Contacts of the helix formed by residues 122 - 134 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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274E TYR 4.6 2.9 + - - -
275E GLU* 2.7 33.4 + - - -
276E PRO* 3.8 13.9 - - - +
363E ASN* 4.7 0.9 - - - +
120F ASN* 3.1 10.2 + - - -
121F ILE* 1.3 75.8 - - - +
123F SER* 1.3 61.1 + - - +
124F THR* 3.5 2.6 + - - -
125F TYR* 3.0 32.5 + - - +
126F MSE 3.1 25.6 + - - +
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Residues in contact with SER 123 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275E GLU* 5.0 1.2 + - - -
335E SER* 3.3 10.7 + - - -
337E HIS* 2.8 27.0 + - - +
338E GLU* 4.0 2.0 - - - -
339E LEU* 4.0 20.5 - - - +
359E VAL* 3.9 22.7 - - - -
360E ASP* 4.3 11.6 + - - +
121F ILE 3.7 4.6 + - - -
122F SER* 1.3 73.2 - - - +
124F THR* 1.3 56.7 + - - +
126F MSE 3.6 11.1 - - - +
127F LYS* 3.0 33.0 + - - +
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Residues in contact with THR 124 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99E SER* 4.1 5.4 - - - +
275E GLU* 4.4 8.8 + - - +
277E ALA* 6.0 5.8 - - + -
335E SER* 3.3 11.0 + - - -
336E THR* 3.3 18.7 + - + +
337E HIS* 3.2 37.9 + - + +
389E LEU* 6.6 0.4 - - + -
122F SER* 3.2 7.2 + - - -
123F SER* 1.3 75.2 + - - +
125F TYR* 1.3 66.1 + - - +
127F LYS* 4.0 0.9 - - - +
128F ASP* 3.0 44.6 + - - +
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Residues in contact with TYR 125 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99E SER* 3.7 18.8 - - - -
100E PHE* 3.7 33.2 - + - -
276E PRO* 3.9 23.3 - - + -
90F ARG* 5.2 3.8 + - - -
116F PHE* 2.6 33.3 + - - +
117F VAL* 4.3 9.0 - - + -
119F GLN* 3.4 18.5 + - - -
120F ASN* 3.6 21.1 - - - +
122F SER* 3.0 28.7 + - - +
124F THR* 1.3 77.3 - - - +
126F MSE 1.3 66.5 + - + +
128F ASP* 3.4 2.9 + - - +
129F LEU* 3.0 26.3 + - + +
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Residues in contact with MSE 126 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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339E LEU* 3.8 12.1 - - + -
359E VAL* 3.1 43.5 - - + -
117F VAL* 3.8 24.0 - - + -
118F GLY 5.7 0.2 - - - -
120F ASN* 4.8 7.9 - - - +
121F ILE* 4.4 2.9 - - - -
122F SER 3.1 25.3 + - - +
123F SER* 3.6 4.5 - - - -
124F THR 3.3 0.2 - - - -
125F TYR* 1.3 80.1 - - + +
127F LYS* 1.3 64.1 + - - +
129F LEU* 3.3 7.7 + - - +
130F MSE 3.2 26.6 + - - +
154F LEU* 5.8 2.7 - - + -
155F ALA* 4.6 11.4 - - - -
158F ILE* 4.0 19.7 - - - -
159F PHE* 3.7 16.0 - - + -
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Residues in contact with LYS 127 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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337E HIS* 3.9 34.3 - - + +
338E GLU 5.6 1.6 - - - +
339E LEU* 4.2 18.6 - - + +
123F SER 3.0 18.4 + - - +
124F THR 4.0 0.7 - - - +
126F MSE 1.3 76.5 - - - +
128F ASP* 1.3 63.7 + - - +
130F MSE 3.3 43.1 + - - +
131F ASP* 3.6 15.5 + - - +
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Residues in contact with ASP 128 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97E ASN 4.9 0.3 - - - +
