 5.3 - - + -
115A MET 3.5 15.2 + - - +
116A THR* 4.0 3.4 - - - +
117A GLY 3.3 0.2 - - - -
118A ALA* 1.3 79.9 - - - +
120A GLU* 1.3 54.9 + - - +
122A ILE* 3.3 11.0 - - - +
123A LYS* 2.7 54.3 - - - +
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Residues in contact with GLU 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 THR* 3.0 29.4 + - + +
117A GLY* 3.1 7.6 + - - +
119A ALA* 1.3 75.1 - - - +
121A GLN* 1.3 65.8 + - - +
123A LYS* 3.2 16.4 + - - +
124A HIS* 3.1 19.6 + - - +
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Residues in contact with GLN 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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23A ILE* 3.3 26.6 - - + +
24A ALA* 3.1 35.3 - - + +
28A CYS* 3.7 22.1 - - + -
117A GLY 2.8 19.1 + - - +
118A ALA* 4.3 2.7 - - - +
120A GLU* 1.3 73.8 - - - +
122A ILE* 1.3 62.5 + - - +
124A HIS* 3.0 29.9 + - - +
125A ILE* 3.0 22.9 + - + +
148A LEU* 5.7 1.1 - - + -
161A ILE* 5.0 8.5 - - + -
163A PHE* 5.5 5.2 - - + -
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Residues in contact with ILE 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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88A TYR* 3.1 43.5 - - + -
92A ILE* 3.9 38.1 - - + -
95A TYR* 5.3 3.6 - - + +
118A ALA 3.0 17.4 + - - +
119A ALA* 3.3 20.0 - - - +
121A GLN* 1.3 77.7 - - - +
123A LYS* 1.3 67.5 + - + +
125A ILE* 2.7 29.4 - - + +
126A LEU* 2.9 27.6 + - + +
163A PHE* 6.5 0.2 - - + -
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Residues in contact with LYS 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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119A ALA* 2.7 42.4 - - - +
120A GLU* 3.2 17.8 + - - +
122A ILE* 1.3 87.8 - - + +
124A HIS* 1.3 61.5 + - - +
126A LEU* 3.6 11.7 + - + +
127A ALA* 3.3 19.9 + - - +
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Residues in contact with HIS 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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120A GLU 3.1 10.9 + - - +
121A GLN* 3.0 26.4 + - - +
123A LYS* 1.3 75.3 - - - +
125A ILE* 1.3 68.8 + - + +
127A ALA* 3.1 9.6 + - - +
128A ASN* 3.0 35.2 + - - -
132A TYR* 4.2 17.8 + + - -
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Residues in contact with ILE 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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88A TYR* 3.5 30.5 - - + +
121A GLN* 3.0 14.5 + - + +
122A ILE* 2.7 37.9 - - + +
124A HIS* 1.3 78.3 - - + +
126A LEU* 1.3 59.5 + - - +
128A ASN 2.7 26.6 + - - +
129A PHE* 2.9 12.8 + - - -
132A TYR* 3.5 35.3 - - + +
148A LEU* 3.5 39.7 - - + -
161A ILE* 4.2 4.5 - - + -
163A PHE* 5.7 4.3 - - + -
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Residues in contact with LEU 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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84A THR 5.2 0.2 - - - +
85A LYS* 4.4 17.8 - - + +
88A TYR* 3.4 30.5 - - + -
89A LYS* 4.0 31.9 - - + +
122A ILE* 2.9 40.6 + - + +
123A LYS* 3.7 13.0 - - + +
125A ILE* 1.3 76.2 - - - +
127A ALA* 1.3 62.3 + - - +
128A ASN 3.0 1.3 + - - -
129A PHE* 3.3 26.7 + - + +
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Residues in contact with ALA 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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123A LYS 3.3 9.0 + - - +
124A HIS* 3.1 14.6 + - + +
125A ILE 3.1 0.8 - - - -
126A LEU* 1.3 77.7 - - - +
128A ASN* 1.3 68.6 + - - +
129A PHE 3.7 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