Contacts of the strand formed by residues 130 - 139 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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42B VAL* 3.8 24.7 - - + -
43B SER 3.8 4.5 - - - +
44B PRO* 4.4 3.1 - - + -
45B GLN* 3.5 7.8 + - - -
53B ALA* 3.9 23.3 - - + +
56B ALA* 6.0 3.4 - - + -
57B VAL* 4.1 19.1 - - + -
124B VAL 3.6 23.8 - - - +
125B PHE* 5.3 2.5 - - - +
127B PHE* 3.1 26.3 + - + +
128B LYS* 3.0 6.7 - - - +
129B ALA* 1.3 89.7 - - + +
131B ARG* 1.3 61.4 + - - +
132B ALA* 4.3 7.6 - - - +
133B LEU* 4.1 18.8 - - + -
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Residues in contact with ARG 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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43B SER* 2.8 28.5 + - - +
44B PRO 3.6 18.9 + - - +
45B GLN* 3.5 32.3 - - - +
46B PRO* 4.4 8.1 - - - -
94B GLU 4.8 10.9 + - - -
95B ASN* 4.9 6.0 + - - +
130B LEU* 1.3 74.4 - - - +
132B ALA* 1.3 65.6 + - + +
306B ASN* 6.0 2.4 - - - +
307B HIS* 5.0 1.7 + - - -
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Residues in contact with ALA 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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41B ARG 4.6 0.2 - - - -
42B VAL* 4.2 0.3 - - - +
43B SER* 3.1 37.4 + - - +
125B PHE 6.0 0.7 - - - -
130B LEU* 3.5 6.6 - - - +
131B ARG* 1.3 84.8 - - + +
133B LEU* 1.3 65.4 + - - +
306B ASN* 3.3 38.6 - - + +
307B HIS* 3.7 12.6 - - + +
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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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40B PHE* 3.8 19.5 - - + -
41B ARG 3.5 16.4 - - - +
42B VAL* 3.7 26.9 - - + -
57B VAL* 4.3 9.4 - - + -
124B VAL* 3.9 26.7 - - + +
125B PHE* 3.1 53.6 - - + +
130B LEU* 4.1 12.8 - - + -
132B ALA* 1.3 78.0 - - - +
134B ARG* 1.3 63.3 + - - +
306B ASN 3.7 2.0 - - - -
307B HIS* 3.2 10.7 + - + +
308B GLY 3.0 18.7 + - - -
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Residues in contact with ARG 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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40B PHE* 3.4 6.8 - - - -
41B ARG* 2.6 47.5 + - + +
125B PHE* 4.5 0.2 - - - -
133B LEU* 1.3 77.7 - - - +
135B LEU* 1.3 63.3 + - - +
136B GLU* 2.9 33.8 + - - -
302B ASP 3.2 22.8 + - - -
304B GLN 3.2 18.2 + - - -
305B LYS* 3.2 28.8 + - - +
306B ASN 3.9 11.2 - - - +
307B HIS 3.9 0.6 + - - -
308B GLY 3.2 24.5 - - - +
309B MET 4.1 2.9 - - - +
310B HIS* 3.4 27.3 - - - +
473B ASP* 2.7 29.5 + - - -
474B THR 5.2 2.0 + - - -
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Residues in contact with LEU 135 (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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38B ALA* 4.0 15.3 - - + -
39B ALA 3.7 9.6 - - - +
40B PHE* 3.9 25.1 - - + -
117B PHE* 4.9 0.9 - - + -
120B ILE* 4.1 9.4 - - + -
121B VAL* 3.8 22.4 - - + -
125B PHE* 4.1 5.6 - - + -
134B ARG* 1.3 71.9 - - - +
136B GLU* 1.3 58.8 + - - +
137B ASP 3.6 21.1 - - - +
138B LEU* 4.2 8.3 - - + -
308B GLY 3.0 12.0 + - - +
309B MET* 3.5 11.8 - - + -
310B HIS* 3.0 26.3 + - - +
313B VAL* 3.9 31.9 - - + +
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Residues in contact with GLU 136 (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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39B ALA* 2.9 18.5 + - + +
41B ARG* 2.8 53.8 + - + +
98B ILE* 4.8 2.7 - - + -
134B ARG* 2.9 32.0 + - - +
135B LEU* 1.3 73.7 - - - +
137B ASP* 1.3 58.7 + - - +
310B HIS* 3.8 6.0 - - - +
312B ARG* 2.8 52.4 + - - +
313B VAL* 3.5 4.8 - - - +
363B TYR* 3.8 30.1 - - + +
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Residues in contact with ASP 137 (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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38B ALA* 3.5 2.9 - - - -
39B ALA* 3.0 23.9 + - + -
135B LEU* 3.6 7.9 - - - +
136B GLU* 1.3 80.5 - - - +
138B LEU* 1.3 77.3 + - - +
312B ARG* 4.0 15.5 - - - +
313B VAL* 3.7 6.4 - - - +
316B LYS* 3.1 28.0 + - - +
348B LEU* 5.5 0.3 - - - +
362B ILE* 3.9 6.4 - - - +
363B TYR* 3.0 45.2 + - + -
364B PHE* 3.4 20.7 + - + +
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Residues in contact with LEU 138 (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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36B ILE* 4.2 5.2 - - + -
37B LEU 3.2 9.2 - - - +
38B ALA* 3.7 26.5 - - + -
116B MET* 4.3 22.4 - - + -
117B PHE* 4.2 14.1 - - + -
120B ILE* 3.7 24.0 - - + -
135B LEU* 4.2 13.7 - - + -
137B ASP* 1.3 84.0 + - - +
139B ARG* 1.3 57.5 + - - +
140B ILE* 3.6 14.6 + - + -
313B VAL* 3.9 26.1 - - + +
316B LYS* 2.6 38.8 + - + +
364B PHE* 3.9 3.1 - - - -
366B GLN* 3.5 1.7 - - - +
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Residues in contact with ARG 139 (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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31B THR* 5.1 2.0 + - - -
32B LEU 3.0 25.7 + - - -
33B ASP* 4.0 19.1 + - - +
35B ASP 2.8 30.5 + - - +
36B ILE* 3.4 2.8 - - - +
37B LEU* 2.7 67.1 + - + +
138B LEU* 1.3 71.0 - - - +
140B ILE* 1.3 71.1 + - - +
141B PRO* 3.3 11.8 - - - +
364B PHE* 3.7 19.4 - - + -
365B THR 3.6 24.4 + - - +
366B GLN* 3.7 4.0 - - - +
367B SER 6.3 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