Contacts of the helix formed by residues 122 - 134 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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274A TYR 4.6 2.7 - - - -
275A GLU* 2.6 33.6 + - - -
276A PRO* 3.9 12.3 - - - +
359A VAL* 4.3 2.0 - - - -
363A ASN* 4.7 1.1 - - - +
120B ASN* 3.0 13.6 + - - +
121B ILE* 1.3 75.2 - - - +
123B SER* 1.3 62.1 + - - +
124B THR* 3.4 3.8 + - - -
125B TYR* 3.1 25.6 + - - +
126B MSE 3.1 26.3 + - - +
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Residues in contact with SER 123 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275A GLU* 5.2 1.0 + - - -
335A SER* 3.2 8.4 + - - -
337A HIS 2.8 26.6 + - - -
338A GLU* 4.1 1.2 - - - -
339A LEU* 4.0 26.7 - - - +
359A VAL* 3.8 25.4 - - - +
360A ASP* 4.1 15.2 + - - +
121B ILE 3.8 4.0 + - - -
122B SER* 1.3 69.2 - - - +
124B THR* 1.3 58.9 + - - +
126B MSE 4.5 0.2 - - - -
127B LYS* 2.8 34.5 + - - +
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Residues in contact with THR 124 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99A SER* 3.9 6.3 - - - +
275A GLU* 4.4 9.8 + - - +
335A SER* 3.2 19.0 + - - -
336A THR* 3.3 17.5 + - + +
337A HIS* 3.2 28.6 + - + -
389A LEU* 6.5 1.3 - - + -
122B SER* 3.2 7.7 + - - -
123B SER* 1.3 80.8 + - - +
125B TYR* 1.3 61.9 + - - +
127B LYS* 4.0 0.3 - - - +
128B ASP* 3.0 45.2 + - - +
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Residues in contact with TYR 125 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99A SER* 3.8 17.9 - - - +
100A PHE* 3.6 35.1 - + - -
276A PRO* 4.0 22.9 - - + -
90B ARG* 5.2 3.1 + - - -
116B PHE* 2.5 32.4 + - - +
117B VAL* 4.2 12.6 - - + -
119B GLN* 3.3 19.4 + - - -
120B ASN* 3.6 21.5 - - - +
122B SER* 3.1 25.4 + - - +
124B THR* 1.3 78.3 - - - +
126B MSE 1.3 62.7 + - + +
128B ASP* 3.7 2.1 - - - +
129B LEU* 2.9 31.2 + - + +
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Residues in contact with MSE 126 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339A LEU* 3.9 15.9 - - + -
359A VAL* 4.2 11.9 - - + -
117B VAL* 3.9 17.9 - - + -
118B GLY 5.2 0.4 - - - +
120B ASN* 3.5 26.7 - - - +
121B ILE* 4.0 13.2 - - - -
122B SER 3.1 17.5 + - - +
125B TYR* 1.3 79.1 - - + +
127B LYS* 1.3 65.6 + - - +
129B LEU* 3.3 6.7 + - - +
130B MSE 3.2 27.1 + - - +
151B GLU 5.2 1.1 - - - +
154B LEU* 5.1 7.6 - - + -
155B ALA* 4.4 23.8 - - + +
158B ILE* 4.0 25.4 - - - -
159B PHE* 3.7 14.8 - - + -
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Residues in contact with LYS 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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337A HIS* 3.8 38.1 - - + +
338A GLU 5.3 2.4 + - - +
339A LEU* 4.1 24.2 - - + +
123B SER 2.8 22.6 + - - +
124B THR 4.0 0.4 - - - +
126B MSE 1.3 72.4 - - - +
128B ASP* 1.3 63.4 + - - +
130B MSE 3.2 33.8 + - + +
131B ASP* 3.7 12.0 + - - +
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Residues in contact with ASP 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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97A ASN 4.9 0.3 - - - +
98A HIS* 3.1 48.8 + - + -
99A SER* 2.7 45.3 + - - -
100A PHE* 3.9 2.4 - - + -
