Contacts of the helix formed by residues 491 - 511 (chain A) in PDB entry 5IVI
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 SER 491 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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487A MET* 3.6 11.3 - - - +
488A PRO* 2.7 39.8 + - - +
490A GLU* 1.3 81.1 - - - +
492A ARG* 1.3 65.1 + - - +
493A GLU* 3.7 13.3 + - - -
494A TYR* 3.1 15.6 + - - +
495A LYS* 3.1 22.3 + - - +
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Residues in contact with ARG 492 (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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448A PHE* 3.2 23.2 - - + -
449A ASP* 3.0 32.5 + - - +
450A SER* 3.6 16.6 - - - +
490A GLU 3.8 1.4 + - - -
491A SER* 1.3 72.3 - - - +
493A GLU* 1.3 72.1 + - - +
495A LYS* 3.5 11.6 + - - +
496A THR* 2.9 32.4 + - - -
543A ASP* 2.8 37.0 + - - +
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Residues in contact with GLU 493 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
448A PHE* 4.1 7.0 - - + -
450A SER* 2.5 37.7 + - - +
452A ASP* 3.3 21.9 - - - +
453A LEU* 4.0 21.1 - - + -
477A TYR* 4.0 6.6 - - + -
487A MET* 3.5 32.0 - - + +
491A SER* 3.7 8.1 - - - -
492A ARG* 1.3 94.0 + - - +
494A TYR* 1.3 66.3 + - - +
496A THR* 3.1 4.3 + - - -
497A ILE* 2.9 26.4 + - - +
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Residues in contact with TYR 494 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A TYR* 3.5 37.8 - + - -
155A LYS* 2.4 38.2 + - - -
487A MET* 4.1 8.0 - - + +
488A PRO 3.3 19.5 - - - +
489A LYS* 3.5 46.7 - - + +
491A SER* 3.1 7.5 + - - +
493A GLU* 1.3 78.0 - - - +
495A LYS* 1.3 64.3 + - + +
497A ILE* 3.1 16.8 + - + +
498A GLU* 3.0 49.6 + - + +
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Residues in contact with LYS 495 (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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489A LYS 4.1 12.8 + - - +
490A GLU* 3.6 26.2 - - - +
491A SER 3.1 18.8 + - - +
492A ARG* 3.7 9.4 - - - +
494A TYR* 1.3 78.2 - - + +
496A THR* 1.3 58.4 + - - +
498A GLU* 3.4 6.3 + - - +
499A ARG* 3.0 48.2 + - - +
519A GLU* 5.3 15.3 - - + +
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Residues in contact with THR 496 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
446A PHE* 4.1 9.9 - - + -
448A PHE* 3.3 33.7 - - + -
477A TYR* 3.8 26.0 - - + -
492A ARG 2.9 18.3 + - - -
493A GLU 3.1 4.0 + - - -
495A LYS* 1.3 75.7 - - - +
497A ILE* 1.3 58.5 + - - +
499A ARG* 3.7 11.7 + - + +
500A MET* 2.9 42.7 + - + +
541A ILE* 5.0 4.9 - - + -
542A SER 4.8 2.5 + - - +
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Residues in contact with ILE 497 (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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51A TYR* 4.2 17.5 - - + +
152A TYR* 3.7 57.0 - - + +
155A LYS* 5.9 4.9 - - + +
453A LEU* 4.1 15.9 - - + -
477A TYR* 3.7 28.2 - - + +
487A MET* 5.3 0.7 - - + -
493A GLU 2.9 20.5 + - - +
494A TYR* 3.4 19.1 - - + +
496A THR* 1.3 76.1 - - - +
498A GLU* 1.3 62.6 + - + +
501A THR* 2.8 32.2 + - + +
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Residues in contact with GLU 498 (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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155A LYS* 4.1 17.9 + - - +
