Contacts of the strand formed by residues 512 - 518 (chain A) in PDB entry 4PE5
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 MET 512 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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398A LEU* 5.4 11.4 - - + -
399A LYS 3.4 2.0 + - - -
400A ILE* 3.3 10.7 - - + -
401A VAL* 2.7 35.0 + - - +
463A LEU* 5.0 6.3 - - - -
466A LEU* 4.8 7.0 - - - -
472A PHE* 5.1 13.0 - - + -
505A LEU* 3.9 2.6 - - - +
510A ALA 3.8 1.0 - - - -
511A ASP* 1.3 81.8 - - + +
513A ILE* 1.3 61.2 + - - +
514A VAL* 3.7 17.4 + - + -
760A ILE* 3.6 20.2 - - + -
761A GLY 3.4 14.8 - - - +
762A MET* 3.7 22.4 - - + -
768A TRP* 4.7 13.9 - - + -
772A VAL* 4.3 17.9 - - + -
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Residues in contact with ILE 513 (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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401A VAL* 3.4 18.4 - - + +
501A MET* 3.7 55.9 - - + -
502A MET* 4.0 9.6 - - + -
505A LEU* 3.7 29.4 - - + -
512A MET* 1.3 71.8 - - - +
514A VAL* 1.3 60.2 + - - +
515A ALA* 3.6 9.7 + - + -
517A LEU* 3.7 28.3 - - + -
527A ILE* 4.5 0.7 - - + -
759A GLY 4.1 1.7 - - - +
760A ILE* 3.6 6.2 - - - -
761A GLY* 2.9 33.8 + - - -
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Residues in contact with VAL 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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400A ILE* 4.4 9.9 - - + -
401A VAL 3.0 9.3 + - - +
402A THR* 3.1 22.7 + - - -
459A CYS* 3.3 38.9 - - + +
460A ILE* 6.0 0.9 - - + +
462A LEU* 5.1 9.4 - - + -
463A LEU* 3.9 36.1 - - + +
466A LEU* 5.3 2.5 - - + -
512A MET* 3.7 20.8 + - + -
513A ILE* 1.3 71.7 - - - +
515A ALA* 1.3 60.2 + - - +
533A PHE* 6.0 1.8 - - + -
760A ILE* 5.0 12.6 - - + -
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Residues in contact with ALA 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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402A THR* 3.6 16.6 - - - +
403A ILE* 4.0 20.6 - - + +
459A CYS* 3.7 11.6 - - - -
501A MET* 4.3 12.6 - - + -
513A ILE* 3.6 6.8 + - + -
514A VAL* 1.3 76.9 - - - +
516A PRO* 1.3 67.2 - - + +
517A LEU* 2.5 22.7 + - - +
533A PHE* 3.7 13.8 - - - -
759A GLY 3.8 3.5 + - - +
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Residues in contact with PRO 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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403A ILE* 5.0 1.1 - - + -
405A GLN* 3.7 33.7 - - + +
408A PHE* 3.5 30.3 - - + -
409A VAL* 4.5 3.6 - - + -
459A CYS* 3.6 15.2 - - - -
484A PHE* 3.6 9.6 - - + -
515A ALA* 1.3 83.4 - - + +
517A LEU* 1.3 56.0 + - - +
518A THR 3.8 0.4 - - - -
533A PHE* 4.7 1.1 - - + -
732A ASP* 4.9 1.3 - - - +
735A VAL* 5.7 1.1 - - + -
758A PHE* 3.8 29.8 - - + -
942A GLY* 3.3 25.0 + - - +
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Residues in contact with LEU 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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484A PHE* 4.8 2.0 - - + -
501A MET* 3.9 20.6 - - + -
502A MET* 5.0 4.7 - - + -
513A ILE* 3.7 40.8 - - + -
515A ALA 2.5 15.1 + - - +
516A PRO* 1.3 69.2 - - - +
518A THR* 1.3 65.3 + - - +
519A ILE* 3.3 1.9 + - - +
523A ARG* 3.3 33.4 - - - +
527A ILE* 4.6 2.0 - - + -
529A PHE* 3.5 33.7 - - + -
758A PHE* 3.3 5.5 - - - +
759A GLY 3.0 29.3 + - - +
761A GLY* 4.1 4.7 - - - +
942A GLY 3.6 1.8 - - - +
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Residues in contact with THR 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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516A PRO 3.7 0.8 + - - -
517A LEU* 1.3 71.2 - - - +
519A ILE* 1.3 65.8 + - - +
520A ASN* 3.4 14.0 + - + +
523A ARG* 3.8 8.7 + - - -
529A PHE* 4.0 6.8 - - - -
538A LEU* 6.1 1.3 - - + -
688A SER* 3.2 23.8 + - - +
732A ASP* 3.8 5.7 + - - +
754A PHE* 3.7 18.4 - - + -
756A SER* 3.3 27.8 - - - +
757A GLY 3.4 5.8 - - - +
758A PHE* 3.4 9.7 - - + -
942A GLY* 2.6 36.6 + - - -
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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