Contacts of the helix formed by residues 535 - 544 (chain A) in PDB entry 5A7R
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 ARG 535 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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519A ASN* 3.0 47.9 + - - +
520A LEU 3.2 25.4 + - - -
521A TYR* 3.3 19.5 - - + +
522A PRO* 5.1 2.2 - - - +
533A GLY 3.5 3.8 + - - -
534A SER* 1.3 72.5 - - - +
536A TRP* 1.3 57.2 + - - +
538A LEU* 3.1 3.0 + - + +
539A ILE* 2.8 44.3 + - + +
560A TYR* 4.0 21.5 + - + -
643A PRO* 4.5 6.1 - - - +
644A ARG* 3.4 24.9 - - - +
1972A SO4 4.1 14.6 + - - -
1985A PPI 3.0 31.3 + - - -
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Residues in contact with TRP 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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514A PRO* 3.5 39.0 + - + +
515A CYS* 3.5 19.4 - - + +
516A SER 5.0 2.7 - - - +
519A ASN 4.2 2.6 + - - -
534A SER* 3.3 7.9 + - - +
535A ARG* 1.3 75.9 - - - +
537A GLU* 1.4 63.8 + - + +
539A ILE* 3.3 24.4 + - + +
540A GLN* 3.0 56.3 + - + +
601A ALA 3.7 21.1 - - - -
602A LEU* 3.5 34.5 + - + -
604A LEU* 4.3 7.9 - - + -
605A PRO* 3.7 18.7 - - + +
636A ASN* 3.9 16.6 - - - -
1987A PPI 4.2 15.8 + - - -
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Residues in contact with GLU 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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534A SER* 3.1 33.9 + - - +
536A TRP* 1.4 80.5 - - + +
538A LEU* 1.3 60.7 + - - +
540A GLN* 3.3 16.9 + - - +
541A THR* 2.9 28.9 + - - +
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Residues in contact with LEU 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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521A TYR* 3.8 37.2 - - + +
534A SER 3.2 11.1 + - - +
535A ARG* 3.1 9.3 + - + +
537A GLU* 1.3 74.3 - - - +
539A ILE* 1.3 66.1 + - - +
541A THR* 3.2 8.3 + - - -
542A ALA* 2.9 27.0 + - + +
559A LYS* 3.6 35.9 - - + +
560A TYR* 4.0 16.4 - - + -
1985A PPI 4.2 10.5 - - + +
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Residues in contact with ILE 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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514A PRO* 4.3 6.5 - - + -
519A ASN* 4.5 2.5 - - - +
535A ARG* 2.8 34.0 + - + +
536A TRP* 3.5 29.8 - - + +
538A LEU* 1.3 73.1 - - - +
540A GLN* 1.3 62.2 + - - +
542A ALA* 3.3 1.2 + - - +
543A LEU* 3.0 46.8 + - + +
560A TYR* 3.6 32.5 - - + -
602A LEU* 4.1 13.7 - - + -
641A THR* 4.0 31.4 - - + +
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Residues in contact with GLN 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 TRP* 3.0 48.1 + - + +
537A GLU* 3.6 19.7 - - - +
538A LEU 3.3 0.2 - - - -
539A ILE* 1.3 75.3 - - - +
541A THR* 1.3 64.3 + - - +
543A LEU 4.1 0.2 - - - -
544A LEU* 3.2 41.6 + - + +
602A LEU* 4.1 30.3 + - + +
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Residues in contact with THR 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 GLU* 2.9 19.1 + - - +
538A LEU* 3.2 10.7 + - - -
540A GLN* 1.3 77.0 - - - +
542A ALA* 1.3 63.4 + - - +
544A LEU* 3.8 6.3 + - - +
545A ASN* 3.2 16.6 + - - +
559A LYS* 6.0 0.2 - - - -
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Residues in contact with ALA 542 (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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538A LEU* 2.9 18.1 + - + +
539A ILE 3.7 3.6 - - - +
541A THR* 1.3 76.9 - - - +
543A LEU* 1.3 59.0 + - - +
545A ASN* 3.0 23.1 + - - +
547A PHE* 4.7 0.5 - - - -
556A ALA* 3.6 39.5 - - - +
559A LYS* 3.9 24.1 + - + +
560A TYR* 3.9 12.6 - - + -
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Residues in contact with LEU 543 (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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539A ILE* 3.0 37.9 + - + +
540A GLN 4.5 1.1 - - - +
542A ALA* 1.3 72.6 - - - +
544A LEU* 1.3 58.5 + - - +
545A ASN 3.2 17.6 + - - +
547A PHE* 3.7 15.7 - - + -
553A LEU* 5.2 0.2 - - + -
556A ALA* 4.3 18.4 - - + -
557A ILE* 5.0 1.1 - - + -
560A TYR* 3.7 24.9 - - + +
598A VAL* 3.8 28.1 - - + +
601A ALA* 5.4 3.4 - - + -
602A LEU* 4.5 10.8 - - + -
639A PHE* 3.8 42.6 - - + -
641A THR* 4.8 1.6 - - + -
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Residues in contact with LEU 544 (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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540A GLN* 3.2 28.4 + - + +
541A THR* 3.8 4.0 + - - +
542A ALA 3.4 0.8 - - - -
543A LEU* 1.3 74.4 - - - +
545A ASN* 1.3 65.5 + - - +
598A VAL* 4.1 10.5 - - + -
599A LYS* 5.3 11.2 - - + -
602A LEU* 3.8 28.3 - - + -
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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