Contacts of the helix formed by residues 514 - 535 (chain A) in PDB entry 4N41
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 514 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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513A ARG* 1.3 73.3 - - - +
515A PRO* 1.3 64.1 - - + +
516A GLN* 4.2 15.5 - - + +
517A GLU* 2.8 61.2 + - + +
518A VAL* 3.1 9.7 + - - +
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Residues in contact with PRO 515 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
484A SER* 3.8 9.0 - - - +
485A PHE* 4.2 4.2 - - - +
486A ARG* 3.9 30.3 - - + +
513A ARG 3.2 10.0 - - - +
514A ILE* 1.3 88.3 - - + +
516A GLN* 1.3 65.8 + - + +
518A VAL* 3.0 5.1 + - + +
519A VAL* 2.9 27.5 + - - +
553A GLU* 3.3 43.7 - - + +
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Residues in contact with GLN 516 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
514A ILE* 3.3 11.1 - - + -
515A PRO* 1.3 80.8 - - + +
517A GLU* 1.3 57.3 + - + +
519A VAL* 3.5 1.6 + - - +
520A TRP* 2.9 29.8 + - - +
552A ASP* 2.8 49.7 + - - +
553A GLU* 3.3 17.4 + - - +
555A ALA* 3.7 1.6 - - - +
556A LEU* 3.6 38.4 + - + +
557A ALA 4.9 0.7 + - - -
93B LYS* 3.2 15.0 + - - +
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Residues in contact with GLU 517 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
513A ARG* 4.0 18.5 + - - +
514A ILE* 2.8 42.9 + - + +
516A GLN* 1.3 76.9 - - + +
518A VAL* 1.3 62.0 + - - +
520A TRP* 4.5 2.2 - - + +
521A ASP* 2.9 39.1 + - - +
556A LEU* 4.0 19.6 - - + +
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Residues in contact with VAL 518 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
485A PHE* 3.7 38.6 - - + +
488A GLY* 4.2 18.8 - - - +
489A GLY 4.5 2.2 - - - +
506A PRO* 4.8 6.7 - - + +
513A ARG* 3.6 51.3 + - + +
514A ILE 3.1 4.9 + - - +
515A PRO* 3.0 8.4 + - + +
517A GLU* 1.3 76.8 - - - +
519A VAL* 1.3 63.4 + - - +
521A ASP* 3.2 2.6 + - - +
522A LEU* 3.0 31.4 + - + +
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Residues in contact with VAL 519 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
477A PHE* 3.9 8.7 - - + -
485A PHE* 3.7 37.0 - - + -
515A PRO 2.9 17.2 + - - +
516A GLN 3.8 1.1 - - - +
518A VAL* 1.3 77.8 - - - +
520A TRP* 1.3 64.3 + - - +
522A LEU* 3.3 9.8 + - - +
523A LEU* 3.0 21.0 + - - +
553A GLU* 3.5 22.7 - - + +
554A PHE* 3.6 37.9 - - + -
557A ALA* 4.1 12.8 - - + -
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Residues in contact with TRP 520 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
516A GLN 2.9 19.5 + - - +
517A GLU* 4.1 2.2 - - + +
519A VAL* 1.3 78.0 - - - +
521A ASP* 1.3 69.6 + - - +
523A LEU* 3.1 27.2 + - + -
524A GLU* 2.8 57.8 + - + +
527A LEU* 4.0 18.8 - - + -
556A LEU* 4.0 24.5 - - + -
557A ALA* 3.9 23.1 - - - +
560A ALA* 3.6 39.5 - - + -
561A LEU 5.0 0.2 - - - -
563A ARG* 5.6 4.1 - - - +
564A GLU* 6.0 2.0 - - - -
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Residues in contact with ASP 521 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
506A PRO* 5.9 5.4 - - + -
507A GLU 6.2 1.1 - - - +
513A ARG* 3.2 30.0 + - - +
517A GLU* 2.9 29.3 + - - +
518A VAL 3.2 4.5 + - - +
520A TRP* 1.3 87.1 + - - +
522A LEU* 1.3 63.3 + - - +
524A GLU* 3.4 8.3 + - - +
525A GLU* 2.9 26.7 + - - +
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Residues in contact with LEU 522 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
477A PHE* 4.2 15.0 - - + -
485A PHE* 4.2 14.8 - - + -
489A GLY 4.0 2.9 - - - +
490A ALA* 3.7 35.7 - - - +
491A ALA* 4.0 11.7 - - + +
504A THR* 3.7 29.3 - - + +
505A LEU 3.7 2.7 - - - -
506A PRO* 3.6 34.1 - - + +
518A VAL* 3.0 24.3 + - + +
519A VAL* 3.6 7.4 - - - +
521A ASP* 1.3 76.5 - - - +
523A LEU* 1.3 60.4 + - - +
525A GLU 3.4 0.2 + - - -
526A THR* 2.9 27.9 + - - -
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Residues in contact with LEU 523 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
473A LEU* 5.6 0.2 - - + -
475A VAL* 4.2 15.7 - - + -
477A PHE* 4.1 13.8 - - + -
519A VAL 3.0 13.1 + - - +
520A TRP* 3.6 23.8 - - + +
522A LEU* 1.3 76.2 - - - +
524A GLU* 1.3 59.3 + - - +
526A THR* 3.0 9.7 + - - -
527A LEU* 2.8 42.3 + - + +
541A VAL* 5.6 1.6 - - + -
543A LEU* 3.9 26.0 - - + -
557A ALA* 3.9 16.4 - - + -
561A LEU* 3.8 35.9 - - + -
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Residues in contact with GLU 524 (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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520A TRP* 2.8 59.8 + - + +
521A ASP* 3.7 8.4 - - - +
523A LEU* 1.3 72.5 - - - +
525A GLU* 1.3 72.6 + - - +
527A LEU* 3.2 7.7 + - + +
528A TRP* 2.9 42.8 + - - +
