Contacts of the helix formed by residues 521 - 541 (chain A) in PDB entry 3U11
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 ASP 521 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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522A SER* 1.3 63.4 + - - +
523A SER* 3.4 9.5 + - - +
524A ARG* 3.8 28.6 - - - +
525A ARG* 3.3 22.5 + - - +
562A LYS* 6.2 1.0 - - - +
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Residues in contact with SER 522 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
521A ASP* 1.3 75.4 - - - +
523A SER* 1.3 60.8 + - - +
524A ARG 3.4 0.2 - - - -
525A ARG* 3.6 7.3 - - - +
526A GLN* 2.9 26.3 + - - +
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Residues in contact with SER 523 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
521A ASP 4.4 6.1 + - - +
522A SER* 1.3 78.8 + - - +
524A ARG* 1.3 63.6 + - - +
525A ARG 3.3 0.4 - - - -
526A GLN* 3.6 2.8 - - - +
527A TYR 3.3 8.1 + - - -
562A LYS* 3.3 17.5 - - - +
563A MET 2.9 44.8 + - - -
564A PHE* 3.4 31.3 - - - -
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Residues in contact with ARG 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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521A ASP* 3.7 31.6 + - - +
522A SER 3.4 0.4 - - - -
523A SER* 1.3 76.1 + - - +
525A ARG* 1.3 64.3 + - - +
527A TYR* 3.6 3.5 + - - +
528A GLN* 3.2 39.1 + - - +
560A GLN 4.3 4.0 + - - -
561A GLY* 3.2 32.6 + - - +
562A LYS* 3.4 40.5 - - + +
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Residues in contact with ARG 525 (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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521A ASP 3.3 13.1 + - - +
522A SER* 3.6 11.0 - - - +
524A ARG* 1.3 75.1 - - - +
526A GLN* 1.3 61.6 + - - +
528A GLN* 3.0 23.9 + - - +
529A GLU* 2.8 56.8 + - - +
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Residues in contact with GLN 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 SER 2.9 18.7 + - - +
523A SER* 3.6 11.9 - - - +
525A ARG* 1.3 75.0 - - - +
527A TYR* 1.3 56.7 + - - +
529A GLU* 3.5 15.7 + - - +
530A LYS* 3.0 51.5 + - - +
563A MET* 3.7 28.2 + - + +
564A PHE* 5.5 1.0 - - - +
565A ASP* 5.6 7.9 - - - +
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Residues in contact with TYR 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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523A SER 3.3 5.5 + - - +
524A ARG 3.7 2.0 - - - +
525A ARG 3.3 0.6 - - - -
526A GLN* 1.3 79.4 - - - +
528A GLN* 1.3 69.6 + - + +
530A LYS* 3.5 1.4 + - - +
531A TYR* 2.8 39.7 + + + +
555A TYR* 3.7 32.4 - + + +
556A GLU* 3.4 35.5 + - - +
559A TYR* 3.7 15.0 - - + -
561A GLY* 3.4 46.3 + - - +
562A LYS 3.7 10.1 - - - -
563A MET* 3.6 23.3 - - + +
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Residues in contact with GLN 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 ARG* 3.2 26.9 + - - +
525A ARG* 3.0 31.5 + - - +
527A TYR* 1.3 88.5 - - + +
529A GLU* 1.3 60.9 + - + +
531A TYR* 3.2 5.1 + - - +
532A LYS* 3.0 42.3 + - - +
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Residues in contact with GLU 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 ARG* 2.8 46.0 + - + +
526A GLN* 3.9 17.3 - - - +
528A GLN* 1.3 73.9 - - - +
530A LYS* 1.3 57.4 + - - +
532A LYS* 3.4 14.6 + - + +
533A GLN* 3.0 31.4 + - - +
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Residues in contact with LYS 530 (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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526A GLN* 3.0 35.3 + - - +
527A TYR 4.0 2.5 - - - +
529A GLU* 1.3 76.2 - - - +
531A TYR* 1.3 59.6 + - - +
533A GLN* 3.4 13.3 + - + +
534A VAL* 3.0 33.6 + - + +
555A TYR* 4.7 12.6 - - + +
563A MET* 3.0 43.4 - - + +
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Residues in contact with TYR 531 (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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527A TYR* 2.8 31.9 + + + +
528A GLN* 3.2 6.5 + - - +
530A LYS* 1.3 75.8 - - - +
