Contacts of the helix formed by residues 552 - 569 (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 ASP 552 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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521F ALA* 3.5 13.3 - - - +
525F LYS* 3.0 28.5 + - - -
548F PRO 3.8 4.0 + - - +
549F TRP* 4.1 9.3 + - - -
551F TYR* 1.3 78.5 - - - +
553F ASP* 1.3 62.9 + - - +
554F GLU* 3.1 6.7 + - - +
555F SER* 2.7 48.3 + - - -
556F CYS* 3.8 6.9 + - - -
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Residues in contact with ASP 553 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
552F ASP* 1.3 75.0 - - - +
554F GLU* 1.3 64.9 + - - +
556F CYS* 3.0 22.7 + - - +
557F ASP* 3.2 17.1 + - - +
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Residues in contact with GLU 554 (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* 3.0 17.0 + - - +
552F ASP* 3.1 10.6 + - - +
553F ASP* 1.3 79.8 - - - +
555F SER* 1.3 51.4 + - - +
557F ASP* 2.8 15.3 + - - +
558F VAL* 2.6 47.3 + - + +
656F PHE* 3.0 39.6 + - - +
657F LEU* 3.7 15.6 - - + +
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Residues in contact with SER 555 (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 4.8 0.2 + - - -
524F TYR* 3.9 18.6 - - - -
525F LYS* 3.7 15.5 - - - +
548F PRO* 3.6 17.9 - - - -
551F TYR* 3.3 16.1 - - - +
552F ASP* 2.7 33.4 + - - -
554F GLU* 1.3 72.2 - - - +
556F CYS* 1.3 56.6 + - - +
558F VAL* 3.6 9.3 - - - +
559F VAL* 2.8 35.3 + - - +
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Residues in contact with CYS 556 (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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296F ARG* 3.6 26.5 - - - -
298F LEU* 3.1 13.8 - - + +
548F PRO* 3.7 10.5 - - - -
549F TRP* 3.5 34.3 - - - -
552F ASP 4.1 5.4 - - - -
553F ASP* 3.0 13.2 + - - +
555F SER* 1.3 75.1 - - - +
557F ASP* 1.3 56.5 + - - +
559F VAL* 3.4 0.6 + - - +
560F ARG* 2.7 49.9 + - - +
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Residues in contact with ASP 557 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
553F ASP* 3.6 14.9 - - - +
554F GLU* 2.8 16.9 + - - +
556F CYS* 1.3 77.2 - - - +
558F VAL* 1.3 53.1 + - - +
560F ARG* 2.4 35.6 + - - +
561F PHE* 2.6 38.5 + - - +
657F LEU* 4.2 20.0 - - + -
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Residues in contact with VAL 558 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
525F LYS* 3.8 35.7 - - + +
528F CYS* 3.9 11.2 - - + -
554F GLU* 2.6 41.8 + - + +
555F SER* 3.6 5.8 - - - +
557F ASP* 1.3 72.0 - - - +
559F VAL* 1.3 62.7 + - - +
561F PHE* 4.4 0.7 - - - -
562F PHE* 3.0 44.2 + - + +
656F PHE* 3.6 29.4 - - + +
657F LEU* 4.3 10.5 - - + +
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Residues in contact with VAL 559 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271F LEU* 4.0 20.9 - - + -
293F MET* 4.8 4.0 - - + -
298F LEU* 4.5 8.7 - - + -
299F PRO* 5.7 0.4 - - + +
524F TYR* 4.3 4.0 - - + +
528F CYS* 3.7 28.5 - - + -
532F LEU* 5.5 4.5 - - + -
539F LEU* 4.8 5.6 - - + -
548F PRO* 3.5 29.4 - - + -
555F SER 2.8 25.6 + - - +
556F CYS 3.9 2.7 - - - +
558F VAL* 1.3 72.4 - - - +
560F ARG* 1.3 62.7 + - - +
562F PHE* 4.6 2.2 - - - +
563F THR* 2.5 43.1 + - - +
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Residues in contact with ARG 560 (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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296F ARG* 2.3 37.7 + - - +
297F ASN* 2.9 34.7 - - - +
298F LEU* 3.2 20.5 - - + +
299F PRO* 4.7 3.8 - - + -
556F CYS* 2.7 26.6 + - - +
557F ASP* 2.4 41.5 + - - +
559F VAL* 1.3 74.1 - - - +
561F PHE* 1.3 62.1 + - - +
563F THR* 4.0 3.1 - - - -
564F GLN* 3.1 47.0 + - - +
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Residues in contact with PHE 561 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
557F ASP 2.6 20.7 + - - +
558F VAL* 3.7 4.3 - - - +
560F ARG* 1.3 74.5 - - - +
562F PHE* 1.3 93.6 + + - +
564F GLN* 3.6 10.2 + - - +
565F LEU* 3.2 30.8 + - + +
639F TRP* 3.7 38.8 - + - -
657F LEU* 3.8 36.1 - - + -
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Residues in contact with PHE 562 (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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528F CYS* 4.6 2.0 - - + +
