Contacts of the helix formed by residues 521 - 533 (chain E) in PDB entry 1XSK
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 ALA 521 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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519E ALA 3.1 9.1 + - - -
520E PRO* 1.3 80.1 - - - +
522E HIS* 1.3 55.1 + - - +
523E VAL 3.1 1.7 - - - +
524E TYR* 3.3 12.4 - - - +
525E LYS* 2.6 45.2 + - + +
551E TYR* 4.0 22.2 - - + +
552E ASP* 4.1 20.2 - - + +
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Residues in contact with HIS 522 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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487E TYR* 2.7 30.1 + + - +
520E PRO* 3.0 31.7 + - + +
521E ALA* 1.3 75.8 - - - +
523E VAL* 1.3 85.1 + - + +
525E LYS* 4.4 4.4 - - - +
526E ARG* 3.2 28.9 + - - +
622E GLU* 3.3 46.0 + - + +
656E PHE* 3.7 24.8 - - + -
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Residues in contact with VAL 523 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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485E ALA 4.2 9.9 - - - +
486E ASN* 4.2 13.2 - - - -
487E TYR* 3.4 34.0 - - + +
490E MET* 4.8 0.7 - - - +
519E ALA* 4.1 12.1 - - + -
520E PRO* 3.6 20.6 - - + -
521E ALA 3.1 0.6 - - - +
522E HIS* 1.3 104.5 + - + +
524E TYR* 1.3 66.6 + - - +
526E ARG* 3.3 3.6 + - - +
527E TRP* 3.0 40.1 + - + +
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Residues in contact with TYR 524 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
512E ILE* 4.4 1.8 - - + -
513E GLY* 3.8 19.5 - - - -
519E ALA* 3.9 14.1 - - + +
521E ALA* 3.0 17.3 + - - +
523E VAL* 1.3 78.8 - - - +
525E LYS* 1.3 63.7 + - - +
527E TRP* 3.2 4.3 + - - +
528E CYS* 3.0 44.3 + - - -
539E LEU* 3.2 23.9 - - + +
546E ARG* 3.1 24.4 + - - -
548E PRO* 3.7 12.3 - - + +
551E TYR* 3.3 43.7 - + + -
555E SER* 3.7 33.9 - - - -
559E VAL* 3.9 9.9 - - + +
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Residues in contact with LYS 525 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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521E ALA* 2.6 33.8 + - - +
522E HIS* 3.9 2.2 - - - +
524E TYR* 1.3 72.9 - - + +
526E ARG* 1.3 64.6 + - - +
528E CYS* 3.1 23.0 + - - +
529E ALA* 3.5 5.2 + - - +
552E ASP* 3.0 19.8 + - - +
554E GLU* 2.9 31.7 + - - -
555E SER* 3.3 30.3 - - - +
558E VAL* 3.4 32.2 - - + +
656E PHE* 3.4 39.9 - - + +
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Residues in contact with ARG 526 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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487E TYR* 3.6 17.7 - - + +
490E MET* 4.3 4.4 - - + +
522E HIS 3.2 15.5 + - - +
523E VAL 3.7 7.0 - - - +
525E LYS* 1.3 78.7 - - - +
527E TRP* 1.3 62.6 + - - +
529E ALA* 3.4 13.7 + - - +
530E PHE* 3.5 11.6 + - - +
618E PRO* 5.6 0.5 - - - +
619E VAL* 3.4 49.8 + - - +
621E THR 3.1 10.6 + - - +
622E GLU 3.1 21.2 + - - -
623E ALA 3.9 1.2 + - - -
624E GLY* 3.2 7.7 - - - +
654E HIS 2.9 24.6 + - - -
655E GLY* 3.3 28.1 + - - -
656E PHE* 3.4 24.6 - - - +
658E SER 3.9 7.7 + - - -
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Residues in contact with TRP 527 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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483E CYS* 3.6 20.9 - - - -
484E TYR 3.4 26.9 - - - -
486E ASN 3.8 9.9 - - - -
489E SER 4.3 1.1 - - - -
490E MET* 3.6 52.6 - - + -
493E SER* 4.1 8.1 - - - -
510E HIS* 3.2 30.8 + + + -
511E ASP 3.3 17.6 + - - -
512E ILE* 3.6 13.0 - - + +
