Contacts of the helix formed by residues 112 - 128 (chain D) in PDB entry 1FS2
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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23D GLN* 3.6 15.5 - - + +
24D SER* 3.5 27.8 - - - -
27D ILE* 6.0 0.2 - - + -
58D VAL* 3.8 9.2 - - + -
61D TRP* 3.8 28.5 - - + -
62D CYS* 3.8 25.6 - - - -
107D ALA* 3.1 9.0 + - - +
110D LEU* 3.7 32.1 - - + -
111D ASP* 1.3 74.7 - - - +
113D LYS* 1.3 67.4 + - - +
114D GLY 4.7 1.1 - - - +
115D LEU* 3.1 18.5 + - + +
116D LEU* 2.9 21.5 + - - +
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Residues in contact with LYS 113 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23D GLN 4.8 0.8 + - - -
25D VAL* 6.4 0.4 - - + -
111D ASP* 3.5 11.3 + - - +
112D ILE* 1.3 72.8 - - - +
114D GLY* 1.3 54.6 + - - +
116D LEU* 3.0 11.1 + - - +
117D ASP* 2.6 52.7 + - + +
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Residues in contact with GLY 114 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61D TRP* 3.5 18.3 - - - -
112D ILE* 3.2 2.4 + - - +
113D LYS* 1.3 81.0 - - - +
115D LEU* 1.3 56.1 + - - +
117D ASP* 2.8 26.5 - - - +
118D VAL* 2.9 16.5 + - - +
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Residues in contact with LEU 115 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58D VAL* 4.4 21.1 - - + -
61D TRP* 3.1 61.8 - - + +
92D PHE* 4.0 10.5 - - + -
103D LEU* 4.7 12.1 - - + +
107D ALA* 3.7 23.3 - - + -
112D ILE* 3.1 18.9 + - + +
114D GLY* 1.3 72.6 - - - +
116D LEU* 1.3 63.3 + - - +
118D VAL* 3.2 5.7 - - + +
119D THR* 3.0 41.1 + - + -
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Residues in contact with LEU 116 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116C LEU* 4.0 23.3 - - + -
104D ILE* 4.1 15.9 - - + +
107D ALA* 3.7 23.1 - - + +
108D ASN* 3.9 18.4 - - - +
111D ASP* 5.2 4.0 - - - -
112D ILE 2.9 12.1 + - - +
113D LYS* 3.3 13.9 - - - +
115D LEU* 1.3 78.3 - - - +
117D ASP* 1.3 63.8 + - - +
119D THR* 3.0 17.7 + - - +
120D CYS* 3.1 29.4 + - - +
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Residues in contact with ASP 117 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123C CYS* 5.2 0.2 - - - -
113D LYS* 2.6 32.0 + - - +
114D GLY* 2.8 20.1 - - - +
116D LEU* 1.3 76.0 - - - +
118D VAL* 1.3 62.0 + - + +
120D CYS* 3.4 4.3 + - - +
121D LYS* 3.3 47.5 + - - +
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Residues in contact with VAL 118 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61D TRP* 4.0 16.6 - - + +
65D HIS* 5.9 0.2 - - - +
85D ILE* 4.3 14.7 - - + +
86D PRO* 4.8 6.7 - - + -
89D ASP* 4.1 28.9 - - + +
92D PHE* 5.9 0.2 - - + -
93D LEU* 4.0 12.3 - - + -
114D GLY 2.9 20.9 + - - +
115D LEU* 3.2 22.4 - - + +
117D ASP* 1.3 73.6 - - + +
119D THR* 1.3 65.7 + - - +
121D LYS* 3.5 10.0 + - + +
122D THR* 2.8 28.4 + - - -
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Residues in contact with THR 119 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93D LEU* 3.8 34.3 - - + -
100D LEU* 4.4 6.3 - - + +
103D LEU* 4.2 16.6 - - + -
104D ILE* 3.2 27.6 - - + +
107D ALA* 4.7 0.2 - - - +
115D LEU* 3.0 33.9 + - + +
116D LEU* 3.0 14.0 + - - -
118D VAL* 1.3 75.5 - - - +
120D CYS* 1.3 61.9 + - - +
122D THR* 3.2 4.7 + - - -
123D VAL* 3.1 26.3 + - - +
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Residues in contact with CYS 120 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116C LEU* 4.5 6.7 - - - -
119C GLY* 4.2 7.6 - - - -
120C ILE* 4.0 34.3 - - - +
123C CYS* 4.3 13.5 - - - -
104D ILE* 4.2 11.9 - - - -
116D LEU* 3.1 38.4 + - - +
117D ASP* 3.8 4.9 - - - +
118D VAL 3.3 0.2 - - - -
119D THR* 1.3 74.7 + - - +
121D LYS* 1.3 60.3 - - - +
123D VAL* 3.1 4.7 + - - +
