Contacts of the strand formed by residues 447 - 452 (chain B) in PDB entry 1GKU
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 GLY 447 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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253B ASN 2.8 11.1 + - - -
254B VAL* 3.7 7.0 - - - -
255B GLU* 3.0 19.6 + - - +
344B ARG 4.1 0.2 - - - -
436B THR* 3.0 32.2 + - - -
446B LYS* 1.3 84.6 - - - +
448B ALA* 1.3 61.7 + - - +
488B LEU* 4.0 5.4 - - - -
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Residues in contact with ALA 448 (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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254B VAL* 3.8 2.5 - - - -
255B GLU 3.5 10.1 - - - +
274B LEU* 4.4 2.9 - - + -
344B ARG 3.9 2.5 + - - +
345B PHE* 3.2 19.3 - - + -
346B ALA* 2.7 33.0 + - - +
436B THR* 3.4 10.0 + - - +
447B GLY* 1.3 75.7 - - - +
449B SER* 1.3 56.0 + - - +
450B PHE* 4.1 14.6 - - + -
484B LEU* 4.3 22.2 - - + -
488B LEU* 4.6 1.3 - - + -
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Residues in contact with SER 449 (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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254B VAL* 3.7 2.4 - - - +
255B GLU 3.1 7.9 + - - +
256B ASP* 3.6 6.9 - - - -
257B VAL* 2.8 29.7 + - - +
346B ALA* 3.5 4.3 - - - -
348B PHE* 3.4 15.8 - - - -
429B TYR* 2.6 40.7 + - - -
433B SER* 3.6 20.1 - - - -
448B ALA* 1.3 74.9 - - - +
450B PHE* 1.3 60.7 + - - +
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Residues in contact with PHE 450 (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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257B VAL* 3.5 38.4 - - + -
259B VAL* 5.4 1.3 - - + -
271B LEU* 3.6 43.7 - - + -
274B LEU* 3.4 32.8 - - + -
345B PHE* 4.2 9.4 - + - -
346B ALA 2.8 21.4 + - - +
347B VAL* 3.3 8.1 - - + +
348B PHE* 2.7 33.4 + - - +
448B ALA* 4.1 11.4 - - + -
449B SER* 1.3 75.3 + - - +
451B LEU* 1.3 56.4 + - - +
452B LEU* 3.9 5.8 - - + -
477B ASP* 5.2 0.7 - - - -
479B VAL* 4.9 3.6 - - + -
481B PHE* 3.9 19.3 - + - -
484B LEU* 4.7 10.1 - - + -
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Residues in contact with LEU 451 (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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257B VAL 2.7 15.4 + - - +
258B ALA* 3.4 1.9 - - + -
259B VAL 2.8 29.6 + - - +
348B PHE* 3.8 11.9 - - + -
350B GLY 3.7 20.0 - - - +
351B CYS* 3.6 28.5 - - - -
352B PRO* 4.4 4.7 - - + -
429B TYR* 4.3 8.7 - - + -
449B SER 3.9 0.2 + - - -
450B PHE* 1.3 71.2 - - - +
452B LEU* 1.3 59.7 + - - +
453B GLU 4.0 0.5 + - - -
459B LEU* 3.8 17.3 - - + +
462B PHE* 3.6 33.0 - - + -
463B ILE* 4.9 0.7 - - + -
474B LYS* 3.8 22.2 - - - +
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Residues in contact with LEU 452 (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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259B VAL* 3.1 22.7 - - + +
261B ASP 3.6 22.4 - - - +
262B GLU* 3.7 16.5 - - + +
267B LEU* 4.9 2.5 - - + -
268B SER* 4.5 21.1 - - - +
271B LEU* 3.8 28.3 - - + -
347B VAL* 4.1 16.2 - - + -
348B PHE 3.1 12.4 + - - +
349B VAL* 4.6 9.2 - - + -
350B GLY* 2.8 31.4 + - - -
450B PHE* 4.0 13.9 - - + +
451B LEU* 1.3 76.1 - - - +
453B GLU* 1.3 60.6 + - - +
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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