337A HIS* 3.3 24.1 + - - -
124B THR* 3.0 27.7 + - - +
125B TYR 3.7 0.7 - - - +
127B LYS* 1.3 76.2 - - - +
129B LEU* 1.3 63.6 + - - +
131B ASP* 3.1 15.1 + - - +
132B VAL 3.7 1.9 + - - -
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Residues in contact with LEU 129 (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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100A PHE* 3.5 23.3 - - + -
78B LEU* 3.8 14.8 - - + -
115B LEU* 3.5 34.8 - - + -
116B PHE 4.1 8.3 - - - +
117B VAL* 3.7 35.9 - - + -
125B TYR* 2.9 21.0 + - + +
126B MSE 3.3 6.7 + - - +
128B ASP* 1.3 73.1 - - - +
130B MSE 1.3 65.9 - - - +
132B VAL* 3.0 14.4 + - + -
133B LEU* 3.2 17.2 + - + +
159B PHE* 4.3 12.1 - - + -
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Residues in contact with MSE 130 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339A LEU* 4.1 24.0 - - + -
126B MSE 3.2 17.6 + - - +
127B LYS* 3.4 27.4 - - + +
128B ASP 3.2 0.6 - - - -
129B LEU* 1.3 76.4 - - - +
131B ASP* 1.3 64.2 + - - +
133B LEU* 3.3 11.0 + - - +
134B GLU* 3.1 23.2 + - - +
158B ILE* 3.6 31.2 - - + -
159B PHE* 3.9 9.2 - - + -
162B LEU* 3.6 33.9 - - + -
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Residues in contact with ASP 131 (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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98A HIS* 2.7 30.4 + - - +
104A LEU* 4.0 10.1 - - + -
108A GLN* 2.9 27.4 + - - +
127B LYS* 3.7 9.7 + - - +
128B ASP* 3.1 15.7 + - - +
130B MSE 1.3 80.0 - - - +
132B VAL* 1.3 61.1 + - - +
134B GLU* 3.4 14.9 - - - +
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Residues in contact with VAL 132 (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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100A PHE* 3.5 41.3 - - + -
103A THR* 4.2 23.6 - - + +
104A LEU* 4.5 11.7 - - + +
108A GLN* 5.1 1.3 - - - +
76B ILE* 3.7 13.1 - - + +
113B GLN* 4.6 5.8 - - - +
115B LEU* 3.8 22.7 - - + -
128B ASP 4.0 4.9 - - - +
129B LEU* 3.0 13.8 + - + +
131B ASP* 1.3 78.3 - - - +
133B LEU* 1.3 60.9 + - - +
134B GLU 3.3 1.8 - - - +
136B LYS* 3.8 13.5 + - - +
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Residues in contact with LEU 133 (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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76B ILE* 3.7 36.3 - - + -
78B LEU* 4.2 11.9 - - + -
129B LEU* 3.2 23.4 + - + +
130B MSE 3.6 9.6 - - - +
131B ASP 3.3 0.2 - - - -
132B VAL* 1.3 76.8 - - - +
134B GLU* 1.3 64.8 + - - +
135B GLY 3.2 0.3 + - - -
136B LYS* 2.9 25.3 + - - +
138B PHE* 4.1 37.5 - - + -
159B PHE* 3.7 36.8 - - + -
162B LEU* 4.8 4.7 - - + -
166B LYS* 5.5 0.7 - - - -
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Residues in contact with GLU 134 (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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108A GLN* 4.6 8.6 + - - +
130B MSE 3.1 11.7 + - - +
131B ASP* 3.4 19.2 - - - +
132B VAL 3.3 2.7 - - - +
133B LEU* 1.3 76.2 - - - +
135B GLY* 1.3 66.6 + - - +
136B LYS* 3.4 10.6 + - - +
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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