Contacts of the helix formed by residues 517 - 534 (chain B) in PDB entry 3IW4
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 LYS 517 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
455B HIS* 3.5 52.3 - - + +
459B ILE 5.3 0.2 - - - +
460B ILE* 4.4 18.1 - - + +
489B MET* 5.3 9.1 + - - +
490B MET* 3.9 21.9 - - + +
516B GLY* 1.3 69.5 - - - -
518B SER* 1.3 62.3 + - - +
519B VAL 3.3 1.6 + - - -
520B ASP* 3.3 14.2 + - - +
521B TRP* 3.6 17.5 - - + +
582B GLY 3.8 18.1 + - - -
583B CYS* 4.8 6.3 - - - +
584B GLY 3.9 19.8 + - - +
585B PRO 5.6 0.2 + - - -
587B GLY* 4.9 4.9 - - - +
588B GLU* 5.5 2.2 + - - +
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Residues in contact with SER 518 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
508B GLU* 2.6 27.3 + - - +
515B TYR* 4.2 0.5 - - - +
516B GLY* 2.7 17.6 + - - -
517B LYS* 1.3 79.4 - - - +
519B VAL* 1.3 62.9 + - - -
521B TRP* 3.0 14.8 + - - +
522B TRP 3.2 3.1 + - - -
577B PRO* 3.9 13.7 - - - +
580B ARG* 2.9 24.0 + - - -
583B CYS* 3.4 29.7 - - - +
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Residues in contact with VAL 519 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
460B ILE* 3.9 19.7 - - + -
462B ARG* 4.3 11.0 - - + -
504B TYR 4.7 1.6 - - - +
506B ALA* 3.7 14.4 - - + +
508B GLU* 3.6 17.3 - - + +
509B ILE* 3.5 35.9 - - + -
515B TYR* 3.5 33.7 - - + -
516B GLY 3.5 1.3 + - - +
518B SER* 1.3 81.3 + - - +
520B ASP* 1.3 60.6 + - - +
522B TRP* 3.3 4.9 + - - +
523B ALA* 2.9 27.3 + - - +
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Residues in contact with ASP 520 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
451B LEU* 4.3 9.0 - - + +
455B HIS* 2.9 34.0 + - + +
460B ILE* 3.7 7.3 - - - +
461B TYR* 2.8 33.4 + - - +
462B ARG* 2.7 31.3 + - - -
463B ASP 4.2 1.7 + - - -
464B LEU* 4.2 6.3 + - + +
517B LYS 3.3 4.0 + - - +
518B SER 3.1 0.6 - - - -
519B VAL* 1.3 76.2 - - - +
521B TRP* 1.3 63.0 - - - +
523B ALA* 3.2 6.3 + - - +
524B TYR* 2.8 29.2 + - - +
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Residues in contact with TRP 521 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
448B SER* 4.8 3.6 - - - -
451B LEU* 3.9 21.1 - - + -
452B PHE* 3.8 34.3 - + - -
455B HIS* 3.8 19.5 - + - -
517B LYS* 3.6 38.3 - - + +
518B SER 3.0 7.4 + - - +
520B ASP* 1.3 74.7 - - - +
522B TRP* 1.3 67.4 + - - +
524B TYR* 3.6 39.0 - + + +
525B GLY 2.9 16.8 + - - -
572B LEU* 3.7 21.0 - - + +
580B ARG* 4.4 7.9 - - - -
581B LEU 4.0 16.4 - - - +
582B GLY* 3.5 31.2 + - - -
583B CYS* 4.5 4.7 - - - -
588B GLU* 5.8 2.9 - - - -
591B VAL* 4.4 14.8 - - + -
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Residues in contact with TRP 522 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
503B ASP 4.9 1.0 + - - -
504B TYR 3.4 21.4 + - - -
505B ILE 3.2 15.5 + - - -
506B ALA* 3.7 13.7 - - + -
507B PRO* 3.6 35.4 - - + -
518B SER 3.2 5.5 + - - -
519B VAL 3.4 9.2 - - - +
520B ASP 3.2 0.2 - - - -
521B TRP* 1.3 76.9 - - - +
