Contacts of the helix formed by residues 515 - 529 (chain D) in PDB entry 1JIQ
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 VAL 515 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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388C GLN 5.4 7.9 - - - +
389C HIS* 6.3 1.6 - - - +
392C TYR* 6.1 1.3 - - + -
393C GLN* 4.6 11.2 - - + +
396C HIS* 5.7 0.9 - - - -
432C GLN* 5.3 2.9 + - - +
358D GLU* 3.8 22.0 - - - +
512D GLN* 3.3 29.4 - - + +
514D GLY* 1.3 78.1 - - - +
516D GLU* 1.3 67.4 + - + +
517D LEU 3.6 0.7 - - - -
518D GLY* 4.0 3.2 + - - -
519D LYS* 3.2 49.4 + - - +
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Residues in contact with GLU 516 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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440C LYS* 4.1 4.7 + - - +
448C GLU* 4.7 2.4 - - - +
466C LYS* 3.1 36.7 + - - -
468C PHE* 4.7 4.0 - - + -
513D TRP* 3.2 31.4 + - + +
514D GLY 3.3 0.2 - - - -
515D VAL* 1.3 82.1 - - + +
517D LEU* 1.3 67.4 + - - +
519D LYS* 3.1 10.2 + - + +
520D GLN* 3.1 48.9 + - + +
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Residues in contact with LEU 517 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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435C ALA* 3.6 34.3 - - + +
438C ARG* 5.5 0.2 - - + -
439C GLY* 3.5 35.7 - - - +
440C LYS* 4.1 11.9 - - + -
468C PHE* 3.6 38.1 - - + -
515D VAL 3.6 0.4 - - - -
516D GLU* 1.3 77.5 - - - +
518D GLY* 1.3 64.2 + - - +
520D GLN* 3.1 21.2 + - - +
521D LEU* 3.0 46.4 + - + +
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Residues in contact with GLY 518 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
396C HIS* 5.1 4.0 + - - -
428C ASN* 5.0 1.7 - - - +
431C ALA* 3.6 8.9 - - - +
432C GLN* 3.5 28.0 - - - -
435C ALA* 4.1 15.2 - - - +
514D GLY 5.3 0.4 + - - -
515D VAL 4.0 3.4 + - - -
516D GLU 3.3 0.8 - - - -
517D LEU* 1.3 78.6 - - - +
519D LYS* 1.3 62.1 + - - +
521D LEU* 3.4 0.4 + - - -
522D ALA* 3.0 25.8 + - - +
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Residues in contact with LYS 519 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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388C GLN* 6.1 2.9 - - - +
389C HIS* 5.3 15.3 - - + -
428C ASN* 5.5 2.7 - - - +
432C GLN* 6.0 1.1 - - - +
157D ILE* 6.4 0.9 - - - -
515D VAL* 3.2 42.7 + - + +
516D GLU* 3.1 9.5 + - + +
518D GLY* 1.3 73.6 - - - +
520D GLN* 1.3 67.7 + - + +
522D ALA* 3.3 5.6 + - - +
523D LYS* 3.1 29.7 + - + +
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Residues in contact with GLN 520 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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440C LYS* 2.6 30.6 + - - +
448C GLU* 3.1 24.6 + - - +
516D GLU* 3.1 26.9 + - + +
517D LEU* 3.4 18.3 - - + +
519D LYS* 1.3 81.0 - - + +
521D LEU* 1.3 70.1 + - + +
523D LYS* 3.4 8.0 + - - +
524D LYS* 3.3 24.7 + - + +
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Residues in contact with LEU 521 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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431C ALA* 3.6 13.0 - - + +
434C GLU* 3.5 32.3 - - + +
435C ALA* 3.7 35.4 - - + +
438C ARG* 5.4 4.7 - - + -
517D LEU* 3.0 34.7 + - + +
518D GLY 4.0 0.4 - - - +
519D LYS 3.3 0.2 - - - -
520D GLN* 1.3 79.2 - - + +
522D ALA* 1.3 63.2 + - - +
524D LYS* 3.3 35.2 + - + +
525D ILE* 3.1 26.3 + - - +
538D HIS* 5.3 0.6 - - + -
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Residues in contact with ALA 522 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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427C ALA* 3.9 12.5 - - + +
