Contacts of the helix formed by residues 520 - 533 (chain F) 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 PRO 520 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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485F ALA 4.1 11.2 - - - +
518F THR 4.0 4.5 - - - +
519F ALA* 1.3 86.2 - - + +
521F ALA* 1.3 66.8 + - - +
522F HIS* 3.3 21.3 - - + +
523F VAL* 2.9 33.1 + - + -
524F TYR 3.2 8.3 + - - -
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Residues in contact with ALA 521 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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519F ALA 3.7 1.8 + - - -
520F PRO* 1.3 70.3 - - - +
522F HIS* 1.3 64.8 + - + +
524F TYR* 3.1 3.3 + - - +
525F LYS* 2.9 34.0 + - - +
551F TYR* 4.0 29.9 - - + +
552F ASP* 3.5 24.9 - - - +
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Residues in contact with HIS 522 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
487F TYR* 2.6 36.2 + + - +
520F PRO* 3.9 20.3 - - + +
521F ALA* 1.3 77.0 - - + +
523F VAL* 1.3 83.3 + - + +
525F LYS* 3.1 3.9 + - - +
526F ARG* 2.9 27.5 + - - +
622F GLU* 3.3 51.1 + - + +
656F PHE* 3.6 24.5 - - + -
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Residues in contact with VAL 523 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
485F ALA 4.2 10.5 - - - -
486F ASN* 4.2 13.9 - - - +
487F TYR* 3.6 37.6 - - + -
490F MET* 4.6 0.3 - - - +
519F ALA* 4.1 13.0 - - + -
520F PRO* 2.9 23.5 + - + +
522F HIS* 1.3 92.0 + - + +
524F TYR* 1.3 57.6 + - - +
526F ARG* 3.4 2.4 + - - +
527F TRP* 2.9 49.9 + - + +
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Residues in contact with TYR 524 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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512F ILE* 4.2 3.6 - - + -
513F GLY* 4.0 19.3 - - - -
519F ALA* 4.5 3.8 - - + +
520F PRO 3.2 4.7 + - - +
521F ALA 3.1 8.6 + - - +
523F VAL* 1.3 80.8 - - - +
525F LYS* 1.3 57.8 + - - +
527F TRP* 3.3 5.6 + - - +
528F CYS* 2.9 49.6 + - - -
539F LEU* 3.4 21.0 - - + +
546F ARG* 3.0 31.8 + - - -
548F PRO* 3.5 18.7 - - + +
551F TYR* 3.6 62.4 - + + -
555F SER* 3.9 22.9 - - - -
559F VAL* 4.3 2.4 - - + +
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Residues in contact with LYS 525 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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521F ALA* 2.9 27.1 + - - +
522F HIS 3.6 1.5 - - - +
524F TYR* 1.3 72.4 - - - +
526F ARG* 1.3 68.0 - - - +
528F CYS* 3.1 14.6 + - - +
529F ALA* 3.4 11.3 + - - +
552F ASP* 3.0 39.4 + - - -
554F GLU* 3.0 29.0 + - - -
555F SER* 3.7 14.6 - - - +
558F VAL* 3.8 25.3 - - + +
656F PHE* 3.4 49.9 - - + +
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Residues in contact with ARG 526 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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487F TYR* 3.5 21.5 - - + +
490F MET* 4.2 5.0 - - + +
522F HIS 2.9 19.7 + - - +
523F VAL 3.7 3.8 - - - +
525F LYS* 1.3 76.2 - - - +
527F TRP* 1.3 61.3 + - - +
529F ALA* 3.6 7.1 + - - +
530F PHE* 3.4 19.9 + - - +
618F PRO* 5.4 0.7 - - - +
619F VAL* 3.3 49.3 + - - +
621F THR 3.1 12.0 + - - +
622F GLU 3.2 14.1 + - - -
623F ALA 4.1 0.4 - - - -
624F GLY* 3.1 13.7 - - - -
654F HIS 2.9 22.8 + - - -
655F GLY* 3.0 27.5 + - - -
656F PHE* 3.6 26.7 + - - +
658F SER 3.8 9.7 + - - -
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Residues in contact with TRP 527 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
483F CYS* 3.7 16.4 - - - -
484F TYR 3.4 26.2 - - - -
485F ALA* 4.2 0.2 - - - -
486F ASN 3.7 18.8 - - - -
489F SER 4.3 1.1 - - - -
490F MET* 3.6 39.9 - - + -
493F SER* 4.2 7.6 - - - -
