Contacts of the strand formed by residues 511 - 520 (chain A) in PDB entry 4M5X
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 THR 511 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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455A VAL* 4.0 16.2 - - + -
456A HIS 3.3 4.0 - - - -
457A SER* 2.7 24.8 + - - +
468A TYR* 6.2 0.2 - - - +
496A HIS* 3.9 18.1 - - + +
497A ASN* 4.0 8.4 - - - +
499A GLY* 4.3 6.2 - - - -
509A HIS* 2.9 30.8 + - - +
510A CYS* 1.3 74.3 - - - +
512A ASN* 1.3 64.8 + - - +
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Residues in contact with ASN 512 (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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408A ARG* 3.2 34.8 - - - +
420A LYS* 2.8 22.9 + - - -
422A ASN* 2.8 34.9 + - - +
455A VAL* 3.4 6.8 - - - +
456A HIS* 2.8 31.7 + - - +
497A ASN* 3.6 13.5 - - - +
499A GLY* 3.8 6.0 - - - -
509A HIS 3.3 20.2 + - - -
510A CYS 3.7 1.4 - - - -
511A THR* 1.3 74.9 - - - +
513A ALA* 1.3 62.5 + - - +
514A TYR* 3.7 0.7 + - - +
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Residues in contact with ALA 513 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
406A LEU* 3.8 19.0 - - + +
408A ARG* 2.8 28.5 + - - +
427A PHE* 3.9 20.9 - - + -
453A VAL* 3.6 27.8 - - + -
454A LEU 3.3 9.0 - - - +
455A VAL* 4.3 1.1 - - - +
497A ASN* 3.3 7.5 + - - +
512A ASN* 1.3 75.2 - - - +
514A TYR* 1.3 59.9 + - - +
515A MET 4.6 0.4 - - - +
516A LEU* 4.1 4.9 - - + -
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Residues in contact with TYR 514 (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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224A TYR* 3.2 30.7 - + + +
227A SER* 4.3 4.3 + - - -
296A VAL* 4.0 28.7 - - + -
405A GLN* 3.6 4.5 - - - +
406A LEU* 2.7 45.0 + - - +
408A ARG* 4.7 4.3 - - - +
409A PHE* 4.1 24.5 - + + -
454A LEU* 2.9 48.8 + - + +
455A VAL 3.6 14.1 - - - -
456A HIS* 3.8 18.8 - - + -
465A TYR* 3.7 17.0 - + - -
512A ASN 5.0 0.2 - - - +
513A ALA* 1.3 74.8 - - - +
515A MET* 1.3 60.1 + - + +
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Residues in contact with MET 515 (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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228A LEU* 4.3 13.9 - - + -
231A THR* 5.0 0.2 - - + -
296A VAL* 3.8 24.9 - - - -
300A CYS* 5.6 1.3 - - + -
403A HIS* 3.7 37.5 - - + +
404A LEU 3.3 12.8 - - - +
405A GLN* 3.3 26.5 - - + +
406A LEU* 4.3 1.1 - - - +
454A LEU* 2.8 51.4 + - + +
513A ALA 3.7 0.4 - - - -
514A TYR* 1.3 93.9 + - + +
516A LEU* 1.3 74.3 + - - +
517A VAL* 3.8 16.4 - - + -
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Residues in contact with LEU 516 (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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360A ILE* 3.7 21.8 - - + -
402A LEU 3.6 1.2 - - - +
403A HIS* 3.7 1.9 - - - -
404A LEU* 2.8 38.7 + - + +
406A LEU* 3.9 14.8 - - + -
427A PHE* 3.6 56.1 - - + -
450A LEU* 4.4 1.6 - - + -
452A ALA 3.5 5.2 - - - +
453A VAL* 3.9 20.2 - - + -
513A ALA* 4.1 5.6 - - + -
515A MET* 1.3 84.0 - - - +
517A VAL* 1.3 64.2 + - - +
518A TYR* 3.9 21.5 - - + -
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Residues in contact with VAL 517 (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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231A THR* 3.5 28.5 - - + -
235A THR* 5.9 1.6 - - - +
401A VAL* 4.0 15.9 - - + -
402A LEU 3.4 2.0 - - - -
403A HIS* 3.5 29.2 - - + +
450A LEU* 3.7 2.4 - - - +
451A HIS* 2.7 51.9 + - + +
452A ALA* 3.0 24.8 + - + +
454A LEU* 4.7 2.5 - - + -
515A MET* 3.8 11.0 - - + -
516A LEU* 1.3 75.5 - - - +
518A TYR* 1.3 60.2 + - - +
519A ILE* 4.8 1.3 - - + -
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Residues in contact with TYR 518 (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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360A ILE* 5.1 1.1 - - + +
401A VAL* 3.6 2.6 - - - -
402A LEU* 2.7 41.0 + - + +
404A LEU* 3.9 20.4 - - + -
427A PHE* 3.8 9.2 - - - +
428A PRO* 2.6 43.8 + - - +
429A GLU 4.0 2.2 - - - -
431A LEU* 3.6 36.5 - - + +
448A TYR* 3.8 21.5 - - + -
449A ILE 3.2 7.6 - - - +
450A LEU* 3.4 35.9 - - + +
516A LEU* 3.9 24.0 - - + -
517A VAL* 1.3 77.9 - - - +
519A ILE* 1.3 64.1 + - - +
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Residues in contact with ILE 519 (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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235A THR* 6.1 0.9 - - + -
400A PRO 3.3 8.7 - - - +
401A VAL* 4.4 13.9 - - + -
448A TYR* 3.5 4.5 - - - -
449A ILE* 2.7 40.9 + - - +
451A HIS* 3.6 38.6 - - + +
517A VAL* 4.8 0.9 - - + -
518A TYR* 1.3 77.7 - - - +
520A ARG* 1.3 76.0 + - - +
521A GLU 3.3 0.3 + - - -
523A LYS* 5.0 0.2 - - + -
524A LEU* 3.7 38.1 - - + -
527A VAL* 3.9 30.7 - - + -
528A LEU* 4.0 6.7 - - + -
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Residues in contact with ARG 520 (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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398A LEU* 3.3 33.2 + - - +
399A PRO 4.9 0.9 - - - -
400A PRO* 2.8 22.8 + - + +
437A LEU* 5.0 6.9 - - - +
441A ASP* 5.5 1.6 - - - +
444A ASP* 2.7 52.9 + - - +
445A PRO 3.7 8.8 + - - +
446A ALA* 3.8 13.8 - - - +
447A ASN 3.6 7.4 - - - +
448A TYR* 3.3 36.2 + - + +
519A ILE* 1.3 71.3 - - - +
521A GLU* 1.3 63.6 + - - +
522A SER* 3.8 12.6 - - - +
523A LYS* 2.8 31.7 + - + +
524A LEU* 3.1 9.4 + - - -
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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