98E HIS* 3.2 40.6 + - + -
99E SER* 2.7 45.2 + - - -
100E PHE* 4.0 0.7 - - - -
337E HIS* 3.1 25.0 + - - -
124F THR* 3.0 25.8 + - - +
125F TYR 3.7 0.7 - - - +
127F LYS* 1.3 78.7 - - - +
129F LEU* 1.3 63.2 + - - +
131F ASP* 3.0 24.9 + - - +
132F VAL* 3.6 2.8 + - - +
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Residues in contact with LEU 129 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100E PHE* 3.6 24.6 - - + -
78F LEU* 4.0 14.8 - - + -
115F LEU* 3.4 37.0 - - + -
116F PHE 4.3 6.5 - - - +
117F VAL* 3.6 35.9 - - + -
125F TYR* 3.0 17.4 + - + +
126F MSE 3.3 8.9 + - - +
128F ASP* 1.3 74.3 - - - +
130F MSE 1.3 66.0 + - - +
132F VAL* 2.9 17.0 + - + +
133F LEU* 3.2 17.5 + - + +
159F PHE* 4.0 13.7 - - + -
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Residues in contact with MSE 130 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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339E LEU* 3.9 29.6 - - + -
126F MSE 3.2 14.8 + - - +
127F LYS* 3.4 33.7 - - + +
128F ASP 3.2 0.4 - - - -
129F LEU* 1.3 76.0 - - - +
131F ASP* 1.3 63.7 + - - +
133F LEU* 3.2 11.8 + - - +
134F GLU* 3.0 22.8 + - - +
158F ILE* 3.6 31.0 - - + -
159F PHE* 3.9 10.3 - - + -
162F LEU* 3.7 29.2 - - + -
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Residues in contact with ASP 131 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98E HIS* 2.8 30.6 + - + +
104E LEU* 4.5 8.7 - - + -
108E GLN* 3.8 16.2 + - - +
127F LYS* 3.6 15.5 + - - +
128F ASP* 3.0 17.0 + - - +
130F MSE 1.3 79.6 - - - +
132F VAL* 1.3 59.2 + - - +
134F GLU* 3.3 31.2 - - - +
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Residues in contact with VAL 132 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100E PHE* 3.6 40.2 - - + -
103E THR* 4.3 15.7 - - + +
104E LEU* 4.2 14.8 - - + -
108E GLN* 5.6 0.7 - - - +
76F ILE* 3.7 2.1 - - + +
113F GLN* 4.3 15.3 - - - +
115F LEU* 3.8 25.8 - - + -
128F ASP 4.0 6.1 - - - +
129F LEU* 2.9 12.1 + - + +
131F ASP* 1.3 77.3 - - - +
133F LEU* 1.3 58.2 + - - +
134F GLU 4.0 0.5 - - - +
136F LYS* 3.0 30.2 + - - +
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Residues in contact with LEU 133 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76F ILE* 3.7 33.4 - - + -
78F LEU* 4.4 11.2 - - + -
115F LEU* 4.8 6.3 - - + -
129F LEU* 3.2 15.0 + - + +
130F MSE 3.2 9.4 + - - +
132F VAL* 1.3 75.8 - - - +
134F GLU* 1.3 66.8 + - - +
135F GLY 3.2 0.5 + - - -
136F LYS* 3.0 24.1 + - - +
138F PHE* 4.3 39.5 - - + -
159F PHE* 3.8 34.5 - - + -
162F LEU* 4.7 6.1 - - + -
166F LYS* 5.3 1.0 + - - +
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Residues in contact with GLU 134 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108E GLN* 4.9 14.7 + - - +
130F MSE 3.0 10.2 + - - +
131F ASP* 3.3 33.1 - - - +
132F VAL 3.2 1.6 - - - +
133F LEU* 1.3 76.7 - - - +
135F GLY* 1.3 64.2 + - - +
136F LYS* 3.3 12.0 + - - +
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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