156A LYS* 4.3 18.2 + - - +
494A TYR* 3.0 54.9 + - + +
495A LYS* 3.8 9.4 - - - +
497A ILE* 1.3 78.7 - - + +
499A ARG* 1.3 57.7 + - + +
501A THR* 3.6 5.7 + - - -
502A GLY* 2.9 27.4 + - - -
518A ILE* 4.6 4.8 - - - +
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Residues in contact with ARG 499 (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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495A LYS* 3.0 35.9 + - + +
496A THR* 3.7 12.3 + - + +
498A GLU* 1.3 75.0 - - + +
500A MET* 1.3 65.7 + - - +
502A GLY* 3.7 0.3 - - - -
503A ILE* 2.9 38.4 + - + +
518A ILE* 4.1 16.5 - - + +
519A GLU* 2.8 48.3 + - + +
520A GLY* 3.7 13.5 - - - -
541A ILE* 5.6 2.5 - - + -
542A SER 3.9 8.1 + - - -
543A ASP* 2.9 31.7 + - - +
544A GLU* 4.3 3.4 - - - +
545A LEU* 4.0 30.1 - - + +
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Residues in contact with MET 500 (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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444A TYR* 5.1 2.2 - - + -
446A PHE* 3.6 36.1 - - + -
474A GLU* 5.2 0.9 - - + -
477A TYR* 3.8 19.3 - - + +
478A PHE* 3.5 35.8 - - + -
496A THR* 2.9 33.7 + - + +
499A ARG* 1.3 75.9 - - - +
501A THR* 1.3 64.4 + - - +
503A ILE* 4.7 2.0 - - - -
504A TRP* 3.0 51.4 + - + +
541A ILE* 3.8 30.5 - - + -
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Residues in contact with THR 501 (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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152A TYR* 4.1 25.7 + - + -
153A PHE* 4.2 29.8 - - + +
156A LYS* 4.2 17.6 - - - +
477A TYR 3.9 13.0 - - - +
478A PHE* 4.2 11.4 - - - +
497A ILE* 2.8 26.8 + - - +
498A GLU* 3.6 7.8 + - - -
500A MET* 1.3 75.8 - - - +
502A GLY* 1.3 56.0 + - - +
504A TRP* 4.0 0.5 - - - +
505A THR* 2.5 39.0 + - - -
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Residues in contact with GLY 502 (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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156A LYS* 4.2 15.7 - - - -
498A GLU 2.9 21.4 + - - -
501A THR* 1.3 78.7 + - - +
503A ILE* 1.3 55.5 + - - +
505A THR* 3.8 0.9 - - - -
506A GLN* 2.9 31.0 + - - +
518A ILE* 3.6 22.8 - - - +
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Residues in contact with ILE 503 (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 MET* 4.3 2.5 - - + -
499A ARG* 2.9 28.2 + - + +
500A MET* 4.7 2.5 - - - -
502A GLY* 1.3 72.5 - - - +
504A TRP* 1.3 85.5 + - + +
506A GLN* 3.3 2.2 + - - +
507A PHE* 2.9 28.1 + - - +
513A PRO* 3.2 38.4 - - + +
518A ILE* 4.3 17.7 - - + -
521A MET* 3.5 29.4 - - + -
526A TRP* 4.0 10.5 - - + -
539A LEU* 5.3 4.0 - - + -
541A ILE* 5.8 4.0 - - + -
545A LEU* 5.8 3.1 - - + -
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Residues in contact with TRP 504 (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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130A LEU* 4.7 5.0 - - + +
153A PHE* 4.3 11.9 - + + -
215A PHE* 3.6 23.1 - + - -
241A ILE* 3.5 34.5 - - + +
243A MET* 3.5 28.8 - - + -
344A MET* 3.9 9.6 - - + -
444A TYR* 3.6 40.4 - + + -
478A PHE* 3.3 26.8 - + + -
500A MET* 3.0 47.5 + - + +
501A THR 4.0 2.7 - - - +
503A ILE* 1.3 97.4 - - + +
505A THR* 1.3 58.3 + - - +
507A PHE* 3.4 5.8 + - - +
508A ALA* 2.9 30.1 + - - +
541A ILE* 5.1 2.9 - - + -
