Contacts of the strand formed by residues 57 - 64 (chain B) in PDB entry 5X6E
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 ILE 57 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136A ILE* 5.5 3.3 - - - +
49B THR* 4.5 17.3 - - + -
50B SER 3.3 9.0 - - - +
51B ILE* 4.2 22.2 - - + -
55B GLY 3.6 13.9 - - - +
56B THR* 1.3 74.7 - - - +
58B MET* 1.3 63.3 + - - +
59B ASN* 4.3 6.5 - - - +
176B TYR* 3.3 53.4 - - + +
180B ILE 5.7 0.3 - - - +
181B ALA* 6.0 3.8 - - - +
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Residues in contact with MET 58 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131A PHE* 3.5 26.9 - - + -
132A ASN* 3.3 35.2 - - - +
135A SER* 3.4 32.8 - - - +
136A ILE* 4.5 15.7 - - + -
49B THR* 3.4 4.0 - - - -
50B SER 3.0 30.4 + - - +
56B THR 5.7 0.2 - - - +
57B ILE* 1.3 76.5 - - - +
59B ASN* 1.3 67.2 + - - +
60B LEU* 3.2 17.1 + - + +
176B TYR* 3.8 6.7 - - - +
177B SER 3.9 1.6 - - - +
178B SER 3.2 28.3 - - - +
179B GLY* 4.8 0.7 - - - +
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Residues in contact with ASN 59 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B LYS* 3.6 10.2 + - + +
48B LEU 3.9 5.4 - - - +
49B THR* 3.2 21.5 - - - +
57B ILE* 4.3 2.4 - - - +
58B MET* 1.3 72.2 - - - +
60B LEU* 1.3 65.5 + - - +
61B GLN 3.5 2.7 - - - +
62B TYR* 3.8 7.8 + - + +
130B LYS* 4.8 0.2 + - - -
173B GLU* 2.8 44.4 + - - +
176B TYR* 2.8 38.1 + - - +
177B SER* 3.3 32.0 + - - +
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Residues in contact with LEU 60 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128A LEU* 4.1 27.4 - - + +
131A PHE* 3.7 25.9 - - + -
132A ASN* 3.7 32.3 - - + +
48B LEU* 3.1 30.7 + - + +
50B SER* 5.0 1.6 - - - -
58B MET* 3.2 16.3 + - + +
59B ASN* 1.3 72.4 - - - +
61B GLN* 1.3 58.1 + - + +
83B TYR* 3.5 38.6 - - + -
130B LYS* 2.7 31.3 + - - +
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Residues in contact with GLN 61 (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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128A LEU* 4.0 14.6 - - + +
47B LYS* 3.6 1.7 - - - +
48B LEU* 2.9 29.5 + - + +
59B ASN* 3.5 3.2 - - - +
60B LEU* 1.3 85.0 - - + +
62B TYR* 1.3 75.3 + - - +
63B TYR* 3.0 33.2 + - + -
123B GLN* 3.3 25.9 + - - +
126B TYR* 3.7 24.0 - - + -
127B SER* 4.5 1.4 + - - -
130B LYS* 4.1 2.7 - - - +
301B GSH 3.1 36.5 - - - +
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Residues in contact with TYR 62 (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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45B ILE* 4.7 2.2 - - + -
46B THR 3.4 16.4 - - - +
47B LYS* 3.8 26.5 - - + -
59B ASN* 3.8 6.4 + - + -
61B GLN* 1.3 89.4 - - - +
63B TYR* 1.3 63.1 + - - +
88B ILE* 4.5 11.5 - - + +
146B GLN* 4.2 9.9 - - - -
150B LEU* 3.9 25.6 - - + -
154B TYR* 3.2 23.1 - + - +
166B LEU* 5.1 11.4 - - + +
168B ASN* 6.2 0.4 - - - -
169B LEU* 4.9 7.5 - - + +
173B GLU* 3.7 25.1 + - - +
174B LEU* 5.9 0.2 - - - -
177B SER* 3.7 16.8 + - - -
301B GSH 2.7 46.2 + - - +
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Residues in contact with TYR 63 (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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128A LEU* 4.6 0.7 - - - +
41B LEU* 4.2 4.7 - - + +
44B GLY 3.9 0.9 - - - +
45B ILE* 3.1 3.5 - - - +
46B THR* 2.6 57.8 + - + +
48B LEU* 4.2 30.3 - - + +
61B GLN* 3.0 39.9 + - + -
62B TYR* 1.3 75.9 - - - +
64B LYS* 1.3 59.8 + - - +
67B PHE* 3.4 43.3 - + + -
69B ILE* 3.6 33.8 - - + +
85B LEU* 5.0 2.0 - - + -
123B GLN* 2.9 28.6 + - - -
154B TYR* 4.3 0.2 - - - -
301B GSH 3.3 7.4 - - - +
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Residues in contact with LYS 64 (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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44B GLY 3.3 5.2 - - - -
45B ILE* 3.7 25.8 - - + -
63B TYR* 1.3 74.4 - - - +
65B GLY* 1.3 73.1 + - - +
67B PHE* 4.4 0.9 - - - +
153B VAL* 3.7 38.9 + - + +
154B TYR* 3.7 18.6 + - + +
156B LYS* 5.2 7.3 - - - +
301B GSH 3.1 40.2 + - + +
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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