Contacts of the helix formed by residues 525 - 537 (chain A) in PDB entry 6HSN
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 SER 525 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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523A ARG 3.3 4.5 + - - -
524A ASP* 1.3 71.9 - - - +
526A ASN* 1.3 73.9 + - - +
527A ARG 3.2 2.7 - - - -
528A SER* 3.1 10.7 + - - -
529A THR* 3.0 28.9 + - - -
628A PRO* 3.9 11.1 - - - +
801A ADP 3.0 19.8 + - - -
804A MPD 4.7 14.3 + - - +
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Residues in contact with ASN 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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505A SER* 4.2 0.9 - - - +
524A ASP* 3.4 1.4 + - - -
525A SER* 1.3 77.3 + - - +
527A ARG* 1.3 58.3 + - - +
529A THR* 4.5 6.1 - - - +
530A LEU* 2.8 41.5 + - + +
571A SER* 3.5 31.5 + - - +
626A GLY 2.9 27.1 + - - -
628A PRO* 3.2 31.5 - - - +
631A ALA* 3.9 11.3 - - + +
632A VAL* 5.8 0.7 - - - +
801A ADP 3.3 24.2 + - - +
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Residues in contact with ARG 527 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
503A VAL* 4.0 22.9 - - + +
505A SER* 3.4 14.0 + - - +
512A ASN* 2.9 27.5 + - - -
513A PRO* 4.1 11.7 - - - +
524A ASP* 2.8 32.0 + - - +
525A SER 3.2 1.0 - - - -
526A ASN* 1.3 78.4 - - - +
528A SER* 1.3 56.7 + - - +
530A LEU* 4.0 0.5 - - - +
531A LEU* 2.8 53.7 + - + +
543A ASN* 2.9 36.9 + - - +
545A GLY* 3.5 34.1 + - - +
546A ILE* 3.5 8.3 - - - +
811A ACT 5.2 6.1 + - - -
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Residues in contact with SER 528 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
513A PRO* 4.3 19.6 - - - +
524A ASP 4.7 1.1 + - - -
525A SER* 3.1 12.6 + - - -
527A ARG* 1.3 79.0 - - - +
529A THR* 1.3 58.5 + - - +
531A LEU* 4.0 6.2 - - - +
532A ALA* 2.9 31.9 + - - +
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Residues in contact with THR 529 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
525A SER* 3.0 21.5 + - - -
526A ASN* 3.9 6.7 - - - -
528A SER* 1.3 77.2 - - - +
530A LEU* 1.3 59.0 + - + +
532A ALA* 3.8 4.6 - - - +
533A THR* 2.9 34.3 + - - +
632A VAL* 3.3 42.0 - - + -
804A MPD 3.9 19.5 - - + +
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Residues in contact with LEU 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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503A VAL* 4.1 19.5 - - + -
504A MET 5.6 0.7 - - - +
526A ASN* 2.8 28.1 + - + +
527A ARG 4.0 1.8 - - - +
529A THR* 1.3 75.1 - - + +
531A LEU* 1.3 65.1 + - - +
533A THR* 3.2 5.9 + - - +
534A ILE* 3.0 29.6 + - - +
569A ILE* 4.1 20.6 - - + -
570A THR 5.3 0.7 - - - -
571A SER* 3.5 26.2 - - - +
624A LEU* 3.9 5.2 - - + -
631A ALA* 3.6 18.2 - - + +
632A VAL* 4.6 4.5 - - + +
635A CYS* 3.5 35.4 - - + -
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Residues in contact with LEU 531 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
503A VAL* 3.6 27.1 - - + -
527A ARG* 2.8 36.9 + - + +
528A SER* 4.0 4.9 - - - +
530A LEU* 1.3 72.0 - - - +
532A ALA* 1.3 57.4 + - - +
534A ILE* 3.3 4.4 + - - +
535A GLN* 2.9 45.8 + - - +
541A THR* 3.5 32.8 - - + +
542A ILE 4.1 9.0 - - - +
543A ASN* 3.5 33.9 - - + +
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Residues in contact with ALA 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 SER 2.9 20.0 + - - +
529A THR* 3.8 5.4 - - - +
531A LEU* 1.3 74.3 - - - +
533A THR* 1.3 58.7 + - - +
535A GLN* 3.3 13.5 + - - +
536A GLU* 2.9 32.9 + - - +
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Residues in contact with THR 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 THR* 2.9 28.9 + - - +
530A LEU* 3.2 8.6 + - - +
532A ALA* 1.3 76.7 - - - +
534A ILE* 1.3 61.6 + - + +
536A GLU* 3.5 14.6 + - - +
537A HIS* 3.1 28.6 + - + +
632A VAL* 4.6 9.2 - - - +
635A CYS* 4.0 21.8 - - - +
636A ASN* 4.2 24.1 + - - +
640A VAL* 4.2 10.5 - - + -
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Residues in contact with ILE 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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501A VAL* 4.0 11.7 - - + -
503A VAL* 5.2 1.6 - - + -
530A LEU 3.0 17.3 + - - +
531A LEU* 3.8 4.0 - - - +
533A THR* 1.3 78.8 - - + +
535A GLN* 1.3 64.9 + - - +
537A HIS* 3.1 16.8 + - + +
538A GLY 3.5 6.4 + - - -
539A TYR* 3.5 23.7 + - + -
541A THR* 3.8 22.2 - - + -
569A ILE* 4.2 16.4 - - + -
635A CYS* 3.8 24.7 - - - -
639A VAL* 4.0 8.7 - - + -
640A VAL* 4.5 6.3 - - + -
643A LEU* 3.7 27.6 - - + -
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Residues in contact with GLN 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 LEU* 2.9 35.6 + - - +
532A ALA* 3.8 12.3 - - - +
534A ILE* 1.3 75.9 - - - +
536A GLU* 1.3 57.5 + - - +
538A GLY* 2.9 20.6 + - - -
539A TYR 4.0 10.3 - - - +
541A THR* 2.9 33.0 + - + +
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Residues in contact with GLU 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 ALA 2.9 17.2 + - - +
533A THR* 3.5 16.0 + - - +
534A ILE 3.2 0.2 - - - -
535A GLN* 1.3 75.8 - - - +
537A HIS* 1.3 62.9 + - - +
538A GLY* 3.3 0.9 + - - -
733A ILE 4.3 1.7 - - - +
735A ARG* 3.2 46.5 + - - +
812A ACT 4.2 14.9 - - - +
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Residues in contact with HIS 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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498A PHE* 5.2 1.6 - - - -
533A THR* 3.1 26.8 + - + -
534A ILE* 3.1 7.3 + - - +
535A GLN 3.0 0.8 - - - -
536A GLU* 1.3 84.1 - - + +
538A GLY* 1.3 59.0 + - - +
539A TYR* 3.5 37.9 + + + -
636A ASN* 4.8 4.5 - - - -
640A VAL* 3.6 41.2 - - + +
644A ARG* 5.2 7.4 - - - -
647A GLN* 5.0 1.2 - - - +
733A ILE* 4.6 17.1 + - - -
735A ARG* 4.9 11.3 + - - -
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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