510F HIS* 3.5 24.5 + + + -
511F ASP 3.3 20.8 + - - -
512F ILE* 3.5 15.3 - - + +
513F GLY* 3.2 26.7 - - - +
514F GLY* 3.8 10.8 - - - -
523F VAL* 2.9 32.6 + - + +
524F TYR 3.6 3.4 - - - +
525F LYS 3.1 0.2 - - - -
526F ARG* 1.3 77.2 - - - +
528F CYS* 1.3 55.2 + - - +
530F PHE* 3.3 9.1 + + - +
531F GLY* 2.7 32.2 + - - -
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Residues in contact with CYS 528 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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512F ILE* 3.5 24.2 - - - -
524F TYR* 2.9 47.6 + - - -
525F LYS* 3.1 9.4 + - - +
527F TRP* 1.3 77.4 - - - +
529F ALA* 1.3 57.6 + - - +
531F GLY 3.3 0.2 + - - -
532F LEU* 2.8 41.0 + - + +
539F LEU* 4.5 1.8 - - - -
555F SER 5.3 0.2 - - - -
558F VAL* 3.9 15.5 - - + +
559F VAL* 3.7 22.9 - - + +
562F PHE* 4.9 1.6 - - - -
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Residues in contact with ALA 529 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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525F LYS 3.4 6.8 + - - +
526F ARG* 3.8 9.9 - - - +
527F TRP 3.3 0.2 - - - -
528F CYS* 1.3 78.5 - - - +
530F PHE* 1.3 65.7 + - - +
532F LEU* 3.3 1.7 + - - +
533F LEU* 3.0 30.1 + - - +
562F PHE* 3.8 39.8 - - + -
656F PHE 5.5 1.6 - - - +
658F SER 5.9 0.7 - - - +
659F LEU* 4.1 20.4 - - + -
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Residues in contact with PHE 530 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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490F MET* 3.9 39.5 - - + -
493F SER* 5.0 1.6 - - - -
494F LEU* 3.8 42.0 - - + -
508F TRP* 4.1 6.7 - + - -
510F HIS* 3.3 28.5 - + - -
526F ARG 3.4 11.2 + - - +
527F TRP* 3.3 12.0 + + - +
529F ALA* 1.3 78.8 - - - +
531F GLY* 1.3 59.2 + - - +
533F LEU* 3.1 15.6 + - - -
534F SER* 2.9 29.9 + - - -
588F MET* 4.0 4.0 - - + -
608F TYR* 3.7 15.3 - + - -
618F PRO* 3.9 28.7 - - + +
620F PHE* 5.6 1.1 - + - -
659F LEU* 4.9 1.7 - - - +
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Residues in contact with GLY 531 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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510F HIS* 3.7 18.8 - - - -
512F ILE* 4.2 12.8 - - - -
527F TRP 2.7 20.0 + - - -
528F CYS 3.7 1.1 - - - -
530F PHE* 1.3 75.5 - - - +
532F LEU* 1.3 60.8 + - - +
533F LEU 3.3 0.5 + - - -
534F SER* 3.3 13.9 + - - -
536F HIS 4.2 0.2 - - - +
537F SER* 2.8 24.5 + - - -
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Residues in contact with LEU 532 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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270F GLY 5.7 0.4 - - - +
271F LEU* 4.1 25.6 - - + +
512F ILE* 4.1 11.9 - - + -
528F CYS* 2.8 29.3 + - + +
529F ALA 4.1 1.1 - - - +
531F GLY* 1.3 73.6 - - - +
533F LEU* 1.3 63.4 + - + +
534F SER 3.2 4.3 + - - +
537F SER* 3.6 10.5 - - - +
559F VAL* 5.2 6.7 - - + +
562F PHE* 3.5 42.6 - - + +
563F THR* 3.9 20.2 - - + +
566F LYS* 3.3 47.5 - - + +
610F LEU* 5.6 0.2 - - - +
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Residues in contact with LEU 533 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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529F ALA 3.0 20.0 + - - +
530F PHE 3.4 5.8 - - - +
531F GLY 3.1 0.8 - - - -
532F LEU* 1.3 83.4 - - + +
534F SER* 1.3 55.3 + - - +
562F PHE* 4.6 10.3 - - + +
565F LEU* 4.4 21.5 - - + -
566F LYS* 5.8 1.3 - - + -
569F MET* 4.7 10.3 - - + -
608F TYR* 2.6 35.5 + - - +
610F LEU* 3.5 31.0 - - + +
616F VAL* 4.1 12.3 - - + -
659F LEU* 3.7 39.5 - - + -
661F VAL* 4.2 13.2 - - + -
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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