Contacts of the helix formed by residues 525 - 535 (chain A) in PDB entry 4EG8
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 525 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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409A LEU* 4.1 7.2 - - + -
416A LEU* 3.8 7.2 - - + +
420A TYR* 3.6 8.3 - - - +
436A VAL* 4.0 10.8 - - + -
439A ALA* 4.6 4.9 - - + -
440A VAL* 3.6 28.5 - - + -
444A LEU* 3.9 28.9 - - + -
521A LYS* 3.0 21.7 + - + +
524A ALA* 1.3 78.8 - - - +
526A TYR* 1.3 82.3 + - + +
527A TRP 3.4 0.9 - - - -
528A PRO* 3.4 3.9 - - - +
529A ALA* 3.3 19.4 + - - +
810A DMS 4.6 5.2 - - - +
812A DMS 4.3 30.5 - - + +
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Residues in contact with TYR 526 (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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409A LEU* 3.8 29.6 - - + -
447A LEU* 3.6 29.9 - - + +
472A TYR* 4.6 7.8 + + - -
474A TRP* 5.4 1.1 - - + -
478A LEU* 4.5 3.1 - - + -
521A LYS* 3.2 17.5 + - + -
522A PHE* 3.5 44.9 - + - +
525A ILE* 1.3 82.4 - - + +
527A TRP* 1.3 65.7 + - - +
529A ALA* 3.0 9.1 + - - +
530A PHE* 2.9 45.3 + + + -
812A DMS 4.1 9.9 - - + -
813A DMS 2.3 47.0 - - + +
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Residues in contact with TRP 527 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344A LEU* 4.7 13.0 - - + -
478A LEU* 3.4 46.9 - - + -
479A THR* 4.2 6.5 - - - -
481A TYR* 3.9 24.0 - + + -
482A LEU* 4.4 7.9 - - + -
508A PHE* 3.7 27.1 - + - -
513A HIS* 3.2 29.2 + + - -
522A PHE 3.0 18.3 + - - +
523A HIS* 3.6 19.1 - + - +
526A TYR* 1.3 76.1 - - - +
528A PRO* 1.4 68.2 - - + +
530A PHE* 3.2 15.2 + + + +
531A LEU* 3.0 55.5 + - + +
539A PRO* 4.1 11.9 - - + +
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Residues in contact with PRO 528 (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 LEU* 3.5 15.7 - - + -
419A TRP* 3.9 14.1 - - + -
523A HIS 3.2 20.0 - - - +
524A ALA 3.2 22.9 - - - +
525A ILE 3.4 11.7 - - - +
527A TRP* 1.4 90.3 - - + +
529A ALA* 1.3 55.0 + - - +
531A LEU* 3.3 3.5 + - + -
532A LEU* 2.8 36.8 + - - +
538A LEU* 3.7 29.1 - - + +
539A PRO* 5.4 1.6 - - + -
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Residues in contact with ALA 529 (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 PHE* 3.7 13.4 - - + -
409A LEU* 3.4 32.1 - - + -
412A PHE* 3.7 21.8 - - + -
416A LEU* 4.1 4.4 - - + +
525A ILE 3.3 7.3 + - - +
526A TYR 3.0 9.3 + - - +
528A PRO* 1.3 78.7 - - - +
530A PHE* 1.3 63.5 + - - +
532A LEU* 3.2 5.9 + - - +
533A SER* 2.9 23.7 + - - -
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Residues in contact with PHE 530 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344A LEU* 5.0 8.3 - - + -
348A LEU* 3.5 27.2 - - + +
407A PHE* 3.6 37.9 - + - -
447A LEU* 3.9 21.8 - - + -
449A VAL* 4.2 13.0 - - + -
472A TYR* 5.8 1.1 - + - -
475A LEU* 3.9 32.3 - - + -
478A LEU* 4.0 15.5 - - + -
526A TYR* 2.9 35.0 + + + -
527A TRP* 3.6 18.8 - + + +
529A ALA* 1.3 74.3 - - - +
531A LEU* 1.3 59.3 - - - +
533A SER* 3.1 3.8 + - - -
534A ALA* 2.9 30.7 + - - +
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Residues in contact with LEU 531 (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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344A LEU* 5.7 2.7 - - + -
508A PHE* 4.0 8.1 - - + -
527A TRP* 3.0 66.8 + - + +
530A PHE* 1.3 76.2 - - + +
532A LEU* 1.3 63.8 + - - +
534A ALA* 3.3 1.8 + - - -
535A GLY 2.9 4.3 + - - -
536A LEU* 2.9 64.8 + - + +
537A PRO 3.8 13.9 - - - +
538A LEU* 3.4 17.0 - - + -
539A PRO* 3.8 16.4 - - + -
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Residues in contact with LEU 532 (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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351A LYS* 5.4 2.6 + - - -
412A PHE* 3.7 19.5 - - + -
415A ARG* 4.0 45.5 + - + +
416A LEU* 4.1 21.1 - - + +
419A TRP* 5.7 0.4 - - + -
528A PRO 2.8 26.1 + - - +
529A ALA 3.6 3.8 - - - +
531A LEU* 1.3 70.9 - - - +
533A SER* 1.3 65.4 + - - +
535A GLY* 3.2 12.4 + - - -
536A LEU 4.8 3.1 - - - +
538A LEU* 4.2 23.3 - - + -
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Residues in contact with SER 533 (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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347A LYS* 5.2 0.5 - - - +
348A LEU* 3.4 19.1 - - - +
351A LYS* 3.2 37.2 + - - +
353A ASP* 2.5 33.0 + - - +
407A PHE* 3.9 5.8 - - - -
412A PHE* 3.6 14.5 - - - -
415A ARG* 5.9 0.2 - - - +
529A ALA 2.9 13.2 + - - -
530A PHE 3.4 8.3 - - - -
532A LEU* 1.3 77.0 - - - +
534A ALA* 1.3 60.5 + - - +
535A GLY 3.2 1.2 + - - -
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Residues in contact with ALA 534 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344A LEU* 3.6 28.9 - - + -
347A LYS* 3.6 40.7 - - + +
348A LEU* 4.0 4.7 - - + -
530A PHE 2.9 16.4 + - - +
531A LEU 4.0 2.7 - - - +
533A SER* 1.3 77.2 - - - +
535A GLY* 1.3 60.5 + - - +
536A LEU* 3.6 15.8 + - + +
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Residues in contact with GLY 535 (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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351A LYS* 6.4 0.2 - - - -
531A LEU 2.9 5.6 + - - -
532A LEU* 3.2 7.5 + - - -
533A SER 3.1 5.4 + - - -
534A ALA* 1.3 79.0 - - - +
536A LEU* 1.3 63.0 + - - +
537A PRO* 4.7 1.0 - - - +
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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