Contacts of the strand formed by residues 448 - 456 (chain A) in PDB entry 1LVK
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 TYR 448 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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166A MET* 3.6 29.2 - - + -
167A LEU* 6.5 0.2 - - - -
170A ARG* 3.4 74.3 + - + +
171A GLN* 4.3 3.4 - - - -
172A ASN* 3.3 18.4 - - - +
246A GLN* 3.6 2.3 - - - -
247A PHE* 2.9 32.0 + - + +
248A ASN 4.4 9.6 - - - -
249A ASN* 4.4 5.4 - - + -
446A LYS* 3.6 9.7 - - - +
447A ALA* 1.3 102.3 - - + +
449A PHE* 1.4 65.5 + - - +
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Residues in contact with PHE 449 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166A MET* 4.2 1.8 - - - +
172A ASN* 2.8 43.9 + - + -
173A GLN 3.0 26.4 + - - -
242A PHE* 4.7 2.5 - + - -
244A GLU* 3.5 36.6 - - + +
245A ILE 3.2 15.3 - - - +
246A GLN* 4.3 1.6 - - - -
247A PHE* 4.1 2.0 - - - -
446A LYS* 3.9 22.0 - - + -
448A TYR* 1.4 77.7 - - - +
450A ILE* 1.3 69.2 + - - +
451A GLY* 3.6 12.3 - - - -
644A THR* 3.9 27.1 - - + -
647A THR* 4.4 3.8 - - - -
648A THR* 3.9 19.7 - - + -
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Residues in contact with ILE 450 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162A ALA* 4.1 6.1 - - + +
163A TYR* 3.8 33.9 - - + +
166A MET* 3.7 11.0 - - - -
173A GLN* 3.2 18.2 - - + +
175A LEU* 4.0 26.2 - - + -
192A VAL* 5.7 0.4 - - + -
196A LEU* 4.1 22.7 - - + -
243A ILE 3.7 0.9 - - - +
245A ILE* 2.9 31.4 + - - +
247A PHE* 3.6 29.2 - - + -
449A PHE* 1.3 79.6 - - - +
451A GLY* 1.3 61.0 + - - +
452A VAL* 4.1 4.1 + - + +
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Residues in contact with GLY 451 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173A GLN 2.9 12.8 + - - -
174A SER* 3.3 4.7 - - - -
175A LEU 2.9 25.8 + - - +
242A PHE* 3.8 24.4 - - - -
243A ILE 3.0 9.0 - - - -
244A GLU* 4.2 3.1 - - - -
449A PHE* 3.6 5.5 - - - -
450A ILE* 1.3 74.5 - - - +
452A VAL* 1.3 63.8 + - - +
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Residues in contact with VAL 452 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175A LEU* 3.4 11.9 - - + +
177A ILE* 3.7 30.5 - - + -
189A THR* 3.9 25.8 - - + +
192A VAL* 3.9 26.0 - - + -
193A ILE* 4.9 8.1 - - + -
241A LYS 3.6 1.4 - - - +
242A PHE* 3.2 5.3 - - - -
243A ILE* 2.6 49.0 + - + +
245A ILE* 5.3 5.2 - - + -
450A ILE* 4.6 9.9 - - + +
451A GLY* 1.3 78.5 - - - +
453A LEU* 1.3 64.6 + - - +
454A ASP 3.9 0.5 + - - -
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Residues in contact with LEU 453 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175A LEU 2.8 13.9 + - - +
176A LEU* 4.3 20.9 - - + -
177A ILE* 2.9 28.8 + - - +
178A THR* 5.1 2.5 - - + -
241A LYS 3.4 4.3 - - - +
242A PHE* 3.7 28.0 - - + -
261A TYR* 4.7 1.6 - - + -
452A VAL* 1.3 77.3 - - - +
454A ASP* 1.3 58.3 + - - +
455A ILE* 3.1 38.8 - - + -
474A THR* 6.0 0.2 - - + -
478A LEU* 4.1 31.9 - - + -
641A LEU* 4.0 22.4 - - + -
645A LEU* 4.6 4.5 - - + -
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Residues in contact with ASP 454 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177A ILE 3.5 3.6 - - - -
185A LYS* 3.1 26.7 - - - +
186A THR* 2.8 26.6 + - - -
189A THR* 3.3 24.0 + - + +
237A SER* 4.4 3.1 + - - -
239A PHE 4.8 1.4 - - - +
240A GLY* 3.8 3.3 - - - -
241A LYS* 2.6 58.2 + - - +
452A VAL 3.9 1.2 + - - +
453A LEU* 1.3 70.5 - - - +
455A ILE* 1.3 73.7 + - - +
998A MG 4.3 1.5 - - - -
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Residues in contact with ILE 455 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177A ILE 3.3 4.9 + - - -
178A THR* 3.3 23.3 - - + -
185A LYS* 3.2 19.4 - - - +
240A GLY* 3.6 15.5 - - - -
241A LYS 2.7 36.1 - - - +
261A TYR* 4.5 7.6 - - + -
453A LEU* 3.1 32.5 - - + -
454A ASP* 1.3 94.0 + - - +
456A SER* 1.3 76.9 + - - +
471A ILE* 4.4 14.1 - - + -
474A THR* 4.9 6.7 - - + -
478A LEU* 4.6 8.5 - - + -
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Residues in contact with SER 456 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178A THR* 4.5 0.4 - - - +
179A GLY 3.5 12.0 + - - -
180A GLU* 5.0 3.7 - - - -
181A SER* 5.4 1.5 + - - -
185A LYS* 3.8 7.5 - - - +
240A GLY* 5.8 0.6 - - - -
455A ILE* 1.3 87.8 - - - +
457A GLY* 1.3 81.3 + - - +
458A PHE 4.4 1.2 + - - -
459A GLU* 3.4 27.1 + - - +
471A ILE* 3.9 12.0 - - - +
475A ASN* 2.9 17.7 + - - +
1000A BEF 5.1 4.7 - - - -
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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