529F ALA* 3.8 25.6 - - + -
532F LEU* 3.5 31.2 - - + +
533F LEU* 4.6 9.5 - - + +
558F VAL* 3.0 36.2 + - + +
559F VAL 4.6 0.2 - - - +
561F PHE* 1.3 97.5 - + - +
563F THR* 1.3 63.3 + - - +
565F LEU* 3.8 13.4 - - + +
566F LYS* 3.1 20.3 + - - +
639F TRP* 3.9 6.5 - + - -
656F PHE 3.8 19.1 - - - -
657F LEU* 3.7 22.4 - - - -
658F SER 4.2 1.1 - - - -
659F LEU* 3.5 33.0 - - + -
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Residues in contact with THR 563 (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* 5.9 0.4 - - - -
271F LEU* 4.0 16.9 - - + +
299F PRO* 3.9 40.3 + - + +
301F HIS* 4.2 12.3 - - + -
532F LEU* 3.9 16.6 - - + +
559F VAL* 2.5 35.9 + - - +
560F ARG 4.0 2.2 - - - -
562F PHE* 1.3 76.4 - - - +
564F GLN* 1.3 64.6 + - - +
566F LYS* 3.6 2.1 + - - +
567F CYS* 3.2 25.7 + - - -
675F ASP 4.8 0.2 - - - -
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Residues in contact with GLN 564 (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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297F ASN 5.4 1.4 + - - -
299F PRO* 5.0 6.7 - - + +
560F ARG* 3.1 38.2 + - - +
561F PHE* 3.8 9.3 - - - +
563F THR* 1.3 76.8 - - - +
565F LEU* 1.3 65.3 + - - +
567F CYS* 3.2 4.2 + - - +
568F ARG* 3.1 26.6 + - - +
675F ASP* 3.0 43.5 + - + +
676F GLN* 3.6 14.7 - - - +
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Residues in contact with LEU 565 (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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533F LEU* 4.4 11.0 - - + -
561F PHE* 3.2 22.6 + - + +
562F PHE* 3.8 22.7 - - + +
563F THR 3.3 0.2 - - - -
564F GLN* 1.3 78.2 - - - +
566F LYS* 1.3 65.2 + - - +
568F ARG* 2.9 22.9 + - + +
569F MET* 2.9 44.1 + - + +
638F LEU* 4.1 13.2 - - + -
639F TRP* 3.5 35.2 - - + -
661F VAL* 5.8 0.4 - - + -
671F LEU* 6.1 3.8 - - + -
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Residues in contact with LYS 566 (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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269F PHE* 2.7 38.5 + - - +
270F GLY* 5.5 0.7 - - - -
532F LEU* 3.3 33.7 - - + +
533F LEU* 5.8 1.5 - - + +
534F SER 3.4 14.2 + - - -
535F SER* 3.0 24.4 + - - +
537F SER* 2.9 25.3 + - - +
562F PHE 3.1 16.4 + - - +
563F THR 3.9 4.3 - - - +
565F LEU* 1.3 80.9 - - - +
567F CYS* 1.3 63.4 + - - +
569F MET* 3.2 18.9 + - - +
570F MET* 3.3 16.4 + - - +
573F LEU* 3.7 16.8 - - + +
678F PRO* 6.3 0.4 - - + -
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Residues in contact with CYS 567 (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* 5.6 2.5 - - - -
301F HIS* 4.4 10.3 - - - -
563F THR* 3.2 18.9 + - - +
564F GLN 3.6 7.6 - - - +
565F LEU 3.1 0.6 - - - -
566F LYS* 1.3 79.9 - - - +
568F ARG* 1.3 60.7 + - - +
570F MET* 3.3 19.5 + - - +
674F ASN 3.6 13.7 - - - +
675F ASP* 3.7 9.2 - - - -
676F GLN 4.0 4.0 - - - -
677F ARG* 3.5 35.2 - - - +
678F PRO* 3.7 10.1 - - - -
680F TYR* 2.9 20.8 + - - -
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Residues in contact with ARG 568 (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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564F GLN 3.1 14.1 + - - +
565F LEU* 2.9 14.6 + - + +
567F CYS* 1.3 75.7 - - - +
569F MET* 1.3 58.2 + - + +
570F MET 3.1 0.7 - - - -
571F PRO* 3.0 8.8 - - - +
671F LEU* 3.5 25.6 - - + +
672F GLY 2.6 54.2 + - - +
673F ASN* 4.8 3.8 - - - +
674F ASN 4.0 2.5 - - - +
675F ASP* 3.6 22.2 - - + -
680F TYR* 3.9 4.7 - - - -
687F ALA* 4.3 5.3 - - - +
3002F SO4 2.9 47.4 + - - -
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Residues in contact with MET 569 (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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533F LEU* 4.7 9.6 - - + -
565F LEU* 2.9 47.2 + - + +
566F LYS* 3.2 5.6 + - - +
568F ARG* 1.3 77.1 - - + +
570F MET* 1.3 52.0 + - - +
571F PRO* 3.3 1.8 - - - -
572F TYR* 3.0 33.4 + - + +
573F LEU* 2.7 57.9 + - + -
610F LEU* 4.4 13.7 - - + -
614F VAL* 4.5 9.0 - - + -
638F LEU* 3.9 21.3 - - + -
661F VAL* 5.7 2.0 - - + -
669F LEU* 6.1 2.9 - - + -
670F ALA 5.0 2.0 - - - -
671F LEU* 5.1 10.5 - - + -
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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