Contacts of the helix formed by residues 544 - 555 (chain A) in PDB entry 1QTE
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 ASN 544 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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538A TYR* 4.0 1.8 + - - -
541A PHE* 3.6 7.4 + - - +
542A GLY 3.2 3.8 - - - +
543A ASN* 1.3 75.8 - - - +
545A ARG* 1.3 58.8 + - - +
546A ILE* 2.9 33.4 + - - +
547A PHE* 3.1 40.0 + - + +
548A SER* 3.0 28.7 + - - -
612A THR* 5.5 1.8 - - - +
613A GLU* 3.6 23.0 - - + +
616A ARG* 4.1 8.5 - - - +
618A TYR* 3.0 28.1 + - - -
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Residues in contact with ARG 545 (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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467A PRO* 5.2 6.1 - - - -
470A TYR* 3.8 25.7 - - + -
538A TYR* 3.8 22.2 - - + +
544A ASN* 1.3 69.5 - - - +
546A ILE* 1.3 63.9 + - - +
548A SER* 3.3 7.9 - - - -
549A SER* 2.7 31.2 + - - -
592A LEU* 3.8 29.0 + - + +
595A ASP* 2.8 48.7 + - - +
608A LEU 2.8 27.9 + - - -
609A MET* 3.6 2.2 - - - +
613A GLU* 2.9 39.9 + - - +
904A GOL 3.2 22.0 + - - -
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Residues in contact with ILE 546 (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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544A ASN* 2.9 9.0 + - - +
545A ARG* 1.3 78.6 - - - +
547A PHE* 1.3 65.2 + - + +
549A SER* 4.0 1.2 - - - -
550A ALA* 3.1 23.7 + - - +
572A ALA* 3.9 19.1 - - + +
575A PHE* 3.7 32.5 - - + -
576A VAL* 3.9 22.7 - - + -
579A ILE* 5.2 2.0 - - + -
588A VAL* 4.2 11.9 - - + +
592A LEU* 3.9 22.2 - - + -
609A MET* 4.0 14.8 - - + -
613A GLU* 4.6 5.4 + - + +
618A TYR* 3.6 25.4 - - + +
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Residues in contact with PHE 547 (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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541A PHE* 3.4 43.5 - + + -
544A ASN* 3.1 27.7 + - + +
546A ILE* 1.3 76.6 - - + +
548A SER* 1.3 57.5 + - - +
550A ALA* 3.4 3.4 + - - +
551A ALA* 2.9 31.1 + - - +
559A VAL* 4.0 10.3 - - + +
563A LEU* 3.5 35.2 - - + -
575A PHE* 3.8 17.7 - + - -
616A ARG* 3.6 33.0 - - - -
618A TYR* 3.4 39.9 - + - -
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Residues in contact with SER 548 (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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470A TYR* 2.7 26.9 + - - -
534A LEU* 4.6 0.8 - - - +
537A VAL* 3.6 17.9 - - - +
538A TYR* 3.6 38.0 - - - -
541A PHE* 4.7 0.4 - - - +
544A ASN 3.0 18.0 + - - -
545A ARG* 3.3 8.0 - - - -
547A PHE* 1.3 73.6 - - - +
549A SER* 1.3 59.8 + - - +
551A ALA* 4.3 1.6 - - - -
552A TYR* 2.9 30.0 + - - +
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Residues in contact with SER 549 (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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470A TYR* 2.8 26.3 + - - -
474A ILE* 4.0 2.9 - - - +
545A ARG 2.7 23.5 + - - -
546A ILE 4.0 2.5 - - - -
548A SER* 1.3 72.6 - - - +
550A ALA* 1.3 67.3 + - - +
552A TYR* 3.3 4.0 + - - +
553A ASN* 3.1 18.2 + - - +
587A TYR* 3.4 27.1 - - - -
588A VAL* 4.1 17.7 - - - -
591A VAL* 3.7 11.4 - - - +
592A LEU* 5.0 1.9 - - - +
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Residues in contact with ALA 550 (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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546A ILE 3.1 19.5 + - - +
547A PHE* 3.8 2.7 - - - +
549A SER* 1.3 76.7 - - - +
551A ALA* 1.3 51.8 + - - +
553A ASN* 3.4 0.7 + - - -
554A ALA* 2.8 38.5 + - - +
559A VAL* 3.6 18.2 - - + -
562A TRP* 4.2 9.0 - - + -
575A PHE* 5.5 3.4 - - + -
579A ILE* 4.6 6.3 - - + -
584A THR* 3.8 18.5 - - + +
588A VAL* 3.8 12.5 - - + +
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Residues in contact with ALA 551 (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 TYR* 4.5 3.3 + - - -
537A VAL* 3.9 18.6 - - + -
541A PHE* 3.8 24.9 - - + -
547A PHE 2.9 18.4 + - - +
548A SER 3.8 4.0 - - - +
550A ALA* 1.3 75.2 - - - +
552A TYR* 1.3 61.8 + - - +
555A GLY* 2.7 30.6 + - - -
556A PRO* 3.9 8.9 - - - +
559A VAL* 3.4 11.1 - - + +
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Residues in contact with TYR 552 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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474A ILE* 4.1 13.0 - - + -
478A GLU* 3.4 17.2 - - - +
495A MET* 2.8 38.8 + - + +
496A GLN 4.9 3.6 - - - -
497A ILE* 4.1 10.4 - - - +
530A GLY* 4.1 17.5 - - - -
533A TYR* 3.8 38.0 - + + -
534A LEU* 3.7 28.3 - - + -
537A VAL* 4.6 2.4 - - + +
548A SER 2.9 18.3 + - - +
549A SER* 3.3 7.6 + - - +
551A ALA* 1.3 77.8 - - - +
553A ASN* 1.3 60.0 + - - +
555A GLY 4.7 0.3 + - - -
587A TYR* 3.3 19.7 - - - +
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Residues in contact with ASN 553 (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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478A GLU* 5.0 1.1 + - - -
549A SER 3.1 15.8 + - - +
550A ALA 3.9 2.0 - - - +
552A TYR* 1.3 81.0 - - - +
554A ALA* 1.3 58.9 + - - +
555A GLY 3.6 0.2 - - - -
583A GLU* 3.0 28.3 + - - +
584A THR* 2.8 37.6 + - + -
587A TYR* 3.7 39.0 - - + -
651A NAG 3.8 12.1 + - - -
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Residues in contact with ALA 554 (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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550A ALA 2.8 19.1 + - - +
553A ASN* 1.3 72.8 - - - +
555A GLY* 1.3 59.5 + - - +
558A ARG* 3.6 23.0 + - + +
559A VAL* 5.5 0.2 - - + -
562A TRP* 3.9 19.1 - - + -
581A PHE* 4.3 10.0 - - + -
584A THR* 3.6 19.3 - - - +
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Residues in contact with GLY 555 (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 TYR* 5.1 0.4 - - - -
551A ALA* 2.7 22.1 + - - -
552A TYR 4.6 0.2 - - - -
553A ASN 3.6 1.2 - - - -
554A ALA* 1.3 75.4 - - - +
556A PRO* 1.3 75.4 - - - +
557A GLY 3.3 2.9 - - - -
558A ARG 3.3 11.6 + - - -
559A VAL* 3.4 13.3 + - - +
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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