Contacts of the helix formed by residues 514 - 528 (chain B) in PDB entry 1N8T
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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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387A GLN 5.4 7.6 - - - +
388A HIS* 6.3 0.9 - - - +
391A TYR* 6.4 1.1 - - + -
392A GLN* 4.8 10.5 - - + +
395A HIS* 5.9 0.7 - - - -
431A GLN* 5.5 1.5 + - - +
357B GLU* 4.4 17.0 - - - +
511B GLN* 3.6 26.0 - - + +
512B TRP 3.1 0.4 - - - -
513B GLY* 1.3 79.3 - - - +
515B GLU* 1.3 72.3 + - + +
516B LEU 3.4 0.8 + - - -
517B GLY* 3.6 3.8 + - - -
518B LYS* 3.4 52.8 + - + +
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Residues in contact with GLU 515 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
439A LYS* 5.1 6.4 + - - +
465A LYS* 3.0 35.3 + - - +
467A PHE* 4.8 4.0 - - + -
512B TRP* 3.3 38.6 + - - +
514B VAL* 1.3 85.3 - - + +
516B LEU* 1.3 63.6 + - - +
518B LYS* 3.3 7.6 + - + +
519B GLN* 3.1 32.3 + - - +
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Residues in contact with LEU 516 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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434A ALA* 3.8 27.1 - - + +
437A LYS* 5.9 2.2 - - + -
438A GLY* 3.7 34.5 - - - +
439A LYS* 4.3 10.8 - - + +
467A PHE* 3.6 47.8 - - + -
514B VAL 3.4 0.8 - - - -
515B GLU* 1.3 77.1 - - - +
517B GLY* 1.3 63.8 + - - +
519B GLN* 3.0 26.3 - - - +
520B LEU* 3.0 44.5 + - + +
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Residues in contact with GLY 517 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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387A GLN* 5.9 0.2 - - - -
395A HIS* 5.2 2.7 - - - -
427A ASN* 4.9 2.3 - - - +
430A ALA* 3.8 6.7 - - - +
431A GLN* 3.7 27.3 + - - -
434A ALA* 4.4 13.5 - - - +
513B GLY 5.1 1.8 + - - -
514B VAL 3.6 5.4 + - - -
515B GLU 3.4 0.2 - - - -
516B LEU* 1.3 79.4 - - - +
518B LYS* 1.3 61.0 + - - +
520B LEU* 4.7 1.6 - - - -
521B ALA* 3.0 25.5 + - - +
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Residues in contact with LYS 518 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387A GLN* 5.8 3.4 - - - +
388A HIS* 5.3 15.5 - - + -
427A ASN* 5.4 3.8 - - - +
431A GLN* 4.9 0.6 - - - +
156B ILE* 6.1 3.7 - - - +
216B GLU* 5.9 3.1 - - - +
514B VAL* 3.4 41.1 + - + +
515B GLU* 3.3 9.3 + - - +
516B LEU 3.3 0.4 - - - -
517B GLY* 1.3 76.1 - - - +
519B GLN* 1.3 63.8 + - - +
521B ALA* 3.3 6.6 + - - +
522B LYS* 3.1 27.2 + - + +
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Residues in contact with GLN 519 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
439A LYS* 2.9 34.6 + - - +
447A GLU* 3.8 13.1 + - - +
515B GLU* 3.1 15.4 + - - +
516B LEU* 3.0 38.2 - - + +
518B LYS* 1.3 76.9 - - - +
520B LEU* 1.3 68.0 + - + +
522B LYS* 3.3 9.9 + - - -
523B LYS* 2.9 36.6 + - - +
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Residues in contact with LEU 520 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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430A ALA* 3.7 12.1 - - + +
433A GLU* 3.2 37.8 - - + +
434A ALA* 3.7 30.3 - - + +
437A LYS* 4.8 16.6 - - + +
516B LEU* 3.0 34.8 + - + +
517B GLY 4.0 0.4 - - - +
519B GLN* 1.3 85.9 - - + +
521B ALA* 1.3 60.1 + - - +
523B LYS* 3.2 15.3 + - + +
524B ILE* 3.2 25.3 + - - +
537B HIS* 5.4 0.8 - - + -
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Residues in contact with ALA 521 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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426A ALA* 3.6 23.1 - - + +
