Contacts of the strand formed by residues 535 - 541 (chain A) in PDB entry 4EJX
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 ILE 535 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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405A VAL* 5.2 0.2 - - - +
406A TYR* 4.2 5.6 - - - -
429A ILE* 3.8 8.1 - - + +
430A LEU* 3.6 7.5 - - + -
431A GLY 3.2 17.3 + - - -
519A MET* 4.1 33.2 - - + -
520A TYR 3.4 15.5 - - - +
521A TYR* 3.9 13.2 - - + -
530A ILE* 4.3 15.7 - - + -
533A GLY* 3.2 11.2 + - - +
534A LEU* 1.3 78.5 - - - +
536A GLY* 1.3 59.0 + - - +
562A PHE* 3.4 37.2 - - + -
566A PHE* 4.4 7.6 - - + -
628A PHE* 3.8 19.1 - - + -
630A ALA* 5.6 1.6 - - + -
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Residues in contact with GLY 536 (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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430A LEU* 4.9 0.2 - - - -
431A GLY 3.9 3.1 - - - -
519A MET* 3.5 4.9 - - - +
520A TYR* 2.7 65.5 + - - -
535A ILE* 1.3 75.7 - - - +
537A PRO* 1.3 70.2 - - - +
628A PHE* 4.3 4.7 - - - -
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Residues in contact with PRO 537 (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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427A LEU* 3.9 2.5 - - + -
430A LEU* 3.8 22.4 - - + -
431A GLY 3.3 20.4 - - - +
432A PRO 3.3 5.2 - - - +
433A VAL* 3.2 29.6 - - + -
434A ILE 3.1 21.3 + - - -
518A LYS 4.0 0.2 - - - +
520A TYR* 3.4 4.6 - - - -
536A GLY* 1.3 84.0 - - - +
538A MET* 1.3 59.2 + - - +
560A TYR* 3.8 19.1 - - + -
628A PHE* 3.7 27.1 - - + -
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Residues in contact with MET 538 (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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433A VAL* 4.6 1.1 - - - -
434A ILE* 3.1 32.5 - - + +
442A ILE* 5.3 0.2 - - - -
458A PRO* 3.8 19.5 - - + -
459A ILE 4.9 4.9 - - - +
461A VAL* 4.7 6.1 - - - -
500A TRP* 3.7 29.8 - - + -
516A LEU 4.0 1.0 - - - +
517A ALA* 4.1 2.6 - - - -
518A LYS* 2.8 49.7 + - + +
519A MET* 3.9 4.0 - - - +
520A TYR* 3.7 26.0 - - + -
537A PRO* 1.3 74.0 - - - +
539A LYS* 1.3 66.8 + - - +
540A ILE* 3.9 26.9 - - + -
560A TYR* 4.4 7.3 - - - -
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Residues in contact with LYS 539 (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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433A VAL* 4.2 3.1 - - + -
434A ILE 2.9 11.8 + - - +
435A TRP* 3.4 23.0 - - + +
436A ALA 3.3 17.0 + - - -
515A CYS* 3.9 16.8 - - + -
516A LEU 3.7 6.5 - - - -
538A MET* 1.3 77.6 - - - +
540A ILE* 1.3 64.3 + - - +
541A CYS* 3.2 18.8 - - - -
546A LEU* 3.9 2.0 - - + +
550A GLY 2.7 29.8 + - - +
551A ARG* 3.6 0.4 - - - +
558A GLU* 2.7 42.6 + - - -
560A TYR* 3.3 23.9 + - + +
626A TYR* 3.8 15.5 - - + -
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Residues in contact with ILE 540 (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 ILE* 5.6 0.4 - - + -
435A TRP 4.9 0.2 - - - -
436A ALA* 3.7 26.5 - - + +
438A VAL* 5.4 0.7 - - + -
442A ILE* 4.3 2.0 - - + -
460A GLY 4.5 9.9 - - - +
461A VAL* 3.6 28.5 - - + -
502A VAL* 3.7 23.8 - - + -
506A VAL 5.5 0.4 - - - +
507A GLY* 5.0 4.3 - - - -
508A PRO* 4.1 22.1 - - + +
515A CYS* 3.9 0.2 - - - -
516A LEU* 3.3 28.2 + - + +
518A LYS* 4.2 23.5 - - + +
538A MET* 3.9 21.5 - - + -
539A LYS* 1.3 70.3 - - - +
541A CYS* 1.3 68.1 + - - +
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Residues in contact with CYS 541 (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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436A ALA 2.8 13.1 + - - +
437A GLU* 3.1 4.7 - - - -
438A VAL* 3.0 25.6 + - - +
508A PRO* 4.9 2.9 - - - -
514A VAL 3.8 6.1 - - - +
515A CYS* 2.0 50.5 - - - -
539A LYS* 3.2 23.1 - - - -
540A ILE* 1.3 79.0 - - - +
542A LYS* 1.3 66.3 + - - +
545A SER* 4.0 6.5 - - - +
546A LEU* 3.9 15.3 - - + -
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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