Contacts of the helix formed by residues 514 - 528 (chain A) in PDB entry 1U0E
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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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357A GLU* 4.0 17.3 - - - +
511A GLN* 3.4 27.1 - - + +
513A GLY* 1.3 79.8 - - - +
515A GLU* 1.3 65.2 + - - +
516A LEU 3.5 0.7 - - - -
517A GLY* 3.9 4.6 + - - -
518A LYS* 3.5 46.9 + - - +
387B GLN 3.7 23.3 - - - +
388B HIS* 5.4 0.9 - - - +
391B TYR* 5.2 1.3 - - + -
392B GLN* 4.4 17.7 - - + +
395B HIS* 5.5 1.1 - - - -
431B GLN* 5.3 2.3 + - - +
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Residues in contact with GLU 515 (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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512A TRP* 3.3 28.2 + - + +
513A GLY 3.4 0.2 - - - -
514A VAL* 1.3 79.0 - - + +
516A LEU* 1.3 66.1 + - - +
518A LYS* 3.1 20.7 + - + +
519A GLN* 3.1 40.0 + - + +
439B LYS* 4.3 7.5 + - - +
447B GLU* 4.6 4.8 - - - +
465B LYS* 4.1 24.6 - - - +
467B PHE* 4.7 3.5 - - + -
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Residues in contact with LEU 516 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
514A VAL 3.5 0.6 - - - -
515A GLU* 1.3 77.2 - - - +
517A GLY* 1.3 64.1 + - - +
519A GLN* 3.1 13.9 + - + +
520A LEU* 2.9 43.6 + - + +
523A LYS* 5.9 0.4 - - - +
395B HIS* 5.5 0.2 - - - +
434B ALA* 3.7 32.1 - - + +
437B LYS* 6.1 0.4 - - + -
438B GLY* 3.5 36.1 - - - +
439B LYS* 3.9 20.2 - - + +
467B PHE* 3.7 37.4 - - + -
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Residues in contact with GLY 517 (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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513A GLY 5.4 0.4 + - - -
514A VAL 3.9 5.5 + - - -
515A GLU 3.3 0.6 - - - -
516A LEU* 1.3 77.9 - - - +
518A LYS* 1.3 60.7 + - - +
520A LEU 3.5 0.4 + - - -
521A ALA* 3.1 25.3 + - - +
395B HIS* 5.2 4.2 + - - -
427B ASN* 4.8 1.6 - - - +
430B ALA* 3.7 8.3 - - - +
431B GLN* 3.4 32.1 + - - -
434B ALA* 4.3 12.6 - - - +
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Residues in contact with LYS 518 (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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214A THR* 6.0 3.0 - - - +
514A VAL* 3.5 41.7 + - - +
515A GLU* 3.1 10.4 + - + +
517A GLY* 1.3 72.3 - - - +
519A GLN* 1.3 66.5 + - + +
521A ALA* 3.4 5.6 + - - +
522A LYS* 3.2 32.9 + - + +
387B GLN* 5.9 2.7 - - - +
388B HIS* 4.5 24.0 + - + -
427B ASN* 5.4 4.3 - - - +
431B GLN* 4.6 0.6 - - - +
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Residues in contact with GLN 519 (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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515A GLU* 3.1 29.9 + - + +
516A LEU* 3.1 13.3 + - + +
518A LYS* 1.3 78.2 - - + +
520A LEU* 1.3 65.0 + - + +
522A LYS* 3.3 18.7 + - + +
523A LYS* 3.3 33.6 + - - +
439B LYS* 2.7 30.0 + - - -
447B GLU* 2.9 28.1 + - - -
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Residues in contact with LEU 520 (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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516A LEU* 2.9 34.6 + - + +
519A GLN* 1.3 76.2 - - - +
521A ALA* 1.3 62.0 + - - +
523A LYS* 3.4 32.8 + - + +
524A ILE* 3.2 27.0 + - - +
537A HIS* 6.5 0.2 - - + -
430B ALA* 3.5 15.5 - - + +
433B GLU* 3.7 25.5 - - + +
434B ALA* 3.6 39.5 - - + +
437B LYS* 4.8 13.5 - - + +
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Residues in contact with ALA 521 (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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517A GLY 3.1 18.2 + - - +