523B ALA* 1.3 63.3 + - - +
525B GLY* 2.8 13.7 + - - -
526B VAL* 2.9 29.1 + - + +
538B PHE* 3.6 34.2 - + - -
550B ILE* 4.2 11.6 - - + +
572B LEU 3.8 15.9 - - - -
573B MET* 3.4 35.2 - - + +
574B THR 3.5 11.4 - - - -
575B LYS* 3.7 6.7 - - + -
580B ARG* 3.6 23.2 - - - +
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Residues in contact with ALA 523 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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462B ARG 6.1 1.1 - - - -
463B ASP 5.8 0.7 - - - +
464B LEU* 3.6 35.7 - - + +
504B TYR* 3.8 22.8 - - + +
519B VAL 2.9 16.9 + - - +
520B ASP* 3.2 6.3 + - - +
522B TRP* 1.3 77.1 - - - +
524B TYR* 1.3 57.9 + - - +
526B VAL* 3.1 6.6 + - - +
527B LEU* 2.8 30.5 + - - +
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Residues in contact with TYR 524 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
444B ALA* 2.7 43.6 + - - +
447B ILE* 3.7 29.6 - - + -
448B SER* 4.1 13.4 - - - -
451B LEU* 4.1 5.4 - - + -
464B LEU* 3.6 15.4 - - + +
520B ASP 2.8 16.9 + - - +
521B TRP* 3.6 22.0 - + + +
523B ALA* 1.3 73.1 - - - +
525B GLY* 1.3 56.8 + - - +
527B LEU* 3.9 5.2 - - + +
528B LEU* 2.7 60.1 + - + +
568B ILE* 4.9 1.8 - - + -
572B LEU* 3.7 26.2 - - + -
591B VAL* 4.6 7.4 - - + -
597B PHE* 3.7 14.4 - - - -
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Residues in contact with GLY 525 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
521B TRP 2.9 6.9 + - - -
522B TRP 2.8 8.4 + - - -
524B TYR* 1.3 78.2 - - - +
526B VAL* 1.3 55.9 + - - +
528B LEU* 3.3 1.8 + - - +
529B TYR* 2.8 30.5 + - - +
569B CYS* 4.8 2.2 - - - -
572B LEU* 3.6 33.0 - - - -
573B MET* 4.1 12.6 - - - +
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Residues in contact with VAL 526 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
503B ASP* 3.8 21.8 - - + +
504B TYR* 3.9 20.0 - - + -
522B TRP* 2.9 44.4 + - + +
523B ALA* 3.4 7.9 - - - +
525B GLY* 1.3 76.0 - - - +
527B LEU* 1.3 64.1 + - - +
529B TYR* 3.2 4.5 + - - +
530B GLU* 3.1 25.7 + - - +
537B PRO* 3.7 27.7 - - + +
538B PHE* 4.9 2.5 - - + -
573B MET* 4.1 12.3 - - - -
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Residues in contact with LEU 527 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
425B LEU* 5.2 1.8 - - + -
447B ILE* 4.2 16.8 - - + -
464B LEU* 3.7 33.2 - - + -
465B LYS 3.9 22.4 - - - +
466B LEU* 4.0 15.4 - - + +
469B VAL* 4.4 9.2 - - + -
504B TYR* 4.2 7.0 - - + -
523B ALA 2.8 15.8 + - - +
524B TYR* 3.9 8.3 - - + +
526B VAL* 1.3 74.3 - - - +
528B LEU* 1.3 73.3 - - + +
530B GLU* 3.0 23.6 + - - +
531B MET* 3.1 34.0 + - + +
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Residues in contact with LEU 528 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
440B ALA 5.5 0.4 - - - +
444B ALA* 3.8 17.9 - - + -
524B TYR* 2.7 58.6 + - + +
525B GLY* 3.6 5.6 - - - +
527B LEU* 1.3 85.1 - - + +
529B TYR* 1.3 60.8 + - - +
531B MET* 3.4 9.4 - - + +
532B LEU* 3.1 40.8 + - + +
568B ILE* 4.2 20.9 - - + -
