Contacts of the helix formed by residues 524 - 536 (chain A) in PDB entry 3S1R
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 524 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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472A LEU* 3.8 37.2 - - + +
473A SER* 4.3 4.7 + - - +
475A THR* 4.4 8.1 - - + -
476A SER* 4.1 19.1 - - - +
522A GLY* 3.4 21.5 + - - +
523A ILE* 1.3 74.7 - - - +
525A GLN* 1.4 82.5 + - + +
527A THR* 3.1 18.7 + - - -
528A LEU* 3.4 8.6 + - - -
650A GLN* 5.7 0.6 - - - +
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Residues in contact with GLN 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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472A LEU* 4.3 17.7 - - + +
524A VAL* 1.4 82.8 - - + +
526A ASP* 1.4 61.5 + - - +
528A LEU* 2.8 12.3 + - - +
529A CYS* 2.8 32.8 + - - +
751A SER* 3.8 19.1 + - - +
752A LYS* 3.8 33.2 - - - +
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Residues in contact with ASP 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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524A VAL 3.7 0.2 + - - -
525A GLN* 1.4 81.1 - - + +
527A THR* 1.3 54.6 + - - +
529A CYS* 3.2 6.5 + - - +
530A GLY* 2.6 36.4 + - - -
654A ASN* 4.7 8.7 - - - +
657A LEU* 3.4 24.8 - - + +
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Residues in contact with THR 527 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
472A LEU* 5.8 3.8 - - - +
523A ILE* 3.6 17.5 - - + +
524A VAL 3.1 12.1 + - - -
526A ASP* 1.3 72.3 + - - +
528A LEU* 1.4 59.8 + - - +
531A ILE* 2.8 32.7 + - - +
649A ILE* 4.3 1.3 - - + +
650A GLN* 3.5 43.1 + - + +
653A VAL* 3.2 23.0 - - + +
654A ASN* 3.4 23.3 + - - +
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Residues in contact with LEU 528 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
523A ILE* 3.4 30.2 - - - +
524A VAL* 3.4 11.2 + - - -
525A GLN 2.8 10.2 + - - +
527A THR* 1.4 77.2 - - - +
529A CYS* 1.3 62.1 + - - +
531A ILE* 3.1 20.3 + - + +
532A ARG* 3.3 7.8 + - - +
618A GLU* 3.7 7.6 - - - -
619A LYS* 3.4 41.1 - - + +
622A VAL* 3.7 13.0 - - + -
749A ALA* 4.0 8.9 - - - +
750A GLY 3.5 28.3 - - - +
751A SER* 3.8 8.1 - - - -
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Residues in contact with CYS 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 GLN 2.8 14.5 + - - +
526A ASP* 3.6 10.5 - - - +
528A LEU* 1.3 72.7 - - - +
530A GLY* 1.3 62.6 + - - +
532A ARG* 3.5 6.3 + - - +
533A LYS* 3.3 32.7 + - - +
657A LEU* 5.3 2.5 - - - -
662A PHE* 3.5 47.3 - - - -
745A GLN* 5.3 2.7 - - - -
746A MET* 4.5 3.6 - - + -
749A ALA* 3.9 13.6 - - - +
751A SER* 3.6 19.8 - - - +
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Residues in contact with GLY 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 ASP 2.6 21.2 + - - -
529A CYS* 1.3 70.6 - - - +
531A ILE* 1.4 54.4 + - - +
533A LYS* 3.3 9.2 + - - +
534A LEU* 2.8 36.0 + - - +
653A VAL* 3.6 12.6 - - - -
656A TRP* 3.6 8.2 - - - -
657A LEU* 4.1 14.8 - - - -
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Residues in contact with ILE 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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523A ILE* 5.1 0.4 - - + -
527A THR 2.8 21.2 + - - +
528A LEU* 3.1 21.7 + - + +
530A GLY* 1.4 71.0 - - - +
532A ARG* 1.4 51.7 + - - +
534A LEU* 3.4 2.7 + - + +
535A THR* 2.8 40.7 + - - +
578A LEU* 3.7 28.9 - - + -
617A VAL* 3.3 32.1 - - + +
622A VAL* 3.9 27.1 - - + -
649A ILE* 3.6 31.4 - - + -
653A VAL* 3.3 13.8 - - + +
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Residues in contact with ARG 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 LEU 3.3 2.3 + - - +
529A CYS* 3.7 9.8 + - - +
530A GLY 3.2 0.4 - - - -
531A ILE* 1.4 78.3 - - - +
533A LYS* 1.3 82.6 + - - +
535A THR* 3.0 18.5 + - - -
536A LEU* 3.3 40.5 - - + +
616A VAL* 3.6 20.8 - - + +
617A VAL 3.3 11.9 - - - +
618A GLU* 4.5 5.4 - - + -
739A ASP* 4.5 4.4 + - - +
745A GLN* 3.2 38.6 + - - +
748A MET* 3.5 37.0 - - - +
749A ALA* 3.6 39.5 - - + +
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Residues in contact with LYS 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 CYS* 3.3 19.5 + - - +
530A GLY 3.5 8.1 - - - +
532A ARG* 1.3 96.8 - - - +
534A LEU* 1.4 51.0 + - - +
536A LEU* 3.4 15.4 - - - +
539A THR* 2.7 30.1 + - - +
656A TRP* 3.6 13.8 - - + -
657A LEU* 4.7 3.8 - - + -
660A ASN* 3.0 27.6 + - - +
661A GLY 3.6 9.5 + - - -
662A PHE* 4.3 24.6 - - + -
745A GLN* 3.5 23.0 + - - +
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Residues in contact with LEU 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 GLY 2.8 20.2 + - - +
531A ILE 3.8 2.7 - - - +
533A LYS* 1.4 70.9 - - - +
535A THR* 1.3 58.0 + - + +
536A LEU 3.4 0.2 - - - -
539A THR* 3.2 18.2 - - + +
541A ILE* 4.4 2.2 - - + -
574A GLY* 3.1 44.7 - - - +
577A ILE* 3.8 15.7 - - + -
578A LEU* 4.1 26.2 - - + -
652A VAL* 4.8 4.5 - - + -
653A VAL* 4.1 28.5 - - + -
656A TRP* 3.6 43.5 - - + +
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Residues in contact with THR 535 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
531A ILE 2.8 23.8 + - - +
532A ARG 3.0 9.3 + - - -
534A LEU* 1.3 74.7 - - + +
536A LEU* 1.3 62.2 + - - +
575A LYS* 3.1 45.1 + - + +
578A LEU* 3.4 32.8 - - + -
602A ASP* 3.9 1.0 - - - +
612A ILE* 5.6 0.2 - - + -
615A GLY 5.1 0.2 - - - -
616A VAL* 3.4 7.0 - - - +
617A VAL* 3.0 38.6 + - + -
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Residues in contact with LEU 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 ARG* 3.3 48.6 + - - +
533A LYS* 3.4 24.9 - - + +
534A LEU 3.4 3.1 - - - +
535A THR* 1.3 81.5 - - - +
537A ARG* 1.4 63.7 + - - +
538A ASP* 3.3 13.5 - - + +
539A THR* 3.4 26.8 + - - +
573A SER* 5.4 0.9 - - - -
574A GLY 4.9 0.9 + - - -
575A LYS* 4.3 4.6 - - - +
616A VAL* 4.2 19.7 - - + -
745A GLN* 6.0 0.2 - - - +
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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