Contacts of the helix formed by residues 122 - 134 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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274C TYR 4.7 2.0 - - - -
275C GLU* 2.8 33.7 + - - -
276C PRO* 3.8 13.3 - - - +
363C ASN* 4.8 1.3 - - - +
120D ASN* 3.0 15.5 + - - +
121D ILE* 1.3 75.0 - - - +
123D SER* 1.3 64.0 + - - +
124D THR 3.5 1.6 + - - -
125D TYR* 3.0 26.5 + - - +
126D MSE 3.1 26.7 + - - +
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Residues in contact with SER 123 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275C GLU* 5.1 1.0 + - - -
335C SER* 3.3 10.6 + - - -
337C HIS 2.9 24.3 + - - -
338C GLU* 4.3 1.2 - - - -
339C LEU* 3.9 20.7 - - - +
359C VAL* 3.8 21.7 - - - +
360C ASP* 4.2 14.1 + - - +
121D ILE 3.7 4.6 + - - -
122D SER* 1.3 72.6 - - - +
124D THR* 1.3 56.5 + - - +
126D MSE 3.9 9.6 - - - -
127D LYS* 2.8 34.6 + - - +
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Residues in contact with THR 124 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99C SER* 3.9 5.8 - - - +
275C GLU* 4.3 10.0 + - - +
335C SER* 3.1 19.2 + - - -
336C THR* 3.4 26.0 + - + +
337C HIS* 3.4 22.1 + - + -
122D SER* 3.2 7.3 + - - -
123D SER* 1.3 79.8 + - - +
125D TYR* 1.3 57.3 + - - +
127D LYS* 3.8 0.5 - - - +
128D ASP* 2.9 49.4 + - - +
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Residues in contact with TYR 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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99C SER* 3.7 19.3 - - - +
100C PHE* 3.7 34.4 - + - -
276C PRO* 4.0 22.4 - - + -
90D ARG* 5.3 2.8 + - - -
116D PHE* 2.6 32.7 + - - +
117D VAL* 4.2 11.7 - - + -
119D GLN* 3.3 16.0 + - - -
120D ASN* 3.6 22.0 - - - -
122D SER* 3.0 26.0 + - - +
124D THR* 1.3 77.8 - - - +
126D MSE 1.3 64.3 + - + +
128D ASP* 3.4 2.6 + - - +
129D LEU* 2.9 27.7 + - + +
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Residues in contact with MSE 126 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339C LEU* 3.9 8.7 - - + -
359C VAL* 3.5 44.4 - - + -
117D VAL* 3.7 19.7 - - + -
118D GLY 5.5 0.4 - - - +
120D ASN* 4.8 10.5 - - - +
121D ILE* 5.0 0.9 - - - -
122D SER 3.1 18.8 + - - +
123D SER* 3.9 6.1 - - - +
125D TYR* 1.3 78.2 - - + +
127D LYS* 1.3 66.0 + - - +
129D LEU* 3.2 4.6 + - - +
130D MSE 3.2 27.4 + - + +
154D LEU* 5.4 3.1 - - + -
155D ALA* 4.2 18.4 - - - -
158D ILE* 3.7 20.0 - - + -
159D PHE* 3.7 21.8 - - + -
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Residues in contact with LYS 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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337C HIS* 3.7 38.1 - - + +
338C GLU 5.2 3.3 + - - +
339C LEU* 4.1 27.1 - - + +
123D SER 2.8 21.1 + - - +
124D THR 3.8 1.3 - - - +
126D MSE 1.3 73.3 - - - +
128D ASP* 1.3 62.3 + - - +
130D MSE 3.3 32.5 + - + +
131D ASP* 3.8 12.6 + - - +
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Residues in contact with ASP 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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97C ASN 4.8 0.2 - - - +
98C HIS* 3.2 51.3 + - + -
99C SER* 2.7 44.4 + - - -
100C PHE* 3.9 1.1 - - - -
337C HIS* 3.2 23.8 + - - -
124D THR* 2.9 26.1 + - - +
125D TYR 3.7 0.7 - - - +
127D LYS* 1.3 74.8 - - - +
129D LEU* 1.3 65.7 + - - +
131D ASP* 3.1 14.9 + - - +
132D VAL* 3.6 3.3 + - - +
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Residues in contact with LEU 129 (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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100C PHE* 3.7 24.2 - - + -
78D LEU* 3.5 28.0 - - + -
115D LEU* 3.4 37.0 - - + -
116D PHE 4.4 5.6 - - - +
117D VAL* 3.7 24.7 - - + -
125D TYR* 2.9 19.4 + - + +
126D MSE 3.2 6.0 + - - +
128D ASP* 1.3 75.8 - - - +
130D MSE 1.3 57.5 + - - +
132D VAL* 2.8 24.9 + - + +
133D LEU* 3.2 16.0 + - + +
159D PHE* 3.9 13.2 - - + -
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Residues in contact with MSE 130 (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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339C LEU* 4.1 26.2 - - + -
126D MSE 3.2 15.0 + - - +
127D LYS* 3.5 28.3 - - + +
128D ASP 3.2 0.8 - - - -
129D LEU* 1.3 76.0 - - - +
131D ASP* 1.3 61.8 + - - +
133D LEU* 3.3 12.4 + - - +
134D GLU* 3.1 25.3 + - - +
158D ILE* 3.5 32.1 - - + -
159D PHE* 4.0 9.0 - - + -
162D LEU* 3.6 31.4 - - + +
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Residues in contact with ASP 131 (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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98C HIS* 2.9 29.3 + - - +
104C LEU* 4.0 11.4 - - + -
108C GLN* 3.1 28.3 + - - +
127D LYS* 4.0 13.3 - - - +
128D ASP* 3.1 14.1 + - - +
130D MSE 1.3 79.9 - - - +
132D VAL* 1.3 60.7 + - - +
134D GLU* 3.6 14.6 + - - +
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Residues in contact with VAL 132 (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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100C PHE* 3.4 40.8 - - + -
103C THR* 4.1 24.0 - - + +
104C LEU* 4.6 11.0 - - + +
108C GLN* 5.5 1.3 - - - -
76D ILE* 3.8 14.0 - - + +
113D GLN* 4.7 4.3 - - - +
115D LEU* 3.7 24.9 - - + -
128D ASP 3.9 5.2 - - - +
129D LEU* 2.8 15.0 + - + +
131D ASP* 1.3 78.6 - - - +
133D LEU* 1.3 60.1 + - - +
134D GLU 3.6 1.6 + - - +
136D LYS* 3.9 12.6 + - - +
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Residues in contact with LEU 133 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76D ILE* 3.8 29.8 - - + -
78D LEU* 4.4 8.7 - - + -
115D LEU* 5.1 0.2 - - + -
129D LEU* 3.2 19.9 + - + +
130D MSE 3.3 8.2 + - - +
132D VAL* 1.3 77.1 - - - +
134D GLU* 1.3 66.5 + - - +
135D GLY 3.3 0.7 + - - -
136D LYS* 3.1 23.3 + - - +
138D PHE* 3.9 46.7 - - + -
159D PHE* 3.8 35.0 - - + -
162D LEU* 4.3 9.6 - - + -
166D LYS* 5.3 1.9 - - - +
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Residues in contact with GLU 134 (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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108C GLN* 4.9 7.1 + - - +
130D MSE 3.1 14.3 + - - +
131D ASP* 3.6 17.8 - - - +
132D VAL 3.3 3.0 - - - +
133D LEU* 1.3 77.4 - - - +
135D GLY* 1.3 64.6 + - - +
136D LYS* 3.3 9.9 + - - +
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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