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Residues in contact with GLU 525 (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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504A THR* 3.6 19.3 - - + -
505A LEU 5.1 3.7 - - - +
521A ASP 2.9 18.0 + - - +
524A GLU* 1.3 87.8 + - - +
526A THR* 1.3 62.2 + - - +
528A TRP* 3.2 20.2 + - - +
529A ALA* 3.0 19.2 + - - +
679A ARG* 3.5 36.7 + - - +
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Residues in contact with THR 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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473A LEU* 3.9 18.4 - - + -
475A VAL* 4.2 14.4 - - + +
491A ALA* 4.6 2.9 - - - +
492A CYS* 5.8 0.5 - - - -
493A ALA* 3.7 30.1 - - + +
502A LEU* 4.6 8.3 - - + +
504A THR* 3.1 17.8 + - - -
522A LEU 2.9 14.9 + - - -
523A LEU* 3.0 14.3 + - - -
525A GLU* 1.3 78.5 - - - +
527A LEU* 1.3 60.6 + - - +
529A ALA* 3.3 4.1 + - - +
530A PHE* 3.0 22.4 + - - +
679A ARG* 4.2 3.4 - - - +
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Residues in contact with LEU 527 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
473A LEU* 4.3 10.5 - - + -
520A TRP* 4.0 33.0 - - + -
523A LEU* 2.8 25.8 + - + +
524A GLU* 3.5 7.2 - - + +
526A THR* 1.3 73.1 - - - +
528A TRP* 1.3 58.5 + - - +
530A PHE* 3.2 6.2 + - - +
531A ARG* 2.9 30.6 + - - +
537A LEU* 4.3 15.7 - - + +
538A PRO* 3.9 30.5 - - + -
541A VAL* 4.4 2.5 - - + -
561A LEU* 4.1 19.7 - - + -
564A GLU* 6.1 1.8 - - + -
566A ILE* 4.3 14.1 - - + -
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Residues in contact with TRP 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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524A GLU* 2.9 29.5 + - - +
525A GLU* 3.2 24.4 + - - +
527A LEU* 1.3 76.3 - - - +
529A ALA* 1.3 58.5 + - - +
531A ARG* 3.3 39.3 + - - +
532A ARG* 2.9 54.5 + - + +
679A ARG* 6.1 0.7 - - - -
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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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500A HIS* 5.7 3.4 - - + -
502A LEU* 3.9 28.0 - - + -
525A GLU 3.0 12.6 + - - +
526A THR 3.7 7.0 - - - +
528A TRP* 1.3 76.0 - - - +
530A PHE* 1.3 67.0 + - - +
532A ARG* 3.1 24.9 + - - +
533A LYS* 3.0 23.0 + - - +
679A ARG* 4.2 12.6 - - + +
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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
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472A GLU* 3.7 45.1 - - + -
473A LEU* 4.2 26.7 - - + -
495A GLY* 4.5 12.6 - - - -
496A GLY* 4.5 1.8 - - - -
500A HIS* 6.4 1.1 - - - -
502A LEU* 5.7 3.2 - - - +
526A THR 3.0 14.1 + - - +
527A LEU* 3.2 11.0 + - - +
529A ALA* 1.3 74.1 - - - +
531A ARG* 1.3 57.8 + - - +
533A LYS* 3.0 7.9 + - + +
534A ALA* 2.9 42.9 + - + +
536A ARG* 3.2 25.1 - - - -
537A LEU 3.7 2.5 - - - -
538A PRO* 3.4 31.6 - - + -
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Residues in contact with ARG 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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527A LEU 2.9 16.7 + - - +
528A TRP* 3.6 38.6 - - - +
530A PHE* 1.3 77.0 - - - +
532A ARG* 1.3 59.9 + - - +
535A GLY* 2.8 29.6 + - - -
536A ARG* 3.2 30.7 - - - +
537A LEU* 4.0 36.1 - - + +
564A GLU* 5.4 3.0 + - - -
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Residues in contact with ARG 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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528A TRP* 2.9 46.6 + - + +
529A ALA* 3.1 26.1 + - - +
531A ARG* 1.3 77.9 - - - +
533A LYS* 1.3 61.8 + - - +
534A ALA 3.7 0.2 + - - -
535A GLY* 4.3 2.4 + - - -
679A ARG* 5.5 6.1 - - - +
680A GLU* 5.2 9.9 + - - -
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Residues in contact with LYS 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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500A HIS* 4.4 29.8 - - + +
529A ALA 3.0 11.7 + - - +
530A PHE* 3.0 8.9 + - + +
532A ARG* 1.3 79.0 - - - +
534A ALA* 1.3 58.3 + - + +
535A GLY 3.7 0.2 - - - -
680A GLU* 6.0 1.1 - - - +
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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
----------------------------------------------------------
530A PHE* 2.9 40.4 + - + +
533A LYS* 1.3 79.3 - - + +
535A GLY* 1.3 60.8 + - - +
536A ARG* 3.1 23.4 + - + +
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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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531A ARG* 2.8 16.5 + - - -
532A ARG 4.3 2.3 + - - -
533A LYS 3.7 1.2 - - - -
534A ALA* 1.3 76.9 - - - +
536A ARG* 1.3 62.3 + - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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