518A LYS* 3.7 6.1 - - - +
519A GLN 3.2 0.2 - - - -
520A LEU* 1.3 76.0 - - - +
522A LYS* 1.3 64.5 + - + +
524A ILE* 3.3 1.2 + - - +
525A GLU* 3.1 33.2 + - - +
426B ALA* 3.7 15.2 - - + +
427B ASN* 3.8 26.0 - - - +
430B ALA* 3.2 13.6 - - + +
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Residues in contact with LYS 522 (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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215A GLN* 6.0 7.9 - - + +
518A LYS* 3.2 21.1 + - + +
519A GLN* 3.3 11.4 + - + +
521A ALA* 1.3 76.1 - - + +
523A LYS* 1.3 60.7 + - + +
525A GLU* 3.9 16.0 - - - +
526A PRO* 3.3 18.2 - - - +
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Residues in contact with LYS 523 (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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516A LEU* 5.9 0.4 - - - +
519A GLN* 3.3 25.6 + - - +
520A LEU* 3.6 35.6 - - + +
521A ALA 3.2 0.4 - - - -
522A LYS* 1.3 77.6 - - + +
524A ILE* 1.3 64.0 + - + +
526A PRO* 3.4 15.8 - - - +
527A GLU* 3.7 15.2 - - - +
537A HIS* 5.3 7.9 - - + -
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Residues in contact with ILE 524 (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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520A LEU 3.2 18.7 + - - +
521A ALA 3.3 4.2 + - - +
523A LYS* 1.3 75.9 - - - +
525A GLU* 1.3 67.5 + - - +
527A GLU* 3.0 17.4 + - - +
528A LEU* 3.3 14.0 + - + +
537A HIS* 3.7 24.9 - - + +
541A THR* 4.3 6.5 - - + -
545A ILE* 4.4 7.4 - - + -
426B ALA* 3.9 13.5 - - + -
429B LEU* 3.8 32.8 - - + -
430B ALA* 3.6 25.4 - - + +
433B GLU* 3.6 19.3 - - - +
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Residues in contact with GLU 525 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215A GLN* 3.4 29.6 + - - +
521A ALA* 3.1 29.6 + - - +
522A LYS* 3.9 14.4 - - - +
524A ILE* 1.3 78.1 - - - +
526A PRO* 1.3 69.9 - - + +
527A GLU 3.4 0.2 + - - -
528A LEU* 3.4 17.6 + - - +
529A GLU 4.1 0.9 + - - -
422B LYS* 3.9 26.8 - - + +
423B ILE* 4.2 24.1 - - + +
426B ALA* 3.6 18.6 - - + +
427B ASN* 4.9 0.7 + - - -
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Residues in contact with PRO 526 (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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522A LYS 3.3 15.0 - - - +
523A LYS* 3.4 11.9 - - - +
525A GLU* 1.3 94.2 - - + +
527A GLU* 1.3 64.2 + - + +
529A GLU* 3.3 39.6 + - - +
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Residues in contact with GLU 527 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
523A LYS* 3.7 18.7 - - - +
524A ILE* 3.0 16.1 + - - +
526A PRO* 1.3 79.6 - - + +
528A LEU* 1.3 59.3 + - - +
529A GLU 3.4 2.4 + - - +
534A VAL* 3.8 25.6 - - + +
536A SER* 2.9 24.1 + - - -
537A HIS* 2.6 29.9 + - - -
545A ILE* 4.2 4.3 - - + +
549A LYS* 2.9 26.4 + - - -
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Residues in contact with LEU 528 (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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524A ILE* 3.7 11.4 - - + +
525A GLU 3.6 6.7 - - - +
526A PRO 3.2 0.6 - - - -
527A GLU* 1.3 76.4 - - - +
529A GLU* 1.3 62.1 + - - +
545A ILE* 4.2 20.2 - - + -
548A ILE* 4.4 19.3 - - + -
549A LYS* 3.6 5.5 - - - +
552A ARG* 2.7 35.4 + - - +
422B LYS* 3.5 39.3 - - + +
425B LEU* 3.9 11.7 - - + -
426B ALA* 3.9 23.3 - - + +
429B LEU* 4.0 19.5 - - + -
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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