Contacts of the helix formed by residues 517 - 534 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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455A HIS* 3.3 47.6 - - + +
459A ILE 6.1 0.2 - - - -
460A ILE* 3.7 15.4 - - + +
489A MET* 5.9 2.2 - - - +
516A GLY* 1.3 70.5 - - - -
518A SER* 1.3 66.1 + - - +
519A VAL* 3.0 2.3 + - - -
520A ASP* 3.0 15.3 + - - +
521A TRP* 3.6 17.4 - - + +
582A GLY 3.1 27.8 + - - -
583A CYS* 4.3 10.3 - - - +
584A GLY 4.4 9.5 + - - -
587A GLY* 5.2 2.8 - - - -
588A GLU 5.5 2.5 - - - +
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Residues in contact with SER 518 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
508A GLU* 2.5 26.9 + - - +
515A TYR* 4.3 1.0 - - - +
516A GLY 2.9 13.3 + - - -
517A LYS* 1.3 81.8 - - - +
519A VAL* 1.3 62.5 + - - +
521A TRP* 3.2 4.9 + - - +
522A TRP 3.2 10.9 + - - -
577A PRO* 3.8 14.5 - - - +
580A ARG* 2.7 26.1 + - - -
583A CYS* 3.4 26.0 - - - -
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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
----------------------------------------------------------
460A ILE* 4.0 21.5 - - + -
462A ARG* 4.1 15.3 - - + -
504A TYR 4.9 0.9 - - - +
506A ALA* 4.2 6.8 - - + +
508A GLU* 3.6 17.0 - - + +
509A ILE* 3.6 32.8 - - + -
515A TYR* 3.5 26.2 - - + -
516A GLY 3.6 11.4 - - - +
518A SER* 1.3 80.9 + - - +
520A ASP* 1.3 69.5 + - - +
522A TRP* 3.4 2.6 + - - +
523A ALA* 3.1 24.1 + - - +
580A ARG* 4.2 1.6 - - - +
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Residues in contact with ASP 520 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
451A LEU* 4.1 9.8 - - + +
455A HIS* 3.2 30.9 + - + +
460A ILE* 3.4 3.0 - - - -
461A TYR* 2.4 42.2 + - - +
462A ARG* 2.6 28.3 + - - -
463A ASP 4.0 2.4 + - - -
464A LEU* 3.7 12.5 + - + +
517A LYS 3.0 5.3 + - - +
519A VAL* 1.3 84.3 - - - +
521A TRP* 1.3 58.5 + - - +
523A ALA* 3.6 4.1 + - - +
524A TYR* 2.9 26.4 + - - +
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Residues in contact with TRP 521 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
448A SER* 4.5 1.8 - - - -
451A LEU* 3.9 24.2 - - + -
452A PHE* 3.5 36.8 - + - -
455A HIS* 3.5 29.5 + + - -
517A LYS* 3.6 25.9 - - - +
518A SER 3.2 5.8 + - - +
519A VAL 3.2 0.4 - - - -
520A ASP* 1.3 76.2 - - - +
522A TRP* 1.3 65.8 + - - +
523A ALA 3.2 0.7 - - - -
524A TYR* 3.3 37.7 - + + +
525A GLY 2.9 17.5 + - - -
572A LEU* 3.3 20.0 - - + +
580A ARG* 4.3 1.6 - - - -
581A LEU 3.8 18.2 - - - +
582A GLY* 3.5 27.0 + - - -
583A CYS* 3.9 12.3 - - - -
588A GLU* 5.3 3.1 - - + -
591A VAL* 4.2 14.4 - - + -
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Residues in contact with TRP 522 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
503A ASP 4.8 1.4 + - - -
504A TYR 3.0 27.5 + - - -
505A ILE 3.3 11.9 + - - -
506A ALA* 3.3 21.3 - - + -
507A PRO* 3.6 33.4 - - + -
518A SER 3.2 3.6 + - - -
519A VAL 3.6 8.3 - - - +
521A TRP* 1.3 76.4 - - - +
523A ALA* 1.3 59.6 + - - +
525A GLY* 2.9 17.7 + - - -
526A VAL* 3.0 24.7 + - + +