513E GLY* 3.3 23.6 - - - +
514E GLY* 3.8 7.6 - - - -
523E VAL* 3.0 21.6 + - + +
524E TYR 3.5 9.2 - - - +
526E ARG* 1.3 75.6 - - - +
528E CYS* 1.3 53.3 + - - +
530E PHE* 3.3 7.8 + + - +
531E GLY* 2.6 33.1 + - - -
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Residues in contact with CYS 528 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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512E ILE* 3.6 21.5 - - + -
524E TYR* 3.0 55.6 + - - -
525E LYS* 3.1 10.3 + - - +
527E TRP* 1.3 77.0 - - - +
529E ALA* 1.3 54.2 + - - +
531E GLY 3.2 0.2 + - - -
532E LEU* 2.7 44.9 + - + +
539E LEU* 4.9 0.7 - - - -
558E VAL* 3.8 14.1 - - + -
559E VAL* 3.9 19.3 - - + -
562E PHE* 5.0 1.3 - - + -
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Residues in contact with ALA 529 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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525E LYS 3.5 4.5 + - - +
526E ARG* 3.4 10.8 + - - +
527E TRP 3.3 0.6 - - - -
528E CYS* 1.3 75.9 - - - +
530E PHE* 1.3 68.8 + - - +
532E LEU* 3.7 0.9 - - - +
533E LEU* 2.9 31.0 + - - +
562E PHE* 3.8 40.7 - - + -
656E PHE 5.8 0.4 - - - +
658E SER 5.9 0.7 - - - +
659E LEU* 3.9 20.9 - - + -
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Residues in contact with PHE 530 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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490E MET* 4.1 37.7 - - + -
493E SER* 5.1 1.3 - - - -
494E LEU* 3.8 41.5 - - + -
508E TRP* 4.1 7.4 - + - -
510E HIS* 3.3 29.4 - + - -
526E ARG 3.5 7.4 + - - +
527E TRP* 3.3 11.8 + + - +
529E ALA* 1.3 76.9 - - - +
531E GLY* 1.3 60.3 + - - +
533E LEU* 3.0 12.5 + - - -
534E SER* 2.8 31.6 + - - -
588E MET* 4.6 3.6 - - - -
608E TYR* 3.5 19.5 - + - -
618E PRO* 3.8 29.8 - - + -
620E PHE* 5.6 0.9 - + - -
659E LEU* 4.7 3.2 - - - +
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Residues in contact with GLY 531 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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510E HIS* 3.8 13.9 - - - -
512E ILE* 3.7 18.2 - - - -
527E TRP 2.6 21.4 + - - -
528E CYS 3.5 1.8 - - - -
529E ALA 3.1 0.2 - - - -
530E PHE* 1.3 74.8 - - - +
532E LEU* 1.3 60.8 + - - +
533E LEU 3.2 1.0 + - - -
534E SER* 3.3 15.6 + - - -
536E HIS 4.2 0.2 - - - +
537E SER* 3.3 19.2 + - - -
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Residues in contact with LEU 532 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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271E LEU* 4.2 19.7 - - + +
512E ILE* 4.1 17.0 - - + -
528E CYS* 2.7 30.1 + - + +
529E ALA 4.1 0.9 - - - +
531E GLY* 1.3 71.9 - - - -
533E LEU* 1.3 61.6 + - + +
534E SER 3.3 2.6 + - - +
537E SER* 3.7 15.9 - - - +
559E VAL* 5.0 6.5 - - + +
562E PHE* 3.7 37.5 - - + +
563E THR* 3.9 27.1 - - + +
566E LYS* 3.1 44.5 - - + +
569E MET* 5.2 0.2 - - - +
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Residues in contact with LEU 533 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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529E ALA 2.9 20.5 + - - +
530E PHE 3.0 7.8 + - - +
532E LEU* 1.3 79.8 - - + +
534E SER* 1.3 53.8 + - - -
562E PHE* 4.5 11.9 - - + +
565E LEU* 4.5 7.0 - - + -
569E MET* 3.5 34.5 - - + -
608E TYR* 2.5 37.7 + - - +
610E LEU* 3.7 24.7 - - + +
616E VAL* 4.3 7.6 - - + -
659E LEU* 3.8 37.2 - - + -
661E VAL* 4.1 19.1 - - + -
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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