Contacts of the helix formed by residues 517 - 534 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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455C HIS* 3.7 41.4 + - + +
459C ILE 5.0 0.7 - - - +
460C ILE* 3.9 19.0 - - + +
489C MET* 6.1 1.6 - - + +
516C GLY* 1.3 69.8 - - - -
518C SER* 1.3 69.1 + - - +
519C VAL 3.1 0.2 - - - -
520C ASP* 2.9 22.5 + - - +
521C TRP* 3.7 18.9 + - - +
582C GLY 3.4 25.7 + - - -
583C CYS* 4.9 4.9 - - + +
584C GLY 5.1 5.7 + - - -
587C GLY* 5.3 0.6 - - - +
588C GLU* 5.3 6.9 - - - +
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Residues in contact with SER 518 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
508C GLU* 2.9 18.5 + - - +
515C TYR* 4.5 0.7 - - - +
516C GLY 3.1 12.5 + - - -
517C LYS* 1.3 80.8 - - - +
519C VAL* 1.3 59.0 + - - +
521C TRP* 2.8 23.0 + - - +
522C TRP 3.4 2.4 + - - -
577C PRO* 3.9 15.2 - - - +
580C ARG* 3.1 20.2 + - - -
583C CYS* 3.3 32.1 - - - -
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Residues in contact with VAL 519 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
460C ILE* 4.2 11.0 - - + -
462C ARG* 4.3 10.5 - - + -
504C TYR 4.7 2.4 - - - +
506C ALA* 3.6 11.1 + - + +
508C GLU* 3.2 27.4 - - + +
509C ILE* 3.6 37.2 - - + -
515C TYR* 3.8 24.2 - - + -
516C GLY 3.5 13.2 - - - +
517C LYS 3.0 0.4 + - - -
518C SER* 1.3 76.0 + - - +
520C ASP* 1.3 63.8 + - - +
522C TRP* 3.6 2.6 + - - +
523C ALA* 3.4 21.8 + - - +
580C ARG* 4.0 2.0 - - - +
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Residues in contact with ASP 520 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
451C LEU* 3.9 10.5 - - + +
455C HIS* 2.7 33.8 + - + +
460C ILE* 3.7 7.7 - - - +
461C TYR* 3.0 31.0 + - - +
462C ARG* 3.0 28.1 + - - -
463C ASP 4.8 0.3 + - - -
464C LEU* 3.6 10.3 - - + +
517C LYS 2.9 12.8 + - - +
518C SER 2.9 0.2 + - - -
519C VAL* 1.3 80.9 - - - +
521C TRP* 1.3 59.9 + - - +
523C ALA* 3.7 3.5 - - - +
524C TYR* 2.9 26.9 + - - +
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Residues in contact with TRP 521 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
448C SER* 4.3 4.9 - - - -
451C LEU* 3.9 21.3 - - + -
452C PHE* 3.4 41.7 - + - -
455C HIS* 3.4 31.1 + + - -
517C LYS* 3.7 18.5 - - - +
518C SER 2.8 7.1 + - - +
520C ASP* 1.3 75.5 - - - +
522C TRP* 1.3 60.6 + - - +
524C TYR* 3.3 46.2 - + + +
525C GLY 3.1 18.5 + - - -
572C LEU* 3.3 20.9 - - + +
580C ARG* 4.2 5.4 - - - -
581C LEU 3.6 17.0 - - - +
582C GLY* 3.4 34.9 + - - -
583C CYS* 4.1 7.2 - - - -
588C GLU* 5.6 1.8 - - - -
591C VAL* 4.5 11.0 - - + -
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Residues in contact with TRP 522 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
503C ASP 4.8 1.2 + - - -
504C TYR 3.3 16.9 + - - -
505C ILE 3.2 14.5 + - - -
506C ALA* 3.3 28.3 - - + -
507C PRO* 3.4 33.9 - - + -
518C SER 3.4 2.8 + - - -
519C VAL 3.8 7.4 - - - +
521C TRP* 1.3 74.9 - - - +
523C ALA* 1.3 55.7 + - - +
524C TYR 3.0 0.7 - - - -
