Contacts of the strand formed by residues 43 - 50 (chain B) in PDB entry 1REI
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 ALA 43 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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87A TYR* 3.9 11.2 - - + -
98A PHE* 3.8 12.1 - - + +
99A GLY 3.3 28.0 - - - +
100A GLN* 4.4 6.9 + - - +
37B GLN 4.3 3.1 - - - +
38B GLN* 4.5 5.0 - - - +
39B THR 4.8 0.9 + - - -
42B LYS* 1.3 85.6 - - - +
44B PRO* 1.3 76.0 - - + +
45B LYS* 3.9 2.4 + - - +
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Residues in contact with PRO 44 (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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38A GLN* 6.0 1.3 - - - +
44A PRO* 6.0 6.7 - - + -
87A TYR* 4.3 13.5 - - + -
96A TYR 5.3 0.5 - - - +
97A THR* 5.6 0.7 - - - -
98A PHE* 3.2 59.0 + - + +
36B TYR* 4.3 14.8 - - + -
37B GLN 3.5 9.2 - - - +
38B GLN* 3.7 25.4 - - + +
43B ALA* 1.3 91.9 - - + +
45B LYS* 1.3 61.1 + - - +
46B LEU 4.2 0.2 + - - -
87B TYR* 5.9 2.9 - - + -
98B PHE* 6.3 2.5 - - + -
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Residues in contact with LYS 45 (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 TYR* 3.4 5.2 - - - -
37B GLN* 2.8 60.4 + - - +
43B ALA 5.0 1.6 - - - +
44B PRO* 1.3 74.9 - - - +
46B LEU* 1.3 72.7 + - - +
47B LEU* 3.4 12.7 + - + +
57B GLY 6.4 0.4 - - - -
58B VAL* 4.6 10.3 - - + -
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Residues in contact with LEU 46 (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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94A LEU* 4.2 4.5 - - + -
95A PRO* 4.8 3.3 - - + +
96A TYR* 3.5 57.1 + - + +
34B ASN* 3.8 15.5 - - + -
35B TRP 3.8 3.8 - - - +
36B TYR* 3.8 27.1 - - + +
44B PRO 4.1 1.0 + - - -
45B LYS* 1.3 76.8 - - - +
47B LEU* 1.3 61.5 + - - +
48B ILE 3.7 23.8 - - - +
49B TYR* 4.5 3.8 - - + -
55B GLN* 3.8 35.3 - - + +
58B VAL* 3.7 14.0 - - - +
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Residues in contact with LEU 47 (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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35B TRP* 2.8 14.2 + - + +
36B TYR 4.5 1.3 - - - -
37B GLN* 3.7 46.4 - - + +
45B LYS* 4.2 8.3 - - + +
46B LEU* 1.3 77.6 - - - +
48B ILE* 1.3 72.6 - - + +
54B LEU* 3.4 7.1 - - - +
55B GLN* 3.3 25.2 + - - +
58B VAL* 3.7 31.8 - - + +
59B PRO* 5.6 0.7 - - + -
62B PHE* 3.7 11.7 - - + -
73B PHE* 3.5 33.4 - - + -
86B TYR* 3.7 8.1 - - + -
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Residues in contact with ILE 48 (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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33B LEU 4.6 0.2 - - - +
34B ASN* 3.3 4.5 - - - -
35B TRP* 2.9 42.0 + - + -
46B LEU* 3.7 6.1 - - - +
47B LEU* 1.3 83.7 - - - +
49B TYR* 1.3 62.9 + - - +
51B ALA* 3.3 33.9 - - - +
52B SER 4.1 2.2 - - - +
53B ASN 3.7 7.2 - - - +
54B LEU* 3.7 20.4 - - + +
55B GLN* 4.6 0.4 - - - -
63B SER* 3.6 26.5 - - - -
64B GLY* 3.7 5.6 - - - +
73B PHE* 3.3 40.2 - - + -
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Residues in contact with TYR 49 (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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94A LEU* 3.8 37.9 - - + -
96A TYR* 4.0 26.6 + + - -
34B ASN* 3.2 23.8 - - - +
46B LEU* 4.5 4.5 - - + -
48B ILE* 1.3 75.4 - - - +
50B GLU* 1.3 83.9 + - + +
51B ALA 3.3 1.2 + - - -
52B SER 3.5 0.2 + - - -
53B ASN* 2.9 43.4 + - + +
55B GLN* 3.4 23.3 + - - +
91B TYR* 3.3 30.2 + + - -
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Residues in contact with GLU 50 (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 LYS* 2.3 58.7 + - + +
32B TYR* 4.2 7.9 - - + -
33B LEU 3.8 2.0 - - - +
34B ASN* 3.4 9.1 + - - -
49B TYR* 1.3 95.4 + - + +
51B ALA* 1.3 59.7 + - - +
52B SER* 2.6 18.4 + - - -
53B ASN* 3.6 16.6 - - - +
91B TYR* 3.4 20.7 + - - +
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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