538A PHE* 3.7 32.0 - + - -
550A ILE* 4.0 13.2 - - + +
572A LEU 3.5 12.1 - - - -
573A MET* 3.2 48.6 - - + +
574A THR 3.5 18.8 - - - -
575A LYS* 4.0 4.9 - - - -
580A ARG* 3.7 11.7 - - - +
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Residues in contact with ALA 523 (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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462A ARG 6.5 0.2 - - - -
464A LEU* 3.9 29.6 - - + +
504A TYR* 3.7 26.1 - - + +
519A VAL 3.1 14.6 + - - +
520A ASP* 3.7 6.3 - - - +
522A TRP* 1.3 77.8 - - - +
524A TYR* 1.3 66.3 + - - +
526A VAL* 3.1 7.0 + - - +
527A LEU* 3.0 24.4 + - - +
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Residues in contact with TYR 524 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
444A ALA* 2.7 48.0 + - + +
447A ILE* 4.2 9.4 - - + -
448A SER* 3.6 23.1 - - - -
451A LEU* 3.6 17.3 - - + -
464A LEU* 3.3 17.9 - - + +
520A ASP 2.9 19.1 + - - +
521A TRP* 3.3 26.7 - + + +
523A ALA* 1.3 78.0 - - - +
525A GLY* 1.3 60.8 + - - +
527A LEU* 3.3 8.7 + - + +
528A LEU* 2.9 34.8 + - + +
568A ILE* 5.0 2.0 - - + -
572A LEU* 3.6 28.0 - - + -
591A VAL* 4.7 7.1 - - + +
597A PHE* 3.5 12.1 - - - -
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Residues in contact with GLY 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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521A TRP 2.9 11.5 + - - -
522A TRP 2.9 6.0 + - - -
524A TYR* 1.3 77.1 - - - +
526A VAL* 1.3 50.1 + - - +
528A LEU* 3.2 7.5 + - - +
529A TYR* 2.7 35.5 + - - +
569A CYS* 4.8 2.4 - - - -
572A LEU* 3.6 25.8 - - - -
573A MET* 4.1 13.4 - - - +
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Residues in contact with VAL 526 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
503A ASP* 3.6 25.6 - - + +
504A TYR* 4.1 18.8 - - + -
522A TRP* 3.0 36.4 + - + +
523A ALA* 3.1 8.2 + - - +
525A GLY* 1.3 74.9 - - - +
527A LEU* 1.3 57.5 + - - +
529A TYR* 3.5 1.7 - - - +
530A GLU* 2.9 32.4 + - - +
537A PRO* 3.6 30.1 - - + -
538A PHE* 4.6 3.4 - - + -
573A MET* 3.8 18.2 - - - -
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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
----------------------------------------------------------
425A LEU* 4.5 0.9 - - + -
444A ALA* 5.6 0.2 - - - -
447A ILE* 3.7 26.7 - - + -
464A LEU* 4.1 20.4 - - + -
465A LYS 4.0 6.3 - - - -
466A LEU* 3.5 40.3 - - + +
469A VAL* 4.3 8.5 - - + -
504A TYR* 4.1 10.1 - - + -
523A ALA 3.0 15.8 + - - +
524A TYR* 3.9 13.5 - - + +
526A VAL* 1.3 75.2 - - - +
528A LEU* 1.3 64.5 + - + +
530A GLU* 3.3 12.2 + - - +
531A MET* 2.8 44.9 + - + +
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Residues in contact with LEU 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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440A ALA* 4.7 2.5 - - + +
444A ALA* 3.7 19.3 - - + -
524A TYR* 2.9 26.4 + - + +
525A GLY 3.2 5.6 - - - +
527A LEU* 1.3 77.2 - - + +
529A TYR* 1.3 64.9 + - - +
531A MET* 3.2 28.5 + - + +
532A LEU* 3.0 39.8 + - + +