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Residues in contact with THR 505 (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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130A LEU* 4.9 3.6 - - - +
153A PHE* 4.4 9.2 - - - -
156A LYS* 3.5 35.6 - - + +
157A ASP* 4.8 2.9 - - + +
158A VAL* 3.6 29.1 - - + +
501A THR 2.5 24.4 + - - -
502A GLY 3.8 2.5 - - - -
504A TRP* 1.3 74.3 - - - +
506A GLN* 1.3 59.7 + - - +
508A ALA* 3.3 6.4 + - - +
509A THR* 2.8 38.0 + - - +
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Residues in contact with GLN 506 (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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502A GLY 2.9 19.7 + - - +
503A ILE* 3.3 4.9 + - - +
505A THR* 1.3 75.4 - - - +
507A PHE* 1.3 62.2 + - - +
509A THR* 3.2 8.0 + - - +
510A THR* 3.0 42.9 + - - +
512A ASN 3.3 11.3 + - - +
513A PRO 4.0 4.7 - - - +
514A TYR 2.9 31.9 + - - +
515A SER* 3.4 25.5 + - - +
518A ILE* 5.8 0.2 - - + -
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Residues in contact with PHE 507 (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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213A THR* 4.8 0.2 - - + -
239A ARG* 3.7 20.3 - - + +
240A GLY 3.6 16.6 - - - -
241A ILE* 3.7 24.0 - - + -
342A PRO* 3.7 7.2 - - + -
343A THR 3.5 38.4 - - - -
344A MET* 3.5 22.7 - - + -
442A TYR* 4.2 7.6 - + - -
503A ILE 2.9 17.6 + - - +
504A TRP 3.7 3.1 - - - +
506A GLN* 1.3 77.6 - - - +
508A ALA* 1.3 61.2 - - - +
511A GLY* 2.7 48.5 + - - -
512A ASN 3.9 7.6 + - - -
513A PRO* 3.7 24.9 - - + -
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Residues in contact with ALA 508 (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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128A PRO* 4.3 6.9 - - + +
130A LEU* 3.6 30.7 - - + -
211A ASN* 3.3 12.0 + - - +
213A THR* 3.2 29.0 + - + +
239A ARG* 2.9 21.1 + - - -
504A TRP 2.9 18.1 + - - +
505A THR 3.6 5.4 - - - +
507A PHE* 1.3 76.6 - - - +
509A THR* 1.3 59.3 + - - +
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Residues in contact with THR 509 (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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128A PRO* 3.5 21.2 - - + +
158A VAL* 5.0 0.2 - - - +
211A ASN* 3.1 19.0 + - - +
239A ARG* 3.1 13.3 + - - -
505A THR* 2.8 26.6 + - - +
506A GLN* 3.5 9.8 + - - +
507A PHE 3.2 0.2 - - - -
508A ALA* 1.3 76.9 - - - +
510A THR* 1.3 72.0 + - + +
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Residues in contact with THR 510 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239A ARG* 3.3 13.2 + - - +
342A PRO* 5.5 0.3 - - - +
506A GLN* 3.0 22.1 + - - +
509A THR* 1.3 94.8 - - + +
511A GLY* 1.3 60.5 + - - +
512A ASN* 3.1 32.0 + - - +
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Residues in contact with GLY 511 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239A ARG* 3.6 9.9 - - - +
342A PRO* 3.8 29.1 - - - +
440A PRO* 4.3 4.2 - - - +
442A TYR* 3.6 17.5 + - - -
507A PHE* 2.7 34.2 + - - -
510A THR* 1.3 72.8 - - - +
512A ASN* 1.3 58.0 + - - +
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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
------------------------------------------------------------
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