Contacts of the strand formed by residues 531 - 538 (chain D) 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 GLU 531 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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535A TYR* 3.9 33.4 - - + +
755A ARG* 4.2 25.1 - - - +
528D PRO* 5.5 0.2 - - - +
529D PHE 4.3 2.3 - - - +
530D ILE* 1.3 92.1 - - - +
532D THR* 1.3 62.8 + - - +
733D ALA* 5.3 0.3 - - - +
734D ALA* 4.3 5.0 + - - +
760D THR 3.4 11.7 - - - +
761D GLY* 3.9 1.8 - - - -
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Residues in contact with THR 532 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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514D THR* 4.5 3.6 - - - +
530D ILE 4.2 0.9 - - - +
531D GLU* 1.3 76.5 - - - +
533D GLY* 1.3 68.5 + - - +
732D ASP* 2.7 39.1 + - - +
733D ALA* 3.1 16.1 + - - -
734D ALA* 3.3 9.3 + - - -
756D VAL* 5.0 3.5 - - - +
759D SER* 3.7 3.6 - - - -
760D THR* 2.7 43.4 + - + +
761D GLY* 3.6 20.0 - - - +
762D TYR* 3.7 20.2 - - + +
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Residues in contact with GLY 533 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
514D THR* 5.6 1.6 - - - -
532D THR* 1.3 88.8 + - - +
534D ILE* 1.3 62.5 + - - -
535D SER* 4.6 0.2 - - - -
691D THR* 4.8 1.9 - - - +
732D ASP* 3.3 9.4 - - - +
733D ALA* 2.7 34.0 + - - +
756D VAL* 4.9 2.2 - - - -
757D PHE 4.0 1.3 - - - -
758D ALA 3.5 14.1 - - - -
759D SER* 4.8 0.4 - - - -
760D THR* 3.7 9.9 - - - -
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Residues in contact with ILE 534 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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533D GLY* 1.3 72.1 - - - -
535D SER* 1.3 67.4 + - - +
536D VAL* 5.8 1.8 - - + -
666D LEU* 6.4 0.7 - - + -
690D SER* 5.6 0.4 - - - +
691D THR* 3.8 37.0 - - + +
694D ASN* 3.7 30.5 - - + -
695D ILE* 4.8 5.4 - - + +
730D ILE* 4.6 13.9 - - + -
731D TYR 3.8 3.1 - - - +
757D PHE* 2.7 57.2 + - + +
758D ALA* 3.9 15.9 + - + +
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Residues in contact with SER 535 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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533D GLY 3.7 0.6 + - - -
534D ILE* 1.3 77.4 + - - +
536D VAL* 1.3 67.3 + - - +
730D ILE* 3.4 3.1 - - - -
731D TYR 2.9 34.3 + - - +
733D ALA* 3.3 34.4 - - - +
736D LEU* 3.3 9.6 - - - +
737D ASN* 5.2 4.3 + - - -
750D THR* 5.7 4.9 - - - -
751D ILE 6.1 0.2 - - - -
755D LYS 3.5 10.1 + - - -
756D VAL* 3.3 15.1 - - - +
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Residues in contact with VAL 536 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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534D ILE* 5.8 2.0 - - + -
535D SER* 1.3 82.2 - - - +
537D MET* 1.3 58.8 + - - +
538D VAL* 3.9 8.9 + - + +
663D VAL* 5.9 0.9 - - + -
728D ALA* 3.7 28.0 - - + -
729D PHE 3.2 12.3 - - - +
730D ILE* 4.1 15.3 - - + -
736D LEU* 4.0 1.6 - - - -
750D THR* 3.4 2.9 - - - -
751D ILE* 2.6 49.8 + - + +
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Residues in contact with MET 537 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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536D VAL* 1.3 75.2 - - - +
538D VAL* 1.3 66.3 + - - +
721D LEU* 5.3 6.1 - - - +
728D ALA* 4.8 0.7 - - - -
729D PHE* 3.3 23.3 + - + +
736D LEU* 3.6 32.2 - - + +
740D ALA* 5.6 1.1 - - + -
748D LEU* 5.3 7.7 - - + +
749D VAL 3.3 20.0 - - - +
750D THR* 4.4 2.2 - - - -
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Residues in contact with VAL 538 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
536D VAL* 3.8 7.5 + - + +
537D MET* 1.3 77.7 - - - +
539D SER* 1.3 70.0 + - - +
661D ASP* 6.0 2.0 - - - +
721D LEU* 6.0 2.0 - - - -
727D ASP 4.3 13.7 - - - +
728D ALA* 4.5 11.2 - - + +
748D LEU* 3.9 4.2 - - - +
749D VAL 3.2 25.2 + - - +
751D ILE* 5.1 3.5 - - + +
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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