Contacts of the strand formed by residues 251 - 255 (chain 3) in PDB entry 5KZ5
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 251 (chain 3).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1343 ALA* 3.7 29.2 - - + -
1383 VAL* 3.9 16.4 - - + -
2283 TYR* 3.5 43.3 - - + +
2293 PHE 3.0 9.9 + - - +
2303 HIS* 3.7 20.0 - - + +
2313 THR* 3.2 16.5 + - - -
2443 VAL* 5.2 0.4 - - - -
2493 ILE* 3.2 14.8 - - - +
2503 ASP* 1.4 83.1 - - - +
2523 MET* 1.3 59.4 + - - +
2683 ILE* 4.1 3.4 - - + -
2693 TYR 3.3 8.7 - - - +
2703 ILE* 3.6 18.4 - - + -
2783 VAL* 3.9 14.8 - - + -
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Residues in contact with MET 252 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1143 ILE* 3.8 17.7 - - + -
2043 THR* 4.4 1.6 - - + +
2313 THR* 3.7 5.6 - - - +
2333 ALA* 3.6 21.1 - - + -
2423 LEU* 3.9 32.3 - - + -
2433 ASP 3.5 19.5 - - - +
2443 VAL* 3.7 27.8 - - + +
2473 MET* 4.8 1.3 - - + -
2493 ILE* 3.8 23.3 - - + -
2513 LEU* 1.3 75.9 - - - +
2533 SER* 1.4 72.3 + - - +
2543 ILE* 5.5 1.3 - - + -
2683 ILE* 3.5 7.9 - - - -
2693 TYR* 3.1 38.1 + - + +
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Residues in contact with SER 253 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1273 ALA* 4.1 3.8 - - - -
1303 SER* 3.2 32.5 + - - -
1313 ASN* 4.0 1.7 + - - -
2303 HIS* 3.9 14.9 + - - -
2313 THR 3.6 4.8 + - - -
2323 ASP* 3.4 24.5 + - - -
2333 ALA* 3.2 27.7 + - - +
2343 ALA* 3.7 7.7 - - - +
2523 MET* 1.4 76.0 - - - +
2543 ILE* 1.3 62.3 + - - +
2673 ALA 3.7 4.9 - - - -
2683 ILE* 4.7 0.9 - - - +
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Residues in contact with ILE 254 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1103 VAL* 6.5 0.7 - - + -
1143 ILE* 5.1 16.6 - - + -
1243 THR* 4.3 2.6 + - - -
1263 GLY 5.4 0.5 - - - +
1303 SER* 4.8 1.4 + - - -
2333 ALA 4.4 1.8 - - - +
2343 ALA* 4.0 6.3 - - - +
2373 VAL* 3.9 29.4 - - + -
2423 LEU* 4.8 12.1 - - + -
2523 MET* 5.5 2.5 - - + -
2533 SER* 1.3 76.7 + - - +
2553 SER* 1.4 66.8 + - - +
2663 GLY* 3.2 17.0 - - - -
2673 ALA* 3.2 27.9 + - + +
2693 TYR* 3.8 23.1 - - + +
3043 LEU* 4.5 23.1 - - + -
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Residues in contact with SER 255 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1253 SER 4.0 4.7 + - - -
1263 GLY* 3.6 24.7 + - - +
1273 ALA* 4.0 10.9 + - - -
2343 ALA* 3.7 27.3 - - - +
2373 VAL* 3.6 24.6 - - - +
2543 ILE* 1.4 75.8 - - - +
2563 GLY* 1.4 64.3 + - - +
2573 HIS* 3.3 16.5 + - - +
2593 ILE* 4.2 1.9 - - - +
2653 VAL 3.6 9.6 - - - -
2663 GLY* 4.3 1.8 - - - -
3043 LEU* 5.3 0.8 - - - +
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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