427A ASN* 4.0 20.9 - - - +
430A ALA* 3.3 16.5 - - + +
215B GLN* 6.1 0.7 - - - +
517B GLY 3.0 19.1 + - - +
518B LYS* 3.7 5.6 - - - +
519B GLN 3.3 0.2 - - - -
520B LEU* 1.3 74.0 - - - +
522B LYS* 1.3 65.1 + - - +
524B ILE* 3.4 1.5 + - - -
525B GLU* 3.0 27.5 + - - +
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Residues in contact with LYS 522 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215B GLN* 3.9 22.1 - - - +
518B LYS* 3.1 16.3 + - + +
519B GLN* 3.3 10.3 + - - +
521B ALA* 1.3 75.8 - - - +
523B LYS* 1.3 75.4 + - - +
525B GLU* 3.3 30.6 + - - +
526B PRO* 3.2 19.8 - - - +
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Residues in contact with LYS 523 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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519B GLN* 2.9 41.4 + - - +
520B LEU* 3.2 16.3 + - + +
521B ALA 3.2 0.4 - - - -
522B LYS* 1.3 91.8 - - - +
524B ILE* 1.3 63.5 + - + +
526B PRO* 3.4 16.7 - - - +
527B GLU* 3.5 18.0 - - - +
537B HIS* 5.1 8.5 - - + -
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Residues in contact with ILE 524 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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426A ALA* 3.8 19.5 - - + -
429A LEU* 3.9 16.2 - - + -
430A ALA* 3.7 27.1 - - + +
433A GLU* 3.6 18.4 - - - +
520B LEU 3.2 17.5 + - - +
521B ALA 3.8 4.3 - - - +
522B LYS 3.3 0.2 - - - -
523B LYS* 1.3 76.5 - - - +
525B GLU* 1.3 67.7 + - - +
527B GLU* 2.8 22.3 + - - +
528B LEU* 3.2 28.9 + - + -
537B HIS* 3.8 21.3 - - + +
541B THR* 4.4 5.4 - - + -
545B ILE* 4.5 5.6 - - + -
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Residues in contact with GLU 525 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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419A LEU* 5.8 1.2 - - - +
422A LYS* 3.9 28.4 - - + +
423A ILE* 4.1 17.2 - - - +
426A ALA* 3.7 21.6 - - + +
427A ASN* 5.0 0.3 + - - -
215B GLN* 2.9 29.8 + - - +
521B ALA* 3.0 22.0 + - - +
522B LYS* 3.3 30.7 + - - +
524B ILE* 1.3 78.1 - - - +
526B PRO* 1.3 69.6 - - + +
528B LEU* 3.3 19.1 + - - +
529B ASP 4.2 1.2 + - - -
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Residues in contact with PRO 526 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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522B LYS 3.2 14.1 - - - +
523B LYS* 3.4 10.8 - - - +
525B GLU* 1.3 92.0 - - + +
527B GLU* 1.3 67.5 + - + +
528B LEU 3.1 2.9 + - - -
529B ASP* 3.3 30.8 + - - +
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Residues in contact with GLU 527 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
523B LYS* 3.5 21.7 - - - +
524B ILE* 2.8 15.3 + - - +
526B PRO* 1.3 79.3 - - + +
528B LEU* 1.3 61.0 + - + +
529B ASP 3.4 2.1 + - - +
534B VAL* 3.7 21.9 - - + +
536B SER* 3.2 20.1 + - - -
537B HIS* 2.6 31.3 + - - -
545B ILE* 4.4 2.5 - - + +
549B LYS* 2.9 27.9 + - - -
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Residues in contact with LEU 528 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
422A LYS* 3.6 38.4 - - + +
425A LEU* 3.8 21.8 - - + -
426A ALA* 3.9 8.1 - - + +
429A LEU* 4.1 11.2 - - + -
524B ILE* 3.2 31.6 + - + +
525B GLU 3.4 10.3 - - - +
526B PRO 3.1 0.6 - - - -
527B GLU* 1.3 78.2 - - + +
529B ASP* 1.3 63.6 + - - +
545B ILE* 4.2 19.1 - - + -
548B ILE* 5.4 5.6 - - + -
549B LYS* 3.7 7.4 - - + +
552B ARG* 2.5 38.7 + - - +
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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