525C GLY* 2.6 26.9 + - - -
526C VAL* 2.8 22.3 + - + +
538C PHE* 3.3 40.2 - + - -
550C ILE* 3.7 8.9 - - + +
572C LEU 3.5 10.3 + - - -
573C MET* 3.2 47.3 - - + +
574C THR 3.8 13.7 - - - -
575C LYS* 3.9 10.8 - - - -
580C ARG* 4.0 10.9 - - - +
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Residues in contact with ALA 523 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
462C ARG 6.5 0.2 - - - -
464C LEU* 3.6 33.4 - - + +
504C TYR* 3.7 21.8 - - + +
519C VAL 3.4 14.6 + - - +
520C ASP* 3.7 5.8 - - - +
522C TRP* 1.3 79.0 - - - +
524C TYR* 1.3 51.8 + - - +
526C VAL* 3.1 8.7 + - - +
527C LEU* 2.7 36.0 + - - +
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Residues in contact with TYR 524 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
444C ALA* 2.3 35.0 + - - +
447C ILE* 3.5 34.3 - - + -
448C SER* 3.5 13.6 - - - -
451C LEU* 3.9 9.2 - - + -
464C LEU* 3.6 10.3 - - + +
520C ASP 2.9 21.5 + - - +
521C TRP* 3.3 34.8 - + + +
523C ALA* 1.3 74.7 - - - +
525C GLY* 1.3 56.5 + - - +
527C LEU* 3.7 4.1 - - + +
528C LEU* 2.8 47.8 + - + +
568C ILE* 5.5 0.9 - - + -
572C LEU* 3.2 32.1 - - + -
591C VAL* 4.7 7.4 - - + -
597C PHE* 3.8 8.7 - + - -
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Residues in contact with GLY 525 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
521C TRP 3.1 4.4 + - - -
522C TRP 2.6 13.5 + - - -
524C TYR* 1.3 73.2 - - - +
526C VAL* 1.3 55.6 + - - -
528C LEU* 3.6 2.5 - - - +
529C TYR* 2.7 32.2 + - - +
569C CYS* 5.5 0.7 - - - -
572C LEU* 3.6 24.0 - - - +
573C MET* 2.9 24.7 - - - +
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Residues in contact with VAL 526 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
503C ASP* 3.7 25.8 - - + +
504C TYR* 3.5 29.6 - - + -
522C TRP* 2.8 40.0 + - + +
523C ALA 3.4 7.2 - - - +
525C GLY* 1.3 70.7 - - - +
527C LEU* 1.3 57.6 + - - +
529C TYR* 3.6 1.6 - - - +
530C GLU* 2.9 39.2 + - - +
537C PRO* 3.8 28.7 - - + +
538C PHE* 4.4 1.3 - - + -
573C MET* 3.6 12.5 - - - +
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Residues in contact with LEU 527 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
425C LEU* 4.6 1.8 - - + -
447C ILE* 4.2 17.0 - - + -
464C LEU* 4.4 9.2 - - + -
465C LYS* 3.6 13.9 - - - +
466C LEU* 3.6 46.7 - - + +
469C VAL* 4.2 13.2 - - + -
504C TYR* 4.4 2.9 - - + -
523C ALA 2.7 16.6 + - - +
524C TYR* 3.7 8.1 - - + +
526C VAL* 1.3 74.2 - - - +
528C LEU* 1.3 75.2 + - + +
530C GLU* 2.9 19.3 + - - +
531C MET* 3.0 36.9 + - + -
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Residues in contact with LEU 528 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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440C ALA 5.9 0.2 - - - -
444C ALA* 3.2 36.8 - - + -
447C ILE* 5.9 0.2 - - + -
524C TYR* 2.8 43.4 + - + +
525C GLY* 3.6 5.4 - - - +
527C LEU* 1.3 80.3 - - + +
529C TYR* 1.3 55.0 + - - +
531C MET* 2.8 36.3 + - + +
532C LEU* 3.0 18.9 + - + +
568C ILE* 3.9 30.7 - - + -
569C CYS* 4.6 6.1 - - - -