428C ASN* 4.0 27.4 - - - +
431C ALA* 3.2 14.9 - - + +
216D GLN* 6.0 1.1 - - - +
518D GLY 3.0 18.3 + - - +
519D LYS* 3.8 5.4 - - - +
520D GLN 3.3 0.2 - - - -
521D LEU* 1.3 72.8 - - - +
523D LYS* 1.3 66.6 + - + +
525D ILE* 3.1 2.4 + - - +
526D GLU* 3.0 33.7 + - - +
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Residues in contact with LYS 523 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216D GLN* 3.4 22.0 + - - +
519D LYS* 3.1 18.8 + - + +
520D GLN* 3.6 10.3 - - - +
521D LEU 3.3 0.2 - - - -
522D ALA* 1.3 78.0 - - + +
524D LYS* 1.3 60.3 + - + +
526D GLU* 3.2 31.1 + - - +
527D PRO* 3.2 18.4 - - - +
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Residues in contact with LYS 524 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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520D GLN* 3.3 17.6 + - - +
521D LEU* 3.3 32.8 + - + +
522D ALA 3.2 0.4 - - - -
523D LYS* 1.3 80.5 - - + +
525D ILE* 1.3 63.4 + - + +
527D PRO* 3.2 17.1 - - - +
528D GLU* 3.6 14.9 - - - +
538D HIS* 4.9 10.5 - - + -
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Residues in contact with ILE 525 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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427C ALA* 4.0 13.0 - - - +
430C LEU* 3.8 30.7 - - + -
431C ALA* 3.8 25.6 - - + +
434C GLU* 3.7 20.9 - - - +
521D LEU 3.1 14.1 + - - +
522D ALA 3.1 5.0 + - - +
524D LYS* 1.3 76.1 - - - +
526D GLU* 1.3 67.7 + - - +
528D GLU* 2.8 20.2 + - - +
529D LEU* 3.3 17.2 + - + +
538D HIS* 3.6 24.5 - - + +
542D THR* 4.3 7.2 - - + -
546D ILE* 4.5 7.4 - - + -
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Residues in contact with GLU 526 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423C LYS* 2.9 33.6 - - + +
424C ILE* 4.3 18.4 - - - +
427C ALA* 3.6 18.8 - - + +
428C ASN* 4.8 2.3 + - - -
216D GLN* 2.8 31.4 + - - +
522D ALA* 3.0 28.2 + - - +
523D LYS* 3.2 31.0 + - - +
525D ILE* 1.3 77.1 - - - +
527D PRO* 1.3 70.6 - - + +
529D LEU* 3.2 13.3 + - - +
530D ASP* 3.9 0.2 - - - +
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Residues in contact with PRO 527 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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423C LYS* 4.5 1.8 - - - +
523D LYS 3.2 11.2 - - - +
524D LYS* 3.2 18.8 - - - +
526D GLU* 1.3 98.9 - - + +
528D GLU* 1.3 61.6 + - + +
530D ASP* 3.4 28.8 + - - +
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Residues in contact with GLU 528 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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524D LYS* 3.6 17.3 - - - +
525D ILE* 2.8 16.4 + - + +
527D PRO* 1.3 77.6 - - + +
529D LEU* 1.3 61.4 + - - +
530D ASP 3.2 2.1 + - - +
535D VAL* 3.8 22.4 - - + +
537D SER* 2.8 24.6 + - - -
538D HIS* 2.6 32.2 + - - -
546D ILE* 4.5 3.0 - - + +
550D LYS* 2.9 27.9 + - - -
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Residues in contact with LEU 529 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423C LYS* 3.5 37.5 - - + +
426C LEU* 4.1 10.8 - - + -
427C ALA* 4.0 19.3 - - + +
430C LEU* 4.1 19.7 - - + -
525D ILE* 3.7 15.7 - - + +
526D GLU 3.2 8.4 + - - +
528D GLU* 1.3 77.3 - - - +
530D ASP* 1.3 62.8 + - - +
546D ILE* 4.1 20.0 - - + -
549D ILE* 5.0 15.0 - - + -
550D LYS* 3.7 4.8 - - + +
553D ARG* 2.6 41.5 + - - +
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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
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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