Contacts of the strand formed by residues 130 - 139 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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42D VAL* 3.8 24.0 - - + -
43D SER 3.7 3.6 - - - +
44D PRO* 4.3 4.7 - - + -
45D GLN* 3.3 13.2 + - - -
53D ALA* 3.9 22.7 - - + +
56D ALA* 6.2 2.9 - - + -
57D VAL* 4.0 20.2 - - + -
124D VAL 3.6 23.3 - - - +
125D PHE* 5.4 2.9 - - - +
127D PHE* 3.2 26.4 + - + +
128D LYS* 3.0 1.3 - - - +
129D ALA* 1.3 89.0 - - + +
131D ARG* 1.3 62.1 + - - +
132D ALA* 4.3 8.1 - - - +
133D LEU* 4.2 19.1 - - + -
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Residues in contact with ARG 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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43D SER* 2.8 26.2 + - - +
44D PRO 3.7 18.2 + - - +
45D GLN* 3.5 30.5 - - - +
46D PRO* 4.5 11.0 - - - +
94D GLU 4.5 13.3 + - - -
95D ASN* 4.7 7.3 + - - +
130D LEU* 1.3 74.7 - - - +
132D ALA* 1.3 66.4 + - + +
307D HIS* 4.9 2.3 + - - -
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Residues in contact with ALA 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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41D ARG 4.6 0.2 - - - -
42D VAL* 4.2 0.7 - - - +
43D SER* 3.1 39.1 + - - +
125D PHE 6.0 0.2 - - - -
130D LEU* 3.5 6.5 - - - +
131D ARG* 1.3 87.0 - - + +
133D LEU* 1.3 63.6 - - - +
306D ASN* 3.3 38.8 - - + +
307D HIS* 3.6 13.7 - - + +
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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
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40D PHE* 3.8 21.5 - - + -
41D ARG 3.5 9.0 - - - +
42D VAL* 3.7 34.8 - - + -
57D VAL* 4.4 10.3 - - + -
124D VAL* 3.8 42.2 - - + +
125D PHE* 3.2 37.4 - - + +
130D LEU* 4.2 11.2 - - + -
132D ALA* 1.3 76.9 - - - +
134D ARG* 1.3 62.4 + - - +
306D ASN 3.8 1.3 - - - -
307D HIS* 3.2 8.4 + - + +
308D GLY 3.0 18.7 + - - -
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Residues in contact with ARG 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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40D PHE* 3.3 6.2 - - - -
41D ARG* 2.7 47.8 + - + +
125D PHE* 4.1 0.4 - - - -
133D LEU* 1.3 77.7 - - - +
135D LEU* 1.3 63.9 + - - +
136D GLU* 3.1 35.5 + - - -
302D ASP 3.1 24.9 + - - -
304D GLN 3.2 18.6 + - - -
305D LYS* 3.3 25.2 + - - +
306D ASN 4.0 10.1 - - - +
307D HIS 3.9 1.1 + - - -
308D GLY 3.2 24.2 - - - +
309D MET 4.0 3.0 - - - +
310D HIS* 3.6 26.0 - - - +
473D ASP* 2.7 31.1 + - - -
474D THR 5.4 1.6 + - - -
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Residues in contact with LEU 135 (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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38D ALA* 4.0 15.7 - - + -
39D ALA 3.7 8.7 - - - +
40D PHE* 4.0 19.1 - - + -
117D PHE* 5.0 1.6 - - + -
120D ILE* 4.1 9.6 - - + -
121D VAL* 3.7 22.2 - - + -
125D PHE* 4.1 10.8 - - + -
134D ARG* 1.3 71.9 - - - +
136D GLU* 1.3 59.9 + - - +
137D ASP 3.6 20.6 - - - +
138D LEU* 4.1 8.7 - - + -
308D GLY 3.0 12.0 + - - +
309D MET* 3.5 11.2 - - + -
310D HIS 3.0 25.8 + - - -
313D VAL* 3.9 32.5 - - + +
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Residues in contact with GLU 136 (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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39D ALA* 2.9 18.7 + - + +
41D ARG* 2.9 56.1 + - + +
98D ILE* 4.9 2.0 - - + -
134D ARG* 3.1 29.2 + - - +
135D LEU* 1.3 74.7 - - - +
137D ASP* 1.3 57.9 + - - +
310D HIS* 3.8 4.7 - - - +
312D ARG* 2.7 54.0 + - - +
313D VAL* 3.6 4.6 - - - +
363D TYR* 3.8 31.2 + - + +
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Residues in contact with ASP 137 (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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38D ALA* 3.6 3.1 - - - -
39D ALA* 3.1 24.3 + - + +
135D LEU* 3.6 7.5 - - - +
136D GLU* 1.3 81.6 - - - +
138D LEU* 1.3 79.0 + - - +
312D ARG* 3.9 14.9 - - - +
313D VAL* 3.8 7.7 - - - +
316D LYS* 3.0 28.9 + - - +
348D LEU* 5.4 0.5 - - - +
362D ILE* 4.0 8.7 - - - +
363D TYR* 3.1 44.4 + - + -
364D PHE* 3.5 17.2 + - + +
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Residues in contact with LEU 138 (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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36D ILE* 4.4 3.6 - - + -
37D LEU 3.1 9.9 - - - +
38D ALA* 3.6 28.9 - - + -
116D MET* 4.1 28.0 - - + -
117D PHE* 4.4 4.7 - - + -
120D ILE* 3.8 26.2 - - + -
135D LEU* 4.1 16.2 - - + -
137D ASP* 1.3 83.6 + - - +
139D ARG* 1.3 57.1 + - - +
140D ILE* 3.6 14.3 + - + +
313D VAL* 3.9 24.7 - - + +
316D LYS* 2.6 37.8 + - + +
364D PHE* 3.9 3.6 - - - -
366D GLN* 3.5 1.9 - - - +
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Residues in contact with ARG 139 (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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31D THR* 5.0 2.0 + - - -
32D LEU 3.0 25.1 + - - -
33D ASP* 4.0 19.3 + - - +
35D ASP 2.8 30.7 + - - +
36D ILE* 3.4 2.8 - - - +
37D LEU* 2.7 65.9 + - + +
138D LEU* 1.3 72.3 - - - +
140D ILE* 1.3 69.5 + - - +
141D PRO* 3.4 10.8 - - - +
364D PHE* 3.6 18.8 - - + -
365D THR 3.5 25.9 + - - +
366D GLN* 3.8 5.4 - - - +
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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