572C LEU* 4.1 13.5 - - + -
596C PHE* 4.0 13.5 - - + -
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Residues in contact with TYR 529 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
525C GLY 2.7 21.7 + - - +
526C VAL* 3.6 3.8 - - - +
528C LEU* 1.3 72.2 - - - +
530C GLU* 1.3 65.7 + - - +
532C LEU* 3.0 4.6 + - + +
533C ALA* 2.8 45.2 + - + +
535C GLN* 3.2 32.7 - - + +
536C PRO 3.6 5.1 + - - -
537C PRO* 3.5 27.9 + - + +
555C VAL* 3.4 25.2 - - + +
556C SER 3.0 20.1 + - - -
557C TYR* 3.8 28.3 - + - -
558C PRO* 4.1 4.7 - - - +
561C LEU* 4.9 3.4 - - + -
569C CYS* 4.4 8.7 - - - -
573C MET* 3.7 12.3 - - + -
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Residues in contact with GLU 530 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
429C ILE* 4.2 5.9 - - + +
466C LEU* 3.3 25.8 - - + +
503C ASP* 5.9 1.5 - - - +
504C TYR* 2.5 43.3 + - - -
526C VAL* 2.9 23.9 + - + +
527C LEU* 2.9 7.1 + - - +
529C TYR* 1.3 74.1 - - - +
531C MET* 1.3 56.6 + - - +
534C GLY* 2.6 34.2 + - - +
535C GLN 3.5 20.8 - - - +
536C PRO* 4.2 20.2 - - + +
537C PRO* 4.6 0.2 - - + -
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Residues in contact with MET 531 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
425C LEU* 4.2 6.3 - - + -
429C ILE* 3.8 19.7 - - + +
434C LYS* 3.4 3.3 - - - +
435C PHE* 2.9 47.2 + - + +
440C ALA* 3.7 27.6 - - + +
443C TYR* 3.7 31.9 - - + -
444C ALA* 3.9 7.4 - - - +
447C ILE* 5.1 0.7 - - + -
466C LEU* 4.8 0.4 - - + -
527C LEU* 3.0 29.6 + - + +
528C LEU* 2.8 48.8 + - + +
530C GLU* 1.3 73.4 - - - +
532C LEU* 1.3 57.7 + - - +
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Residues in contact with LEU 532 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
434C LYS* 3.4 22.1 + - - +
435C PHE 4.4 5.8 - - - +
437C GLU* 3.9 23.3 - - + +
440C ALA* 3.1 34.1 - - + -
528C LEU* 3.0 19.2 + - + +
529C TYR* 3.0 5.4 + - + +
531C MET* 1.3 78.3 - - - +
533C ALA* 1.3 60.5 - - + +
561C LEU* 4.0 26.5 - - + +
565C ALA* 3.5 31.6 - - + -
569C CYS* 4.6 16.2 - - - -
596C PHE* 4.1 15.5 - - + -
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Residues in contact with ALA 533 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
434C LYS* 4.1 12.1 - - - +
529C TYR* 2.8 46.3 + - + +
532C LEU* 1.3 78.8 - - + +
534C GLY* 1.3 59.9 + - - +
535C GLN* 3.1 14.1 + - + +
558C PRO* 4.4 21.2 - - + +
561C LEU* 4.8 4.5 - - + -
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Residues in contact with GLY 534 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
429C ILE* 4.9 6.3 - - - +
433C GLY 3.5 24.3 - - - +
434C LYS* 3.9 3.3 - - - +
530C GLU* 2.6 25.4 + - - -
532C LEU 3.6 1.2 - - - -
533C ALA* 1.3 72.4 - - - +
535C GLN* 1.3 70.4 + - - +
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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) + - + + + + + -
------------------------------------------------------------
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