Contacts of the helix formed by residues 112 - 128 (chain B) in PDB entry 1FQV
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 ILE 112 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23B GLN* 4.1 14.8 - - + +
24B SER* 3.8 18.8 - - - -
58B VAL* 3.3 33.9 - - + -
61B TRP* 4.2 4.0 - - + -
62B CYS* 4.0 20.4 - - - -
107B ALA* 2.9 15.6 + - - +
110B LEU* 3.7 24.7 - - + +
111B ASP* 1.3 75.1 + - - +
113B LYS* 1.3 67.2 + - - +
114B GLY* 3.0 3.7 + - - +
115B LEU* 3.7 24.9 - - + +
116B LEU* 2.9 23.4 + - - +
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Residues in contact with LYS 113 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B VAL* 6.0 0.6 - - - +
111B ASP* 3.7 9.2 + - - +
112B ILE* 1.3 71.2 - - - +
114B GLY* 1.3 64.0 + - - +
116B LEU* 3.7 15.0 - - + +
117B ASP* 3.0 55.8 + - + +
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Residues in contact with GLY 114 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61B TRP* 3.1 21.6 - - - -
112B ILE* 3.0 4.6 + - - +
113B LYS* 1.3 82.4 - - - +
115B LEU* 1.3 59.3 + - - +
117B ASP* 3.3 16.1 + - - +
118B VAL* 3.6 8.5 + - - +
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Residues in contact with LEU 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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58B VAL* 5.4 10.3 - - + -
61B TRP* 3.0 63.1 - - + +
92B PHE* 4.1 9.2 - - + -
93B LEU* 4.8 0.9 - - + -
103B LEU* 4.1 15.9 - - + +
107B ALA* 3.1 28.0 - - + +
112B ILE* 3.1 15.4 + - + +
114B GLY* 1.3 70.1 - - - +
116B LEU* 1.3 61.8 + - - +
117B ASP 3.2 2.0 - - - -
118B VAL* 3.3 13.2 - - + +
119B THR* 2.9 39.7 + - + +
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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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116A LEU* 4.1 16.8 - - + -
119A GLY* 5.9 1.1 - - - -
104B ILE* 4.5 3.8 - - + -
107B ALA* 3.9 16.8 - - + +
108B ASN* 4.1 28.9 - - - +
111B ASP* 5.3 6.7 - - - +
112B ILE 2.9 16.7 + - - +
113B LYS* 3.7 16.8 - - + +
115B LEU* 1.3 77.6 - - - +
117B ASP* 1.3 59.0 + - - +
119B THR* 3.1 11.3 + - - +
120B CYS* 3.0 38.2 - - - -
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Residues in contact with ASP 117 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123A CYS* 4.6 2.4 - - - -
113B LYS* 3.0 33.5 + - - +
114B GLY* 3.4 13.1 - - - +
115B LEU 3.2 0.2 - - - -
116B LEU* 1.3 76.2 - - - +
118B VAL* 1.3 66.3 + - - +
120B CYS* 3.5 3.6 + - - +
121B LYS* 3.0 70.7 + - - +
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Residues in contact with VAL 118 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61B TRP* 3.7 12.3 - - + +
85B ILE* 4.0 15.6 - - + +
86B PRO* 5.0 4.0 - - + -
89B ASP* 3.5 26.0 - - + +
93B LEU* 4.0 11.7 - - + -
114B GLY 3.6 4.7 - - - +
115B LEU* 3.3 42.6 - - + +
117B ASP* 1.3 79.9 - - - +
119B THR* 1.3 53.6 + - - +
121B LYS* 3.4 6.9 + - + +
122B THR* 2.6 38.4 + - - -
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Residues in contact with THR 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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93B LEU* 4.0 14.8 - - + -
100B LEU* 4.3 5.0 - - + +
103B LEU* 4.2 17.3 - - + -
104B ILE* 3.5 26.8 - - - +
115B LEU* 2.9 45.4 + - + +
116B LEU* 3.1 11.8 + - - -
118B VAL* 1.3 76.6 - - - +
120B CYS* 1.3 65.5 + - - +
122B THR* 3.3 8.3 + - - -
123B VAL* 3.1 27.4 + - - +
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Residues in contact with CYS 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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116A LEU* 4.4 2.9 - - - -
119A GLY* 4.0 8.3 - - - -
120A ILE* 3.8 38.5 - - - +
123A CYS* 3.8 16.4 - - - -
104B ILE* 4.4 10.1 - - - -
116B LEU* 3.0 44.5 + - - +
117B ASP* 3.9 2.5 - - - +
119B THR* 1.3 80.7 + - - +
121B LYS* 1.3 61.5 + - - +
123B VAL* 3.2 4.4 + - - +
124B ALA* 2.8 26.5 + - - +
