Contacts of the helix formed by residues 516 - 529 (chain A) in PDB entry 5I0H
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 THR 516 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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514A GLN 4.0 9.2 - - - +
515A ALA* 1.3 76.7 - - - +
517A ASP* 1.3 64.7 + - - +
518A SER* 3.4 10.6 + - - -
519A THR* 2.9 40.0 + - + +
520A LEU 3.0 7.1 + - - -
561A LEU* 3.4 15.9 - - - +
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Residues in contact with ASP 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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516A THR* 1.3 74.7 - - - +
518A SER* 1.3 56.5 + - - +
520A LEU* 3.4 8.2 + - - +
521A LEU* 2.9 29.5 + - - +
557A VAL* 3.1 37.9 - - + +
558A ARG* 3.6 8.3 - - + +
559A GLY* 2.7 24.7 + - - -
560A ILE* 3.8 2.0 - - - +
561A LEU* 2.9 35.4 + - - +
562A GLU 5.4 0.5 + - - -
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Residues in contact with SER 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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516A THR* 3.1 10.0 + - - -
517A ASP* 1.3 75.9 - - - +
519A THR* 1.4 64.9 + - - +
521A LEU* 3.3 7.2 + - - +
522A GLU* 3.1 34.8 + - - +
557A VAL* 5.3 1.3 - - - -
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Residues in contact with THR 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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509A GLU* 3.0 16.9 + - - -
514A GLN 5.4 1.8 - - - +
515A ALA* 3.6 5.3 - - - -
516A THR* 2.9 40.8 + - + +
518A SER* 1.4 73.0 - - - +
520A LEU* 1.3 64.3 + - - +
522A GLU* 3.4 20.3 + - - +
523A LYS* 3.2 32.5 + - - +
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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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505A LEU* 3.8 16.4 - - + +
506A ILE* 3.9 17.9 - - + -
509A GLU* 3.6 31.2 + - + -
516A THR 3.0 14.0 + - - +
517A ASP* 3.4 11.9 - - - +
519A THR* 1.3 77.1 + - - +
521A LEU* 1.4 58.3 + - - +
523A LYS* 3.0 6.7 + - + +
524A LEU* 2.9 48.3 + - + +
557A VAL* 5.1 3.6 - - + -
560A ILE* 3.9 30.3 - - + -
561A LEU* 3.9 20.2 - - + -
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Residues in contact with LEU 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 ASP 2.9 17.1 + - - +
518A SER* 3.3 6.5 + - - +
520A LEU* 1.4 71.8 - - - +
522A GLU* 1.3 66.2 + - - +
524A LEU* 3.3 6.0 + - + -
525A HIS* 2.9 59.4 + - + +
534A TYR* 4.4 2.2 - - - +
541A VAL 3.2 27.4 - - - +
542A ASN* 3.6 21.8 - - - +
543A ASN 3.8 10.5 - - - +
544A PHE* 3.9 11.7 - - + -
557A VAL* 3.6 24.2 - - + -
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Residues in contact with GLU 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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518A SER* 3.1 25.1 + - - +
519A THR* 3.6 20.0 - - - +
520A LEU 3.3 0.2 - - - -
521A LEU* 1.3 74.5 - - - +
523A LYS* 1.4 56.4 + - + +
525A HIS* 3.5 7.1 + - - +
526A SER* 2.8 39.2 + - - +
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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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505A LEU* 4.0 21.7 - - + +
508A GLU* 6.5 0.7 - - + -
509A GLU* 3.2 41.9 + - + +
519A THR* 3.2 15.0 + - - +
520A LEU* 3.0 11.2 + - + +
522A GLU* 1.4 76.2 - - + +
524A LEU* 1.3 65.4 + - - +
526A SER* 3.9 5.2 - - - -
527A GLN* 3.0 28.4 + - - +
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Residues in contact with LEU 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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502A LEU* 3.9 28.9 - - + +
505A LEU* 3.8 31.6 - - + -
506A ILE* 4.7 4.9 - - + -
520A LEU* 2.9 39.4 + - + +
521A LEU* 3.3 11.6 + - + +
523A LYS* 1.3 75.7 - - - +
525A HIS* 1.4 56.5 + - - +
528A HIS* 2.9 36.5 + - - +
534A TYR* 3.3 17.4 + - + +
544A PHE* 3.8 37.9 - - + -
557A VAL* 4.6 0.9 - - + -
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Residues in contact with HIS 525 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
521A LEU* 2.9 38.1 + - + +
522A GLU* 3.8 5.8 - - - +
524A LEU* 1.4 76.4 - - - +
526A SER* 1.4 57.5 + - - +
529A ALA* 3.0 36.1 + - - +
534A TYR* 2.7 34.3 + - - -
536A LYS* 3.7 45.5 + - + +
537A PRO* 3.9 9.1 + - + +
541A VAL* 5.4 1.8 + - - -
543A ASN 3.4 26.1 + - - -
544A PHE* 4.1 1.3 - - + -
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Residues in contact with SER 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 GLU* 2.8 26.1 + - - +
523A LYS* 3.9 5.8 - - - -
525A HIS* 1.4 76.5 - - - +
527A GLN* 1.3 60.8 + - - +
529A ALA* 4.6 2.1 + - - +
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Residues in contact with GLN 527 (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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498A LYS* 5.8 2.4 - - - +
500A LEU* 3.6 40.5 - - + +
505A LEU* 3.8 10.9 - - + +
523A LYS 3.0 17.7 + - - +
526A SER* 1.3 77.8 - - - +
528A HIS* 1.3 88.2 + - + +
529A ALA 3.8 0.7 - - - -
530A ASN 5.3 0.9 + - - -
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Residues in contact with HIS 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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495A LEU* 3.5 22.3 - - + +
498A LYS* 4.1 17.1 + - - -
500A LEU 2.8 29.5 + - - -
501A GLY* 3.8 13.3 - - - -
502A LEU* 3.7 18.2 - - + -
505A LEU* 3.5 10.6 - - + +
524A LEU 2.9 19.4 + - - +
525A HIS 4.0 0.2 - - - -
527A GLN* 1.3 95.0 + - + +
529A ALA* 1.3 58.9 + - - +
530A ASN 3.1 3.4 - - - -
531A ASN* 2.8 29.6 + - + +
534A TYR* 3.3 32.1 - - + +
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Residues in contact with ALA 529 (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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525A HIS 3.0 22.0 + - - +
526A SER* 4.6 2.6 + - - +
527A GLN 3.8 1.2 - - - -
528A HIS* 1.3 74.0 - - - +
530A ASN* 1.4 65.6 + - - +
531A ASN 3.8 4.0 + - - +
534A TYR* 3.9 15.8 - - - +
536A LYS* 4.4 23.8 + - + +
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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