Contacts of the helix formed by residues 122 - 134 (chain A) in PDB entry 3IFS
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 SER 122 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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120A ASN* 3.0 15.5 + - - -
121A ILE* 1.3 74.8 - - - +
123A SER* 1.3 65.1 + - - +
124A THR* 3.5 2.3 + - - -
125A TYR* 3.0 26.2 + - - +
126A MSE 3.1 26.6 + - - +
274B TYR 4.7 2.0 - - - -
275B GLU* 2.6 32.9 + - - -
276B PRO* 3.8 14.1 - - - +
363B ASN* 4.7 0.7 - - - +
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Residues in contact with SER 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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121A ILE 3.7 4.6 + - - -
122A SER* 1.3 72.4 - - - +
124A THR* 1.3 55.6 + - - +
126A MSE 3.8 1.2 - - - +
127A LYS* 2.9 33.1 + - - +
275B GLU* 5.0 1.4 + - - -
335B SER* 3.1 12.1 + - - -
337B HIS* 2.5 29.4 + - - +
338B GLU* 4.0 1.6 - - - -
339B LEU* 4.0 25.6 - - - +
359B VAL* 3.8 26.4 - - - +
360B ASP* 4.4 10.6 + - - +
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Residues in contact with THR 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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122A SER* 3.2 6.2 + - - -
123A SER* 1.3 79.1 + - - +
125A TYR* 1.3 62.4 + - - +
128A ASP* 3.0 45.0 + - - +
99B SER* 4.0 5.8 - - - +
275B GLU* 4.4 9.0 + - - +
335B SER* 3.1 18.4 + - - -
336B THR* 3.3 17.7 + - + +
337B HIS* 3.2 30.4 + - + +
389B LEU* 6.5 0.7 - - + -
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Residues in contact with TYR 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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90A ARG* 5.4 2.9 + - - -
116A PHE* 2.6 32.6 + - - +
117A VAL* 4.2 12.6 - - + -
119A GLN* 3.3 19.1 + - - -
120A ASN* 3.6 24.2 - - - +
122A SER* 3.0 26.4 + - - +
124A THR* 1.3 77.5 - - - +
126A MSE 1.3 62.6 + - + +
128A ASP* 3.3 2.4 + - - +
129A LEU* 2.8 32.6 + - + +
99B SER* 4.0 16.8 - - - +
100B PHE* 3.6 33.8 - + - -
276B PRO* 4.0 18.8 - - + -
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Residues in contact with MSE 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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117A VAL* 4.0 16.6 - - + -
118A GLY 5.3 0.4 - - - +
120A ASN* 3.5 26.9 - - - +
121A ILE* 3.9 7.2 - - + -
122A SER 3.1 26.2 + - - +
125A TYR* 1.3 79.5 - - + +
127A LYS* 1.3 64.1 + - - +
129A LEU* 3.3 5.7 + - - +
130A MSE 3.2 26.3 + - - +
151A GLU 5.3 1.3 - - - +
154A LEU* 5.4 4.5 - - + -
155A ALA* 4.5 21.1 - - + +
158A ILE* 4.1 24.7 - - - -
159A PHE* 3.6 21.0 - - + -
339B LEU* 3.8 16.6 - - + -
359B VAL* 4.2 11.9 - - + -
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Residues in contact with LYS 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 SER 2.9 18.3 + - - +
124A THR 4.1 1.1 - - - +
126A MSE 1.3 75.6 - - - +
128A ASP* 1.3 64.4 + - - +
130A MSE 3.3 31.8 + - + +
131A ASP* 3.6 11.8 + - - +
337B HIS* 3.8 35.9 + - + +
338B GLU 3.0 20.9 + - - +
339B LEU* 3.0 35.6 - - + +
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Residues in contact with ASP 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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124A THR* 3.0 26.2 + - - +
125A TYR 3.6 3.1 - - - +
