Contacts of the strand formed by residues 450 - 460 (chain A) in PDB entry 4CFE
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 450 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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441A ARG* 3.9 42.2 - - + -
442A ARG 3.6 2.2 - - - +
443A LYS* 3.9 39.6 + - + +
448A GLY 4.3 9.0 - - - -
449A ASN* 1.3 80.9 - - - +
451A VAL* 1.3 62.2 + - - +
452A LYS* 4.0 8.9 + - - +
535A HIS* 6.1 1.4 - - - -
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Residues in contact with VAL 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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441A ARG* 3.3 1.4 - - - -
442A ARG* 2.6 53.9 + - + +
444A ASN* 4.4 8.7 - - + +
449A ASN* 4.4 7.2 - - + +
450A TYR* 1.3 77.4 - - - +
452A LYS* 1.3 62.6 + - - +
535A HIS 5.4 0.7 - - - +
538A ASP* 3.4 59.7 - - + +
539A PHE* 4.2 6.7 - - + +
542A MET* 3.4 21.4 - - - +
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Residues in contact with LYS 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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439A ARG* 3.1 41.2 - - - +
440A VAL 3.3 15.3 - - - +
441A ARG* 3.8 27.3 - - + +
450A TYR* 5.2 9.2 - - - +
451A VAL* 1.3 78.1 - - - +
453A MET* 1.3 63.0 + - - +
471A SER* 4.7 0.5 - - - -
472A ILE* 3.5 45.3 + - + +
473A ASP 5.7 3.8 - - - -
535A HIS* 5.9 0.2 - - - -
539A PHE* 5.3 1.6 - - - -
542A MET* 4.9 1.1 - - - -
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Residues in contact with MET 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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428A PHE* 5.1 0.9 - - + -
439A ARG* 3.7 1.7 - - - -
440A VAL* 3.1 52.3 + - + +
451A VAL* 6.2 0.2 - - + -
452A LYS* 1.3 75.8 - - - +
454A SER* 1.3 66.1 + - - +
455A LEU* 4.1 8.1 - - + -
469A PHE* 3.9 16.2 - - + -
470A LYS 3.3 13.0 - - - +
472A ILE* 3.5 14.4 - - - +
539A PHE* 4.0 14.1 - - + -
542A MET* 4.2 23.6 - - + +
543A CYS* 3.6 28.0 - - - -
546A LEU* 3.7 32.5 - - + -
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Residues in contact with SER 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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437A HIS* 3.7 27.8 + - - -
438A LEU 3.6 4.8 + - - -
439A ARG* 5.4 2.0 - - - -
453A MET* 1.3 74.6 - - - +
455A LEU* 1.3 64.8 + - - +
456A GLN* 4.2 1.6 + - - +
468A ASP* 3.4 5.0 - - - +
469A PHE* 3.6 1.9 - - - -
470A LYS* 2.6 62.9 + - - +
472A ILE* 3.9 13.9 - - - -
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Residues in contact with LEU 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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416A MET* 6.3 0.7 - - + -
419A VAL* 5.5 4.0 - - + -
423A MET* 3.6 31.4 - - + -
436A TYR 3.7 1.0 - - - +
437A HIS* 3.2 7.6 - - - -
438A LEU* 2.8 50.3 + - + +
440A VAL* 4.0 12.5 - - + +
453A MET* 4.1 7.4 - - + -
454A SER* 1.3 76.7 + - - +
456A GLN* 1.3 61.5 + - - +
467A LEU* 3.9 25.4 - - + -
468A ASP 3.4 13.9 - - - +
469A PHE* 3.5 31.9 - - + -
546A LEU* 3.9 15.5 - - + -
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Residues in contact with GLN 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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434A ASN* 4.8 5.1 + - - +
436A TYR* 3.0 23.8 + - - +
437A HIS* 2.5 41.3 + - + +
454A SER* 5.3 1.6 - - - +
455A LEU* 1.3 75.0 - - - +
457A LEU* 1.3 65.8 + - - +
458A TYR* 3.4 34.8 - - + +
466A LEU 3.7 0.7 - - - +
467A LEU* 3.6 5.2 - - - +
468A ASP* 2.7 46.8 + - + +
204B PRO* 3.3 33.3 - - - +
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Residues in contact with LEU 457 (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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412A PRO* 4.1 17.5 - - + +
415A ILE* 4.2 24.9 - - + -
416A MET* 3.9 21.9 - - + +
436A TYR* 3.1 47.2 + - + +
456A GLN* 1.3 86.3 + - - +
458A TYR* 1.3 64.1 - - - +
465A TYR* 3.9 19.5 - - + -
466A LEU 3.3 23.8 - - - +
467A LEU* 4.1 8.0 - - + +
203B PRO* 4.2 4.8 - - + +
204B PRO* 3.6 11.1 - - - +
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Residues in contact with TYR 458 (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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169A PHE* 4.7 7.8 - - - -
189A LEU* 3.8 22.5 - - + +
456A GLN* 3.4 35.6 - - + +
457A LEU* 1.3 74.7 - - - +
459A LEU* 1.3 61.8 + - - +
465A TYR* 3.2 19.6 - - - +
466A LEU* 2.7 30.3 + - + +
468A ASP* 3.6 29.0 + - + -
203B PRO* 4.7 2.7 - - - -
204B PRO* 3.3 23.8 - - + -
205B ILE 3.8 1.1 - - - -
206B LEU* 3.5 42.0 - - + -
207B PRO* 3.6 18.3 - - + +
210B LEU* 4.5 7.5 - - + +
238B HIS* 5.5 1.6 - - - -
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Residues in contact with LEU 459 (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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458A TYR* 1.3 76.4 - - - +
460A VAL* 1.3 63.7 + - - +
461A ASP 3.8 22.3 + - - +
462A ASN* 4.5 9.4 - - - +
464A SER 4.4 1.8 - - - +
465A TYR* 3.6 31.9 - - + +
203B PRO* 4.0 20.6 - - + +
204B PRO 3.0 13.3 + - - +
205B ILE* 3.7 30.5 - - + +
206B LEU* 3.1 18.9 + - - +
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Residues in contact with VAL 460 (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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407A ARG* 4.3 23.3 - - - +
459A LEU* 1.3 78.0 - - - +
461A ASP* 1.3 73.0 + - + +
462A ASN 3.1 2.8 + - - +
464A SER* 2.6 43.0 + - - +
465A TYR 4.5 0.2 - - - -
466A LEU* 3.7 36.3 - - + +
206B LEU* 3.7 24.5 - - + -
211B LEU* 5.7 6.1 - - + -
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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