Contacts of the strand formed by residues 130 - 139 (chain C) in PDB entry 1IR1
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 LEU 130 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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42C VAL* 4.0 12.6 - - + -
43C SER 3.8 4.7 - - - +
44C PRO* 4.4 3.4 - - + -
45C GLN* 3.4 13.6 + - - -
53C ALA* 3.8 32.8 - - + +
56C ALA* 5.9 3.8 - - + -
57C VAL* 4.1 20.4 - - + -
124C VAL 3.7 23.6 - - - +
125C PHE* 5.5 2.9 - - - +
127C PHE* 3.1 26.2 + - + +
128C LYS* 3.0 1.6 - - - +
129C ALA* 1.3 90.8 - - + +
131C ARG* 1.3 61.7 + - - +
132C ALA* 4.2 7.9 - - - +
133C LEU* 4.3 19.3 - - + -
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Residues in contact with ARG 131 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43C SER* 2.7 26.9 + - - +
44C PRO 3.1 25.4 + - - +
45C GLN* 3.6 29.4 - - - +
46C PRO* 4.2 11.0 - - - -
94C GLU* 4.4 9.9 + - - +
95C ASN* 3.6 29.6 + - - +
96C GLN* 6.0 0.8 - - - +
130C LEU* 1.3 74.2 - - - +
132C ALA* 1.3 65.5 + - + +
307C HIS* 5.0 1.7 + - - -
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Residues in contact with ALA 132 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41C ARG 4.6 0.2 - - - -
42C VAL* 4.2 0.7 - - - -
43C SER* 3.1 39.2 + - - +
125C PHE 6.0 0.4 - - - -
130C LEU* 3.5 8.0 - - - +
131C ARG* 1.3 84.5 - - + +
133C LEU* 1.3 64.4 + - - +
306C ASN* 3.4 37.2 - - + +
307C HIS* 3.7 12.6 - - + +
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Residues in contact with LEU 133 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40C PHE* 3.9 20.0 - - + -
41C ARG 3.5 9.4 - - - +
42C VAL* 3.7 34.8 - - + -
57C VAL* 4.4 10.5 - - + -
124C VAL* 3.7 39.9 - - + +
125C PHE* 3.1 36.6 - - + +
130C LEU* 4.3 11.7 - - + -
132C ALA* 1.3 78.5 - - - +
134C ARG* 1.3 63.0 + - - +
306C ASN 3.6 2.4 + - - -
307C HIS* 3.2 10.3 + - - -
308C GLY 3.0 18.5 + - - -
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Residues in contact with ARG 134 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40C PHE* 3.4 6.8 - - - -
41C ARG* 2.7 46.3 + - + +
125C PHE* 4.5 0.2 - - - -
133C LEU* 1.3 76.4 - - - +
135C LEU* 1.3 62.6 + - - +
136C GLU* 3.0 36.0 + - - -
302C ASP 3.0 25.1 + - - -
304C GLN 3.1 19.1 + - - -
305C LYS* 3.3 26.4 - - - +
306C ASN 3.9 11.0 - - - +
307C HIS 3.9 0.8 + - - -
308C GLY 3.1 26.0 - - - +
309C MET 4.0 3.0 - - - +
310C HIS* 3.5 24.6 - - - +
473C ASP* 2.8 30.3 + - - -
474C THR 5.2 1.2 + - - -
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Residues in contact with LEU 135 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38C ALA* 4.0 17.3 - - + -
39C ALA 3.7 8.5 - - - +
40C PHE* 3.8 24.9 - - + -
117C PHE* 5.1 1.1 - - + -
120C ILE* 3.9 10.5 - - + -
121C VAL* 3.7 23.3 - - + -
125C PHE* 4.1 4.3 - - + -
134C ARG* 1.3 71.8 - - - +
136C GLU* 1.3 58.0 + - - +
137C ASP 3.6 18.8 - - - +
138C LEU* 4.0 11.7 - - + -
308C GLY 2.9 13.0 + - - +
309C MET* 3.5 10.8 - - + -
310C HIS 3.0 25.3 + - - -
313C VAL* 4.0 28.0 - - + +
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Residues in contact with GLU 136 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39C ALA* 2.9 18.9 + - + +
41C ARG* 2.9 51.1 + - + +
98C ILE* 4.9 2.2 - - + -
134C ARG* 3.0 32.9 + - - +
135C LEU* 1.3 73.4 - - - +
137C ASP* 1.3 58.3 + - - +
310C HIS* 3.7 6.5 - - - +
312C ARG* 2.8 53.5 + - - +
313C VAL* 3.5 4.9 - - - +
363C TYR* 3.8 30.3 - - + +
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Residues in contact with ASP 137 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39C ALA* 3.1 24.2 + - + +
135C LEU* 3.6 3.5 - - - +
136C GLU* 1.3 80.4 - - - +
138C LEU* 1.3 84.8 + - - +
312C ARG* 3.9 15.7 - - - +
313C VAL* 3.8 7.9 - - - +
316C LYS* 3.1 28.1 + - - +
348C LEU* 5.5 0.5 - - - +
362C ILE* 3.9 8.3 - - - +
363C TYR* 3.1 45.5 + - + -
364C PHE* 3.4 18.9 + - + +
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Residues in contact with LEU 138 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36C ILE* 4.4 7.9 - - + -
37C LEU 3.2 6.7 - - - +
38C ALA* 3.6 23.8 - - + -
116C MET* 4.1 30.3 - - + -
117C PHE* 4.5 4.3 - - + -
120C ILE* 3.9 22.7 - - + -
135C LEU* 4.0 14.1 - - + -
137C ASP* 1.3 89.2 + - - +
139C ARG* 1.3 56.1 + - - +
140C ILE* 3.6 11.6 + - + -
313C VAL* 4.0 26.4 - - + +
316C LYS* 2.6 39.6 + - + +
364C PHE* 4.0 3.4 - - - -
366C GLN* 3.4 2.4 - - - +
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Residues in contact with ARG 139 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31C THR* 5.1 2.4 + - - -
32C LEU 3.0 24.2 + - - -
33C ASP* 3.9 18.9 + - - +
35C ASP 2.8 31.3 + - - +
36C ILE* 3.4 3.1 - - - +
37C LEU* 2.7 62.1 + - + +
138C LEU* 1.3 69.2 - - - +
140C ILE* 1.3 71.0 + - - +
141C PRO* 3.4 10.8 - - - +
364C PHE* 3.6 25.0 - - + -
365C THR 3.6 26.3 + - - +
366C GLN* 3.8 4.9 - - - +
367C SER 6.2 0.2 - - - +
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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
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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