124D ALA* 2.8 27.0 + - - +
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Residues in contact with LYS 121 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123C CYS* 3.6 20.2 - - + -
80D LYS* 4.0 15.2 - - - +
81D ARG 4.2 4.3 - - - +
82D THR* 4.2 22.7 - - - +
84D ASP* 2.6 32.2 + - - +
85D ILE* 4.1 18.8 - - + -
117D ASP* 3.3 37.9 + - - +
118D VAL* 3.9 8.1 - - + +
120D CYS* 1.3 77.2 - - - +
122D THR* 1.3 56.7 + - - +
124D ALA* 3.2 10.0 + - - +
125D ASN* 2.9 33.3 + - - -
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Residues in contact with THR 122 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85D ILE* 3.6 16.2 - - + +
90D GLN* 6.2 0.3 - - - -
93D LEU* 3.2 31.7 - - + +
100D LEU* 4.3 9.4 - - + -
118D VAL 2.8 18.6 + - - -
119D THR* 3.4 9.4 - - - -
120D CYS 3.1 0.6 - - - -
121D LYS* 1.3 75.9 - - - +
123D VAL* 1.3 63.4 + - - +
125D ASN* 3.7 6.3 + - - +
126D MET* 3.3 38.4 + - + +
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Residues in contact with VAL 123 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109C TRP* 4.1 18.2 - - + -
120C ILE* 4.0 24.7 - - + -
139C TRP* 6.2 0.7 - - + -
100D LEU* 4.2 11.4 - - + -
104D ILE* 3.6 23.3 - - + -
119D THR 3.1 14.0 + - - +
120D CYS 3.1 5.9 + - - +
122D THR* 1.3 74.4 - - - +
124D ALA* 1.3 69.6 + - - +
126D MET* 2.8 19.8 + - - +
127D ILE* 3.2 14.5 + - + +
139D PHE* 3.7 27.4 - - + -
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Residues in contact with ALA 124 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120C ILE* 4.0 12.5 - - - +
123C CYS* 3.6 28.3 - - + +
124C LEU* 3.9 14.9 - - + +
81D ARG 5.3 1.6 - - - +
120D CYS 2.8 13.6 + - - +
121D LYS* 3.2 10.3 - - - +
123D VAL* 1.3 75.7 - - - +
125D ASN* 1.3 62.6 + - - +
127D ILE* 2.9 21.8 + - - +
128D LYS* 3.0 18.0 + - + +
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Residues in contact with ASN 125 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81D ARG 2.8 23.2 + - - -
82D THR* 2.9 27.3 - - - +
85D ILE* 4.3 5.7 - - - +
121D LYS 2.9 16.4 + - - +
122D THR* 4.0 6.7 - - - +
123D VAL 3.2 0.2 - - - -
124D ALA* 1.3 77.2 - - - +
126D MET* 1.3 62.3 + - + +
127D ILE 3.3 0.3 + - - -
128D LYS* 3.1 38.2 + - - +
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Residues in contact with MET 126 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93D LEU 6.1 1.3 - - - +
95D VAL 6.0 2.2 - - - +
97D GLN* 5.5 12.3 - - + -
100D LEU* 3.7 29.4 - - + -
122D THR* 3.3 24.8 + - + +
123D VAL* 2.8 14.7 + - - +
125D ASN* 1.3 73.8 - - + +
127D ILE* 1.3 58.4 + - - +
128D LYS 4.3 0.7 - - - +
130D LYS* 2.9 37.3 - - - +
138D THR* 6.3 0.2 - - - -
139D PHE* 3.6 29.4 - - + -
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Residues in contact with ILE 127 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120C ILE* 3.8 29.4 - - + -
121C PHE* 4.7 1.8 - - + -
124C LEU* 4.3 15.0 - - + -
131C LYS* 3.3 8.4 + - - +
132C VAL* 3.4 29.2 - - + -
139C TRP* 4.0 24.9 - - + -
123D VAL* 3.5 13.5 - - + +
124D ALA* 2.9 8.6 + - - +
126D MET* 1.3 77.6 - - - +
128D LYS* 1.3 69.3 + - - +
129D GLY 3.3 0.3 + - - -
130D LYS* 3.0 20.3 + - - +
135D ILE* 3.5 17.0 - - + +
139D PHE* 4.2 15.3 - - + -
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Residues in contact with LYS 128 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123C CYS 5.1 6.7 - - - +
124C LEU* 3.8 18.4 - - + -
125C CYS* 4.5 15.0 - - - +
128C GLU* 3.3 29.5 + - - +
81D ARG* 4.3 9.6 - - - +
124D ALA* 3.0 15.8 + - + +
125D ASN* 3.1 42.7 + - - +
126D MET 4.3 2.4 - - - +
127D ILE* 1.3 78.7 - - - +
129D GLY* 1.3 58.9 + - - +
130D LYS* 3.3 4.2 + - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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