Contacts of the strand formed by residues 253 - 261 (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 ILE 253 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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196A LEU* 4.0 20.6 - - + +
197A ALA* 4.0 15.0 - - - +
200A ALA* 3.1 18.1 + - + +
202A ARG* 3.0 22.1 + - - +
211A LEU* 4.0 11.3 - - + +
212A GLU* 4.3 15.5 - - + +
215A ILE* 3.7 30.5 - - + -
245A ILE* 3.7 20.2 - - + -
246A GLN 3.2 10.8 - - - +
247A PHE* 3.6 17.3 - - + -
252A PHE* 1.3 69.8 - - - +
254A SER* 1.3 62.2 - - - +
255A GLY 3.8 7.0 - - - +
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Residues in contact with SER 254 (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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202A ARG* 4.4 7.2 - - - +
211A LEU* 3.6 12.9 - - - +
246A GLN* 2.5 20.2 + - - +
247A PHE 3.1 21.5 + - - -
248A ASN* 3.8 18.8 - - - -
252A PHE 3.2 1.1 + - - -
253A ILE* 1.3 74.7 - - - +
255A GLY* 1.3 54.8 + - - -
441A LEU 4.5 0.7 - - - +
443A SER* 4.0 18.8 - - - -
445A ARG 5.7 1.1 - - - -
446A LYS* 4.2 7.6 - - - +
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Residues in contact with GLY 255 (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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211A LEU* 3.8 11.7 - - - +
215A ILE* 4.0 5.4 - - - +
245A ILE* 3.9 1.0 - - - -
246A GLN* 2.9 32.7 + - - +
253A ILE* 3.6 9.0 - - - +
254A SER* 1.3 83.7 + - - +
256A ALA* 1.3 64.0 + - - +
441A LEU 3.2 13.9 - - - -
443A SER* 4.7 0.2 - - - -
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Residues in contact with ALA 256 (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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215A ILE* 4.2 17.3 - - + -
243A ILE* 5.1 2.2 - - + -
244A GLU 2.9 15.3 - - - +
245A ILE* 3.9 17.9 - - + -
246A GLN* 3.4 9.3 + - - -
255A GLY* 1.3 76.9 - - - +
257A SER* 1.3 63.6 + - - +
258A ILE* 6.1 0.7 - - + -
438A ASN* 4.3 0.9 - - - +
441A LEU* 3.0 22.7 + - + +
442A CYS* 3.2 24.9 + - - +
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Residues in contact with SER 257 (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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242A PHE 3.8 0.9 - - - +
243A ILE* 3.4 4.2 - - - +
244A GLU* 2.7 52.4 + - - +
246A GLN* 3.8 11.4 - - - -
256A ALA* 1.3 77.7 - - - +
258A ILE* 1.3 68.2 + - - +
438A ASN* 3.4 17.2 + - - -
442A CYS* 4.0 10.6 - - - +
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Residues in contact with ILE 258 (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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218A ALA* 4.3 11.4 - - + -
219A ASN* 5.0 8.3 - - - +
222A LEU* 3.8 31.9 - - + -
239A PHE* 5.8 0.2 - - + -
241A LYS* 4.5 12.1 - - + -
242A PHE 3.6 4.9 - - - +
243A ILE* 4.3 17.7 - - + -
256A ALA* 6.1 0.9 - - + -
257A SER* 1.3 79.5 + - - +
259A GLN* 1.3 74.4 + - - +
260A SER* 4.5 2.0 - - - +
434A VAL* 3.4 18.0 - - + +
437A ILE* 4.2 23.6 - - + -
438A ASN* 2.8 31.3 + - - +
441A LEU* 5.1 5.6 - - + -
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Residues in contact with GLN 259 (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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241A LYS* 3.1 7.3 - - - +
242A PHE* 2.8 49.2 + - + +
257A SER 4.3 0.2 - - - -
258A ILE* 1.3 76.9 + - - +
260A SER* 1.4 75.1 + - - +
261A TYR* 3.0 44.8 - - + +
637A GLN* 3.7 22.6 + - - +
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Residues in contact with SER 260 (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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222A LEU* 6.3 0.4 - - - -
239A PHE* 4.0 9.6 - - - -
240A GLY 3.2 8.1 - - - -
241A LYS* 4.5 0.4 - - - +
258A ILE* 4.2 3.6 + - - +
259A GLN* 1.4 90.6 - - - +
261A TYR* 1.3 65.7 + - - +
263A LEU* 6.3 0.2 - - - -
430A PHE* 3.7 33.4 - - - -
431A LEU* 4.9 10.7 - - - +
434A VAL* 4.2 15.7 - - - +
637A GLN* 4.8 1.4 - - - +
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Residues in contact with TYR 261 (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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239A PHE* 3.3 3.6 - - - +
240A GLY* 2.7 49.6 + - - +
241A LYS 4.1 1.3 - - - -
242A PHE* 3.8 21.6 - - + +
259A GLN* 3.0 49.1 - - + +
260A SER* 1.3 78.7 - - - +
262A LEU* 1.3 72.4 + - + +
263A LEU* 3.3 2.6 + - - -
453A LEU* 4.7 7.0 - - + -
455A ILE* 4.5 6.5 - - + -
634A TYR* 5.4 11.0 - + + -
637A GLN* 4.0 34.8 + - + -
638A LEU* 5.9 0.7 - - - -
641A LEU* 4.0 25.8 - - + +
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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