569B CYS* 4.3 4.7 - - - -
572B LEU* 3.9 10.3 - - + -
596B PHE* 4.2 14.6 - - + -
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Residues in contact with TYR 529 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
525B GLY 2.8 14.2 + - - +
526B VAL 3.4 8.5 - - - +
527B LEU 3.1 0.2 - - - -
528B LEU* 1.3 75.5 - - - +
530B GLU* 1.3 54.1 + - - +
532B LEU* 3.1 4.9 + - + +
533B ALA* 2.7 52.9 + - + +
535B GLN* 3.1 33.0 - - + +
536B PRO 3.8 4.1 + - - -
537B PRO* 3.4 31.9 - - + +
555B VAL* 3.9 8.6 - - + +
556B SER 3.4 20.1 + - - -
557B TYR* 3.7 28.7 - + - -
558B PRO* 3.7 11.5 - - + +
561B LEU* 5.0 2.9 - - + -
569B CYS* 4.3 11.4 - - - -
573B MET* 3.8 21.5 - - + -
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Residues in contact with GLU 530 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
643A LEU* 3.7 15.8 - - + +
646A ALA* 4.2 8.1 - - - +
647A ASN* 3.4 12.5 - - - +
429B ILE* 3.8 3.9 - - + +
466B LEU* 3.3 25.4 - - + +
503B ASP* 6.0 0.2 - - - +
504B TYR* 3.0 32.7 + - - -
526B VAL* 3.2 15.8 - - - +
527B LEU* 3.0 13.6 + - - +
529B TYR* 1.3 72.1 - - - +
531B MET* 1.3 63.8 + - - +
534B GLY* 2.5 34.2 + - - -
535B GLN 3.2 25.1 - - - +
536B PRO* 4.5 6.5 - - + +
537B PRO* 4.5 1.7 - - + +
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Residues in contact with MET 531 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
425B LEU* 4.0 14.6 - - + -
429B ILE* 3.4 15.9 - - + +
434B LYS* 3.6 4.2 - - - +
435B PHE* 3.1 47.8 + - + -
440B ALA* 3.3 30.5 - - + +
443B TYR* 3.8 20.0 - - + -
444B ALA* 3.6 24.9 - - + +
447B ILE* 5.3 0.7 - - + -
466B LEU* 4.8 2.7 - - + -
527B LEU* 3.1 28.7 + - + +
528B LEU* 3.4 14.8 - - + +
530B GLU* 1.3 82.4 - - - +
532B LEU* 1.3 62.8 + - - +
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Residues in contact with LEU 532 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
434B LYS* 2.9 25.3 - - - +
435B PHE 4.4 4.5 - - - +
437B GLU* 4.4 18.6 - - + +
440B ALA* 3.5 26.2 - - + -
528B LEU* 3.1 31.1 + - + +
529B TYR* 3.1 10.5 + - + +
531B MET* 1.3 80.6 - - - +
533B ALA* 1.3 59.1 + - + +
561B LEU* 4.0 22.1 - - + +
565B ALA* 3.4 36.3 - - + -
569B CYS* 4.6 8.7 - - - -
596B PHE* 4.1 9.4 - - + -
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Residues in contact with ALA 533 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
434B LYS* 4.0 10.1 - - - +
529B TYR* 2.7 52.9 + - + +
532B LEU* 1.3 73.9 - - + +
534B GLY* 1.3 60.4 + - - +
535B GLN* 3.0 16.7 + - + +
558B PRO* 4.1 21.7 - - + +
561B LEU* 4.9 1.8 - - + -
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Residues in contact with GLY 534 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
643A LEU* 3.8 25.3 - - - +
429B ILE* 5.0 1.1 - - - -
433B GLY 3.1 27.4 - - - +
434B LYS* 3.6 5.5 - - - +
530B GLU 2.5 23.0 + - - -
532B LEU 3.6 1.2 - - - -
533B ALA* 1.3 71.8 - - - +
535B GLN* 1.3 67.4 + - - +
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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