Contacts of the helix formed by residues 109 - 123 (chain B) in PDB entry 1HF0
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 GLU 109 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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17A LYS* 6.1 0.4 - - - +
18A GLN* 3.3 37.3 - - + +
21A ILE* 3.8 34.9 - - + +
22A LYS* 3.1 41.9 + - - +
108B ILE* 1.3 76.7 - - - +
110B THR* 1.3 67.1 + - - +
111B ASN* 4.3 6.4 + - + +
112B ILE* 3.1 32.6 + - + +
113B ARG* 2.9 18.9 + - - +
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Residues in contact with THR 110 (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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17A LYS* 3.9 23.0 + - - +
108B ILE 3.6 2.7 + - - -
109B GLU* 1.3 70.8 - - - +
111B ASN* 1.3 55.7 + - - +
113B ARG* 2.9 13.2 + - + +
114B VAL* 2.8 42.4 + - + +
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Residues in contact with ASN 111 (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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14A LYS* 5.8 5.9 - - - +
18A GLN* 4.2 19.0 + - - +
109B GLU* 4.3 4.8 + - + +
110B THR* 1.3 78.9 - - - +
112B ILE* 1.3 74.7 + - + +
113B ARG 3.0 1.6 - - - -
114B VAL* 3.0 17.1 + - - +
115B ALA* 2.9 23.0 + - - +
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Residues in contact with ILE 112 (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 LYS* 5.0 4.5 - - - +
108B ILE* 4.1 10.3 - - + -
109B GLU* 3.1 46.1 + - + +
111B ASN* 1.3 78.1 - - + +
113B ARG* 1.3 59.9 + - - +
115B ALA* 3.0 9.7 + - - +
116B LEU* 2.8 49.6 + - + +
138B LEU* 4.0 30.7 - - + +
140B MET* 4.3 23.1 - - + -
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Residues in contact with ARG 113 (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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108B ILE* 3.9 16.8 - - + +
109B GLU 2.9 11.8 + - - +
110B THR* 3.0 14.8 - - - +
112B ILE* 1.3 80.0 - - - +
114B VAL* 1.3 56.0 + - - +
116B LEU* 3.6 7.2 - - + +
117B GLU* 2.7 53.3 + - + +
148B TRP* 3.4 33.7 - - + +
152B ARG* 4.9 5.0 - - - +
155B LYS* 5.1 11.9 - - - +
16N A 5.3 8.5 + - - -
17N A 5.6 4.0 - - - -
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Residues in contact with VAL 114 (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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110B THR* 2.8 25.8 + - + +
111B ASN* 3.0 23.3 + - - +
113B ARG* 1.3 75.0 - - - +
115B ALA* 1.3 60.6 + - + +
117B GLU* 3.7 6.6 - - - +
118B LYS* 2.9 31.1 + - + +
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Residues in contact with ALA 115 (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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111B ASN 2.9 11.7 + - - +
112B ILE* 3.2 9.4 - - - +
114B VAL* 1.3 77.9 - - + +
116B LEU* 1.3 57.2 + - - +
118B LYS* 3.0 10.0 + - - +
119B SER* 2.7 36.2 + - - -
138B LEU* 4.3 23.8 - - + -
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Residues in contact with LEU 116 (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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108B ILE* 4.5 6.7 - - + -
112B ILE* 2.8 41.7 + - + +
113B ARG* 3.6 6.7 - - - +
115B ALA* 1.3 71.9 - - - +
117B GLU* 1.3 57.8 + - - +
119B SER* 3.2 7.0 + - - -
120B PHE* 2.8 29.5 + - - +
134B ILE* 4.1 11.0 - - + -
138B LEU* 3.7 20.6 - - + -
140B MET* 5.1 0.2 - - + -
145B ILE* 3.9 21.3 - - + -
148B TRP* 3.6 49.8 - - + +
149B PHE* 4.2 16.1 - - + -
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Residues in contact with GLU 117 (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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113B ARG* 2.7 46.3 + - - +
114B VAL* 3.7 7.6 - - - +
116B LEU* 1.3 71.8 - - - +
118B LYS* 1.3 67.1 - - - +
120B PHE* 3.2 10.3 + - - +
121B LEU* 3.1 31.6 + - + +
148B TRP* 3.8 3.9 - - - -
152B ARG* 2.8 46.0 + - - -
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Residues in contact with LYS 118 (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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114B VAL* 2.9 22.6 + - + +
115B ALA* 3.3 8.7 - - - +
117B GLU* 1.3 74.8 - - - +
119B SER* 1.3 66.0 + - - +
121B LEU* 3.0 21.9 + - + +
122B GLU* 3.3 26.1 + - - +
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Residues in contact with SER 119 (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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115B ALA 2.7 15.7 + - - -
116B LEU* 3.4 11.2 - - - -
118B LYS* 1.3 74.0 - - - +
120B PHE* 1.3 62.9 + - - +
122B GLU* 3.0 25.6 + - - +
123B ASN* 3.1 15.3 + - - +
126B PRO* 5.9 0.5 - - - +
134B ILE* 3.9 19.9 - - - +
149B PHE* 3.8 16.4 - - - -
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Residues in contact with PHE 120 (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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116B LEU 2.8 16.9 + - - +
117B GLU* 3.2 15.7 + - - +
119B SER* 1.3 73.5 - - - +
121B LEU* 1.3 60.9 + - + +
123B ASN 3.6 5.2 - - - -
124B GLN* 2.6 89.5 + - + +
148B TRP* 4.1 9.9 - - + -
149B PHE* 3.9 12.5 - + + -
152B ARG* 3.6 61.2 - - + -
153B ARG* 4.1 17.0 - - + -
156B GLU* 4.1 15.3 - - + -
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Residues in contact with LEU 121 (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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117B GLU* 3.1 26.0 + - + +
118B LYS* 3.0 14.3 + - + +
120B PHE* 1.3 87.9 - - + +
122B GLU* 1.3 64.0 + - - +
124B GLN* 3.1 16.1 + - - +
152B ARG* 5.8 1.1 - - - +
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Residues in contact with GLU 122 (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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118B LYS* 3.3 26.3 + - - +
119B SER* 3.0 16.2 + - - +
121B LEU* 1.3 83.2 - - - +
123B ASN* 1.3 63.6 + - + +
124B GLN* 4.3 0.7 + - - -
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Residues in contact with ASN 123 (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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119B SER* 3.1 12.5 + - - +
120B PHE* 3.5 7.0 - - - +
121B LEU 3.4 0.4 - - - -
122B GLU* 1.3 85.4 - - + +
124B GLN* 1.3 62.5 + - - +
125B LYS* 2.8 24.3 + - - +
126B PRO* 3.6 18.7 - - + +
130B GLU* 3.4 29.7 + - - -
149B PHE* 4.0 1.9 - - - -
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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