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Residues in contact with LYS 121 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123A CYS* 3.4 20.9 - - + +
85B ILE* 4.1 20.6 - - + -
117B ASP* 3.0 53.3 + - - +
118B VAL* 3.8 6.3 - - + +
120B CYS* 1.3 73.1 - - - +
122B THR* 1.3 60.5 + - - +
124B ALA* 3.3 8.8 - - - +
125B ASN* 2.8 36.5 + - - +
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Residues in contact with THR 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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85B ILE* 3.8 14.3 - - + +
90B GLN* 6.2 0.2 - - - -
93B LEU* 3.0 31.6 - - + +
100B LEU* 4.0 23.8 - - + -
118B VAL 2.6 24.1 + - - -
119B THR* 3.3 8.1 - - - -
120B CYS 3.1 0.2 - - - -
121B LYS* 1.3 78.4 - - - +
123B VAL* 1.3 60.8 + - - +
125B ASN* 3.2 7.4 + - - +
126B MET* 3.1 35.7 + - + +
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Residues in contact with VAL 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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109A TRP* 3.5 16.2 - - + -
120A ILE* 3.5 29.4 - - + -
139A TRP* 6.1 0.4 - - + -
100B LEU* 3.5 14.1 - - + -
104B ILE* 3.5 22.2 - - + -
119B THR 3.1 14.9 + - - +
120B CYS 3.2 7.6 + - - +
122B THR* 1.3 73.0 - - - +
124B ALA* 1.3 64.5 + - - +
126B MET* 3.2 9.5 + - - +
127B ILE* 3.1 23.3 + - + +
139B PHE* 3.6 24.7 - - + -
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Residues in contact with ALA 124 (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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120A ILE* 4.0 7.2 - - - +
123A CYS* 3.4 30.3 - - + +
124A LEU* 3.7 20.0 - - + +
120B CYS 2.8 14.4 + - - +
121B LYS* 3.3 9.9 - - - +
122B THR 3.1 0.2 - - - -
123B VAL* 1.3 78.8 - - - +
125B ASN* 1.3 65.9 + - - +
127B ILE* 3.3 5.4 + - - +
128B LYS* 3.1 27.5 + - - +
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Residues in contact with ASN 125 (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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85B ILE* 3.8 20.3 - - - +
121B LYS* 2.8 20.6 + - - +
122B THR* 3.5 7.4 - - - +
124B ALA* 1.3 77.1 - - - +
126B MET* 1.3 62.4 + - + +
128B LYS* 3.6 43.7 + - - +
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Residues in contact with MET 126 (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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109A TRP* 5.3 0.7 - - - -
93B LEU 5.2 3.6 - - - +
95B VAL 5.2 8.7 - - - +
97B GLN* 5.5 9.0 - - + +
100B LEU* 3.4 35.2 - - + -
122B THR* 3.1 23.0 + - + +
123B VAL* 3.4 8.3 - - - +
124B ALA 3.2 0.4 - - - -
125B ASN* 1.3 77.6 - - + +
127B ILE* 1.3 62.2 + - - +
128B LYS 3.6 3.1 - - - +
130B LYS* 3.2 35.8 - - - +
139B PHE* 3.8 28.0 - - + -
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Residues in contact with ILE 127 (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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120A ILE* 4.1 20.0 - - + -
121A PHE* 4.7 1.6 - - + -
124A LEU* 4.5 13.2 - - + -
128A GLU* 5.3 1.1 - - + +
131A LYS* 3.1 18.7 + - - +
132A VAL* 3.4 22.4 - - + -
139A TRP* 3.7 28.5 - - + -
123B VAL* 3.1 14.7 + - + +
124B ALA* 3.3 6.3 + - - +
126B MET* 1.3 75.6 - - - +
128B LYS* 1.3 66.5 + - - +
130B LYS* 3.2 15.2 + - - +
135B ILE* 3.3 27.4 - - + -
139B PHE* 3.6 19.1 - - + -
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Residues in contact with LYS 128 (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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123A CYS 4.1 19.7 + - - -
124A LEU* 4.1 2.0 - - - +
125A CYS* 4.1 13.9 - - - +
128A GLU* 3.7 34.4 + - + +
131A LYS* 3.6 6.7 - - - +
124B ALA* 3.1 15.1 + - - +
125B ASN* 3.6 42.3 - - - +
126B MET 3.3 4.4 - - - +
127B ILE* 1.3 77.5 - - - +
129B GLY* 1.3 58.7 + - - +
130B LYS* 3.2 5.5 + - - +
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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