Contacts of the helix formed by residues 525 - 535 (chain A) in PDB entry 6A5T
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 525 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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473A LEU* 3.1 49.4 - - + +
474A SER* 4.6 8.1 - - - +
476A THR* 4.0 17.0 - - - +
477A SER* 4.3 12.1 - - - +
523A GLY* 5.0 3.1 - - - +
524A ILE* 1.3 85.6 - - - +
526A GLN* 1.3 81.6 + - + +
527A ASP 3.1 2.0 + - - -
528A THR* 3.4 6.7 + - - +
529A LEU* 3.1 17.4 + - - -
651A GLN* 5.0 4.0 - - - +
752A SER* 6.1 0.2 - - - -
835B GLN* 4.6 5.2 - - + +
836B GLU* 5.4 1.6 - - + +
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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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525A VAL* 1.3 78.4 - - + +
527A ASP* 1.3 69.4 + - - +
529A LEU* 3.4 3.8 + - - +
530A CYS 3.1 13.2 + - - -
752A SER* 3.5 17.2 + - - +
753A LYS* 3.0 34.2 - - - +
835B GLN* 5.3 2.9 - - + -
836B GLU* 2.6 52.8 + - + +
1013B ASN* 5.5 0.7 - - - +
1015B HIS* 3.1 41.5 + - + +
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Residues in contact with ASP 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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525A VAL 3.1 1.0 + - - -
526A GLN* 1.3 74.3 - - - +
528A THR* 1.3 57.6 + - - +
529A LEU 2.5 6.1 + - - -
530A CYS* 2.5 27.3 + - - +
531A GLY* 2.8 10.5 + - - -
655A ASN* 5.1 0.4 - - - +
658A LEU* 4.3 16.0 - - + +
663A PHE* 4.7 1.6 - - - -
829B CYS* 2.8 37.0 - - - +
832B GLY* 4.6 4.4 - - - -
834B ASN* 4.0 2.3 - - - +
835B GLN* 3.7 26.9 + - + +
1013B ASN* 3.6 15.4 + - - -
1015B HIS* 2.7 26.1 + - - -
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Residues in contact with THR 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 23.6 - - + -
525A VAL* 3.4 5.4 + - - +
527A ASP* 1.3 76.4 - - - +
529A LEU* 1.3 56.3 + - - +
531A GLY* 4.7 0.4 - - - +
532A VAL* 2.9 29.2 + - - +
650A ILE* 4.3 8.3 - - + +
651A GLN* 3.8 35.0 + - + +
654A VAL* 3.6 19.1 - - + +
655A ASN* 3.5 25.2 + - - +
658A LEU* 5.9 0.9 - - - -
835B GLN* 3.7 10.0 + - - +
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Residues in contact with LEU 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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524A ILE* 3.9 23.5 - - + +
525A VAL 3.1 12.4 + - - +
526A GLN 3.5 8.3 - - - +
527A ASP 2.5 4.6 + - - -
528A THR* 1.3 71.3 - - - +
530A CYS* 1.3 69.4 + - - +
532A VAL* 3.0 17.0 + - + +
533A ARG* 3.0 19.9 + - - +
619A ASP* 4.5 4.5 - - - -
620A LYS* 4.4 21.8 - - + +
623A VAL* 4.3 17.9 - - + -
624A GLY* 5.6 1.6 - - - +
750A ALA* 3.2 25.6 - - + +
751A GLY 3.9 3.1 - - - +
752A SER* 3.5 22.7 - - - +
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Residues in contact with CYS 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 3.1 2.6 + - - -
527A ASP* 2.5 11.2 + - - +
529A LEU* 1.3 76.5 - - - +
531A GLY* 1.3 65.3 + - - +
533A ARG* 3.3 4.1 + - - +
534A LYS* 3.0 26.7 + - - +
663A PHE* 4.1 23.3 - - + -
746A GLN* 4.8 3.4 - - - -
747A MET* 3.5 32.5 - - + -
750A ALA* 4.1 13.5 - - + -
752A SER* 4.3 2.0 - - - +
1015B HIS* 3.8 24.2 - - + +
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Residues in contact with GLY 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 ASP 2.8 12.5 + - - -
530A CYS* 1.3 72.3 - - - +
532A VAL* 1.3 51.3 + - - -
533A ARG 2.4 18.3 + - - -
534A LYS* 2.5 21.4 + - - -
535A MET* 2.9 11.1 + - - -
654A VAL* 3.8 13.5 - - - -
657A TRP* 5.5 1.6 - - - -
658A LEU* 4.2 24.4 - - - +
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Residues in contact with VAL 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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524A ILE* 5.7 2.0 - - + -
528A THR* 2.9 26.0 + - + +
529A LEU* 3.0 20.8 + - + +
531A GLY* 1.3 67.5 - - - -
533A ARG* 1.3 59.8 + - - +
535A MET* 4.2 7.0 - - + -
536A THR* 3.3 21.2 + - + -
579A LEU* 3.5 39.9 - - + -
618A VAL* 3.8 12.5 - - + +
623A VAL* 4.7 12.8 - - + -
650A ILE* 4.9 8.5 - - + -
654A VAL* 3.3 25.0 - - + +
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Residues in contact with ARG 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 LEU 3.0 6.9 + - - +
530A CYS* 3.5 7.9 + - - +
531A GLY 2.4 11.5 + - - -
532A VAL* 1.3 71.6 - - - +
534A LYS* 1.3 96.2 + - - +
535A MET 2.8 2.5 + - - -
536A THR* 2.8 15.8 + - - -
537A LEU* 3.4 45.6 + - - +
617A VAL* 3.8 20.7 - - + +
618A VAL 3.7 19.1 - - - +
619A ASP* 4.5 2.2 - - + -
746A GLN* 3.7 36.3 + - - +
749A SER* 4.3 12.2 + - - -
750A ALA* 3.6 33.4 - - + +
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Residues in contact with LYS 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 CYS* 3.0 18.5 + - - +
531A GLY* 2.5 13.5 + - - +
533A ARG* 1.3 95.2 - - - +
535A MET* 1.3 61.1 + - - +
536A THR 3.5 0.2 + - - -
537A LEU* 3.6 14.0 + - + +
540A THR* 3.4 10.9 + - - -
657A TRP* 4.5 10.6 - - + -
658A LEU* 5.6 2.5 - - + -
661A ASN* 4.0 20.2 + - - +
662A GLY 4.5 7.9 - - - -
663A PHE* 4.1 25.1 - - + +
743A ASN* 5.5 1.0 + - - -
746A GLN* 3.1 38.5 + - - +
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Residues in contact with MET 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 GLY 2.9 11.9 + - - +
532A VAL* 4.4 7.0 - - + -
533A ARG 2.8 0.2 + - - -
534A LYS* 1.3 80.0 - - - +
536A THR* 1.3 79.0 + - + +
540A THR* 2.8 30.4 + - + +
542A ILE* 4.9 1.8 - - + -
550A MET* 4.1 9.4 - - - -
575A GLY* 4.1 21.3 - - - +
578A LEU* 4.8 5.4 - - + -
579A LEU* 4.3 14.4 - - + +
653A VAL* 4.7 4.9 - - + -
654A VAL* 4.6 20.9 - - + -
657A TRP* 3.5 60.5 - - + +
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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