127A LYS* 1.3 79.8 - - - +
129A LEU* 1.3 61.9 + - - +
131A ASP* 3.1 13.8 + - - +
132A VAL* 3.7 3.8 + - - +
97B ASN 4.9 0.2 - - - +
98B HIS* 3.2 52.4 + - + -
99B SER* 2.7 39.1 + - - -
100B PHE* 3.9 1.1 - - - -
337B HIS* 3.2 24.2 + - - -
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Residues in contact with LEU 129 (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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78A LEU* 3.7 15.9 - - + -
115A LEU* 3.6 33.0 - - + -
116A PHE 4.2 5.8 - - - +
117A VAL* 3.7 35.9 - - + -
125A TYR* 2.8 20.2 + - + +
126A MSE 3.3 6.2 + - - +
128A ASP* 1.3 74.4 - - - +
130A MSE 1.3 62.4 + - - +
132A VAL* 3.0 16.2 + - + +
133A LEU* 3.2 15.1 + - + +
159A PHE* 4.0 12.3 - - + -
100B PHE* 3.5 31.1 - - + -
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Residues in contact with MSE 130 (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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126A MSE 3.2 12.0 + - - +
127A LYS* 3.4 23.8 - - + +
128A ASP 3.2 0.4 - - - -
129A LEU* 1.3 75.7 - - - +
131A ASP* 1.3 62.5 + - - +
133A LEU* 3.3 12.2 + - - +
134A GLU* 3.3 19.9 + - - +
158A ILE* 3.5 32.8 - - + -
159A PHE* 3.8 13.9 - - + -
162A LEU* 3.7 32.5 - - + -
339B LEU* 4.0 26.7 - - + -
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Residues in contact with ASP 131 (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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127A LYS* 3.9 12.0 - - - +
128A ASP* 3.1 12.6 + - - +
130A MSE 1.3 80.2 - - - +
132A VAL* 1.3 60.1 + - - +
134A GLU* 3.3 14.2 - - - +
98B HIS* 2.7 30.5 + - - +
104B LEU* 4.0 11.4 - - + -
108B GLN* 3.1 31.0 + - - +
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Residues in contact with VAL 132 (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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76A ILE* 3.8 8.6 - - + +
113A GLN* 4.4 9.9 - - - +
115A LEU* 3.9 25.4 - - + -
128A ASP 3.9 4.3 - - - +
129A LEU* 3.0 10.9 + - - +
131A ASP* 1.3 75.0 - - - +
133A LEU* 1.3 60.8 + - - +
134A GLU 3.2 2.6 + - - +
136A LYS* 3.9 12.5 + - - +
98B HIS* 4.8 1.8 - - + -
100B PHE* 3.5 41.3 - - + -
103B THR* 3.6 29.6 - - + +
104B LEU* 4.9 7.0 - - + +
108B GLN* 5.5 1.1 - - - -
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Residues in contact with LEU 133 (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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76A ILE* 3.9 35.2 - - + -
78A LEU* 4.5 8.7 - - + -
115A LEU* 4.4 8.3 - - + -
129A LEU* 3.2 15.3 + - + +
130A MSE 3.3 10.5 + - - +
132A VAL* 1.3 75.0 - - - +
134A GLU* 1.3 64.3 + - - +
135A GLY 3.3 0.7 + - - -
136A LYS* 3.1 24.3 + - - +
138A PHE* 4.2 39.4 - - + -
159A PHE* 3.8 35.0 - - + -
162A LEU* 4.9 5.4 - - + -
166A LYS* 5.1 1.2 + - - -
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Residues in contact with GLU 134 (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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130A MSE 3.3 9.5 + - - +
131A ASP* 3.3 18.2 - - - +
132A VAL 3.2 3.7 - - - +
133A LEU* 1.3 76.5 - - - +
135A GLY* 1.3 72.9 + - - +
136A LYS* 3.3 13.0 + - - +
108B GLN* 4.4 10.8 - - - +
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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