568A ILE* 3.6 33.0 - - + -
569A CYS* 4.5 9.2 - - - -
572A LEU* 4.1 14.4 - - + -
596A PHE* 4.4 13.7 - - + -
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Residues in contact with TYR 529 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
525A GLY 2.7 20.8 + - - +
526A VAL 3.5 5.2 - - - +
528A LEU* 1.3 73.7 - - - +
530A GLU* 1.3 57.8 + - - +
532A LEU* 3.0 5.5 + - + +
533A ALA* 2.8 45.7 + - + +
535A GLN* 3.3 24.3 - - + +
536A PRO 3.5 6.3 + - - -
537A PRO* 3.4 32.4 + - + +
555A VAL* 3.7 20.0 - - + +
556A SER 3.9 8.3 + - - -
557A TYR* 4.1 17.3 - + - -
558A PRO* 3.7 20.1 - - + +
561A LEU* 5.2 3.1 - - + -
569A CYS* 4.4 10.2 - - - -
573A MET* 3.9 22.0 - - + -
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Residues in contact with GLU 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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429A ILE* 4.4 7.2 - - + +
466A LEU* 3.0 27.5 - - + +
503A ASP* 5.4 2.4 - - - +
504A TYR* 2.6 40.0 + - - -
526A VAL* 2.9 20.7 + - - +
527A LEU* 3.3 7.5 + - - +
529A TYR* 1.3 75.8 - - - +
531A MET* 1.3 64.2 + - - +
534A GLY* 2.9 25.0 + - - -
535A GLN 3.3 23.1 - - - +
536A PRO* 4.0 23.2 - - + +
537A PRO* 4.6 0.7 - - + -
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Residues in contact with MET 531 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
425A LEU* 4.1 12.8 - - + -
429A ILE* 3.9 18.5 - - + +
434A LYS* 3.7 3.3 - - - +
435A PHE* 3.1 54.9 + - + +
440A ALA* 3.7 22.2 - - + +
443A TYR* 3.7 22.2 - - + -
444A ALA* 3.9 10.8 - - + +
466A LEU* 4.7 0.9 - - + -
527A LEU* 2.8 34.5 + - + +
528A LEU* 3.3 32.5 - - + +
529A TYR 3.1 0.4 - - - -
530A GLU* 1.3 78.4 - - - +
532A LEU* 1.3 59.8 + - - +
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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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434A LYS* 3.4 24.4 - - - +
435A PHE 4.4 6.8 - - - +
437A GLU* 4.2 21.5 - - + +
440A ALA* 3.7 23.8 - - + -
528A LEU* 3.0 31.4 + - + +
529A TYR* 3.0 5.6 + - + +
531A MET* 1.3 78.4 - - - +
533A ALA* 1.3 58.3 + - + +
534A GLY 3.6 0.2 - - - -
561A LEU* 4.2 26.8 - - + +
565A ALA* 4.3 23.1 - - + -
569A CYS* 4.1 24.2 - - - -
596A PHE* 4.6 10.8 - - + -
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Residues in contact with ALA 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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434A LYS* 4.1 12.4 + - - +
529A TYR* 2.8 49.1 + - + +
532A LEU* 1.3 74.6 - - + +
534A GLY* 1.3 58.5 + - - +
535A GLN* 3.0 17.4 + - + +
558A PRO* 4.3 19.1 - - + +
561A LEU* 5.3 4.3 - - + -
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Residues in contact with GLY 534 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
429A ILE* 4.7 4.7 - - - +
433A GLY 3.3 26.5 - - - +
434A LYS* 4.0 1.0 - - - +
530A GLU* 2.9 18.8 + - - -
532A LEU 3.6 1.4 - - - -
533A ALA* 1.3 76.7 - - - +
535A GLN* 1.3 69.9 + - - +
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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