532A LYS* 1.3 58.9 + - + +
534A VAL* 3.1 22.9 + - + +
535A GLU* 2.8 58.1 + - + +
538A MET* 3.8 13.0 - - + +
551A ILE* 4.6 0.9 - - + -
552A HIS* 3.3 49.9 + + - +
555A TYR* 3.9 36.1 - + + -
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Residues in contact with LYS 532 (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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528A GLN* 3.0 27.3 + - - +
529A GLU* 3.4 16.3 + - + +
531A TYR* 1.3 75.8 - - + +
533A GLN* 1.3 61.5 + - + +
535A GLU* 3.6 18.0 + - - +
536A GLN* 2.9 38.6 + - - +
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Residues in contact with GLN 533 (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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529A GLU* 3.0 17.7 + - + +
530A LYS* 3.5 20.4 - - + +
532A LYS* 1.3 76.0 - - - +
534A VAL* 1.3 57.5 + - + +
536A GLN* 3.5 28.6 + - - +
537A TYR* 3.0 25.7 + - - +
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Residues in contact with VAL 534 (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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530A LYS* 3.0 21.3 + - + +
531A TYR* 3.3 21.3 - - + +
533A GLN* 1.3 74.0 - - + +
535A GLU* 1.3 65.7 + - - +
537A TYR* 3.0 10.2 + - + +
538A MET* 2.8 30.9 + - + +
551A ILE* 3.7 30.7 - - + -
555A TYR* 3.2 32.1 - - + +
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Residues in contact with GLU 535 (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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531A TYR* 2.8 44.6 + - + +
532A LYS* 3.6 29.9 - - - +
534A VAL* 1.3 72.4 - - - +
536A GLN* 1.3 59.0 + - + +
538A MET* 3.1 18.2 + - + +
539A SER* 2.9 26.9 + - - -
548A ARG* 5.0 1.4 + - - -
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Residues in contact with GLN 536 (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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532A LYS* 2.9 28.4 + - - +
533A GLN* 3.8 27.1 + - - +
534A VAL 3.2 0.4 - - - -
535A GLU* 1.3 73.7 - - + +
537A TYR* 1.3 66.7 + - - +
539A SER* 3.8 6.6 - - - +
540A PHE* 2.9 27.4 + - - +
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Residues in contact with TYR 537 (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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533A GLN 3.0 14.6 + - - +
534A VAL* 3.0 13.4 + - + +
536A GLN* 1.3 75.5 - - - +
538A MET* 1.3 67.6 + - + +
540A PHE* 3.8 2.8 - - - +
541A HIS* 3.1 68.9 + + + +
543A LEU* 3.9 22.8 - - + +
551A ILE* 6.0 1.1 - - + -
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Residues in contact with MET 538 (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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531A TYR* 3.8 21.8 - - - +
534A VAL* 2.8 20.3 + - + +
535A GLU* 3.5 25.1 - - + +
537A TYR* 1.3 77.2 - - + +
539A SER* 1.3 63.1 + - - +
542A LYS 3.2 1.9 + - - -
543A LEU* 3.0 51.1 + - + -
548A ARG* 3.5 48.9 - - + +
551A ILE* 3.8 30.7 - - + -
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Residues in contact with SER 539 (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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535A GLU 2.9 13.5 + - - -
536A GLN* 3.3 9.6 + - - -
538A MET* 1.3 75.8 - - - +
540A PHE* 1.3 60.5 + - - +
542A LYS* 2.8 26.9 + - - +
548A ARG* 3.8 20.4 + - - +
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Residues in contact with PHE 540 (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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536A GLN 2.9 17.7 + - - +
537A TYR* 3.8 4.9 - - - +
539A SER* 1.3 77.3 - - - +
541A HIS* 1.3 84.0 + + + +
542A LYS* 3.2 13.9 + - - +
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Residues in contact with HIS 541 (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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537A TYR* 3.1 68.4 + + - +
540A PHE* 1.3 97.6 - + - +
542A LYS* 1.3 70.2 + - - +
543A LEU* 2.9 27.0 + - + +
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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