Contacts of the helix formed by residues 514 - 525 (chain D) in PDB entry 1JLH
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 514 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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387C GLN 5.6 6.3 - - - +
391C TYR* 5.9 2.5 - - + -
392C GLN* 4.3 14.6 - - + +
431C GLN* 5.5 1.2 + - - -
357D GLU* 4.5 13.2 - - - +
511D GLN* 3.3 32.8 - - + +
512D TRP 2.9 1.4 + - - -
513D GLY* 1.3 82.8 - - - +
515D GLU* 1.3 74.9 + - + +
516D LEU 3.6 1.1 + - - -
517D GLY* 3.9 3.7 + - - -
518D LYS* 3.7 17.7 + - - +
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Residues in contact with GLU 515 (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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439C LYS* 4.9 4.6 + - - +
465C LYS* 2.8 39.2 + - - +
467C PHE* 4.7 4.0 - - + -
511D GLN 5.3 0.2 - - - +
512D TRP* 3.2 34.6 + - + +
514D VAL* 1.3 84.0 - - + +
516D LEU* 1.3 67.4 + - - +
518D LYS* 3.2 6.6 + - - +
519D GLN* 3.0 39.4 + - + +
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Residues in contact with LEU 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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395C HIS* 5.2 0.2 - - + -
434C ALA* 3.6 30.5 - - + +
437C ARG* 5.1 3.1 - - - +
438C GLY* 3.6 33.7 - - - +
439C LYS* 4.3 17.5 - - + -
467C PHE* 3.6 40.3 - - + -
514D VAL 3.6 0.8 - - - -
515D GLU* 1.3 76.0 - - - +
517D GLY* 1.3 65.2 + - - +
519D GLN* 2.9 23.6 + - + +
520D LEU* 3.0 35.8 + - + +
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Residues in contact with GLY 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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387C GLN* 5.9 0.2 - - - -
395C HIS* 5.0 3.6 + - - -
427C ASN* 5.5 0.9 - - - -
430C ALA* 3.6 9.0 - - - +
431C GLN* 3.5 28.4 + - - -
434C ALA* 4.0 15.4 - - - +
467C PHE* 5.4 0.4 - - - -
513D GLY 5.6 0.2 + - - -
514D VAL 3.9 4.5 + - - -
515D GLU 3.4 1.0 - - - -
516D LEU* 1.3 79.0 - - - +
518D LYS* 1.3 61.1 + - - +
520D LEU 3.4 0.3 + - - -
521D ALA* 3.1 24.3 + - - +
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Residues in contact with LYS 518 (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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387C GLN* 5.9 0.4 + - - -
427C ASN* 5.4 3.4 - - - -
431C GLN* 4.6 0.8 - - - +
213D THR 5.1 1.2 + - - -
214D THR* 4.7 8.1 - - - +
215D GLN* 4.0 38.6 - - - +
216D GLU* 4.7 9.6 + - - +
514D VAL 3.7 12.2 + - - +
515D GLU* 3.2 8.8 + - - +
516D LEU 3.2 1.0 - - - -
517D GLY* 1.3 72.6 - - - +
519D GLN* 1.3 65.8 + - + +
521D ALA* 3.5 6.5 + - + +
522D LYS* 3.2 34.6 + - + +
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Residues in contact with GLN 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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439C LYS* 2.6 30.8 + - - +
447C GLU* 3.1 23.7 - - - +
515D GLU* 3.0 35.7 + - + +
516D LEU* 2.9 18.6 + - + +
518D LYS* 1.3 79.6 - - - +
520D LEU* 1.3 68.4 + - + +
522D LYS* 3.4 13.7 + - - +
523D LYS* 3.5 20.7 + - - +
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Residues in contact with LEU 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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430C ALA* 3.5 15.5 - - + +
433C GLU* 3.6 28.3 - - + +
434C ALA* 3.5 40.8 - - + +
437C ARG* 4.9 13.7 - - - +
516D LEU* 3.0 31.1 + - + +
517D GLY 3.9 0.4 - - - +
519D GLN* 1.3 77.9 - - + +
521D ALA* 1.3 64.8 + - - +
523D LYS* 3.2 33.0 + - - +
524D ILE* 3.1 25.6 + - - +
537D HIS* 5.3 1.2 - - + -
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Residues in contact with ALA 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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426C ALA* 3.7 18.3 - - + +
427C ASN* 4.0 22.7 - - - +
430C ALA* 3.1 16.4 - - + +
215D GLN* 6.0 1.1 - - - +
517D GLY 3.1 17.9 + - - +
518D LYS* 3.9 5.8 - - + +
519D GLN 3.4 0.2 - - - -
520D LEU* 1.3 77.3 - - - +
522D LYS* 1.3 64.6 + - + +
524D ILE* 3.2 1.0 + - - -
525D GLU* 3.0 33.1 + - - +
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Residues in contact with LYS 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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215D GLN* 3.6 17.2 + - - +
518D LYS* 3.2 30.0 + - + +
519D GLN* 3.5 11.7 - - - +
520D LEU 3.2 0.4 - - - -
521D ALA* 1.3 78.4 - - + +
523D LYS* 1.3 62.1 + - + +
525D GLU* 2.8 40.3 + - - +
526D PRO* 3.3 18.0 - - - +
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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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519D GLN* 3.5 14.0 + - - +
520D LEU* 3.2 37.9 + - - +
522D LYS* 1.3 79.0 - - + +
524D ILE* 1.3 62.4 + - + +
526D PRO* 3.4 16.8 - - - +
527D GLU* 3.5 15.0 - - - +
537D HIS* 5.3 8.5 - - + -
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Residues in contact with ILE 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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426C ALA* 4.1 10.1 - - + +
429C LEU* 3.9 29.6 - - + -
430C ALA* 3.8 24.5 - - + +
433C GLU* 3.5 21.8 - - - +
520D LEU 3.1 15.1 + - - +
521D ALA 3.8 4.3 - - - +
523D LYS* 1.3 77.9 - - - +
525D GLU* 1.3 67.1 + - - +
527D GLU* 2.9 23.0 + - - +
528D LEU* 3.4 16.8 + - + +
537D HIS* 3.6 20.6 - - + +
541D THR* 4.1 11.0 - - + -
545D ILE* 4.4 6.7 - - + -
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Residues in contact with GLU 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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422C LYS* 2.8 33.6 + - + +
423C ILE* 4.1 20.3 - - + +
426C ALA* 3.6 18.1 - - + +
427C ASN* 5.1 0.2 + - - -
215D GLN* 2.9 27.9 + - - +
521D ALA* 3.0 21.6 + - - +
522D LYS* 2.8 37.6 + - - +
524D ILE* 1.3 77.3 - - - +
526D PRO* 1.3 68.7 - - + +
528D LEU* 3.2 14.8 + - - +
529D ASP* 4.0 0.3 - - - +
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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