Contacts of the helix formed by residues 551 - 567 (chain A) in PDB entry 1XBA
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 551 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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482A MET* 6.1 0.7 - - - +
486A GLU* 3.5 50.3 + - - +
489A ASN* 5.9 0.3 + - - -
490A PHE 4.1 10.9 + - - -
491A VAL* 3.7 7.2 - - - +
519A LEU* 5.0 6.8 - - - +
524A ASN 4.6 2.2 + - - -
550A SER* 1.3 74.2 - - - +
552A LYS* 1.3 59.0 + - - +
554A ASP* 3.1 13.4 + - - +
555A VAL* 3.0 23.1 + - - +
619A PHE* 3.5 9.1 - - - -
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Residues in contact with LYS 552 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
486A GLU* 5.4 0.7 - - - +
550A SER* 3.0 12.5 + - - +
551A SER* 1.3 77.8 - - - +
553A SER* 1.3 64.1 + - - +
555A VAL* 3.1 12.5 + - - +
556A TRP 3.3 0.9 + - - -
613A VAL* 3.3 36.5 + - + +
614A GLU* 3.6 14.7 + - - +
616A ARG* 2.8 51.0 + - - +
617A PRO 3.7 19.1 - - - +
618A GLY* 4.0 10.1 - - - +
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Residues in contact with SER 553 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
538A TRP 4.8 0.3 - - - +
540A ALA* 4.3 4.3 + - - +
542A GLU* 2.8 21.9 + - - +
543A CYS* 3.4 25.5 - - - -
548A LYS 3.7 1.4 + - - -
549A PHE* 3.6 10.0 - - - -
550A SER* 2.9 34.1 + - - -
552A LYS* 1.3 75.7 - - - +
554A ASP* 1.3 62.5 + - - +
556A TRP* 3.4 6.2 + - - +
557A SER* 3.3 21.6 + - - -
616A ARG* 3.6 3.0 - - - +
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Residues in contact with ASP 554 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
482A MET* 3.8 10.7 - - + +
490A PHE 4.5 0.9 - - - +
491A VAL* 3.5 11.3 - - - +
492A HIS* 2.7 34.4 + - - +
493A ARG* 2.9 28.3 + - - +
495A LEU* 3.5 9.7 - - + +
549A PHE* 6.0 0.5 - - - -
550A SER 3.2 9.3 + - - +
551A SER* 3.1 13.8 + - - +
553A SER* 1.3 78.1 - - - +
555A VAL* 1.4 59.7 + - - +
557A SER* 3.3 9.8 + - - -
558A PHE* 2.8 27.2 + - - +
619A PHE* 3.6 13.2 - - + -
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Residues in contact with VAL 555 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
551A SER 3.0 17.8 + - - +
552A LYS* 3.1 10.7 + - - +
554A ASP* 1.4 76.8 - - - +
556A TRP* 1.3 62.0 - - - +
558A PHE* 3.1 6.0 - - - +
559A GLY 3.1 16.1 + - - -
608A CYS* 3.5 32.1 - - - +
616A ARG* 4.1 5.4 - - + -
617A PRO* 3.4 27.8 - - + +
618A GLY* 3.9 14.4 - - - +
619A PHE* 3.6 29.2 - - + -
622A VAL* 4.0 9.2 - - + -
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Residues in contact with TRP 556 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
537A LYS 5.0 1.6 + - - -
538A TRP 3.4 17.1 + - - -
539A TYR 3.4 17.9 + - - -
540A ALA* 3.7 15.0 - - + -
541A PRO* 3.5 29.8 - - + -
552A LYS 3.3 3.2 + - - -
553A SER 3.4 9.6 - - - +
555A VAL* 1.3 75.0 - - - +
557A SER* 1.4 63.0 + - - +
559A GLY* 2.9 18.2 + - - -
560A VAL* 3.3 20.6 + - + +
573A TYR* 4.7 3.2 + - - -
585A LEU* 3.5 35.5 - - + +
590A ARG* 4.0 13.9 - - - -
608A CYS 3.6 13.4 + - - +
609A TRP* 3.4 53.8 + + + -
610A THR 3.7 16.6 - - - -
611A TYR 4.0 1.1 - - - -
616A ARG* 3.9 9.0 - - - +
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Residues in contact with SER 557 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
493A ARG* 5.8 0.7 - - - -
494A ASP 5.8 0.2 + - - -
495A LEU* 3.4 34.4 + - - +
538A TRP* 2.7 31.0 + - - +
539A TYR* 4.4 9.0 - - - -
553A SER 3.3 10.1 + - - -
554A ASP* 3.3 14.5 + - - -
556A TRP* 1.4 75.3 - - - +
558A PHE* 1.3 66.3 + - - +
560A VAL* 3.2 6.4 + - - +
561A LEU* 2.9 22.2 + - - +
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Residues in contact with PHE 558 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
475A VAL* 3.5 24.7 - - + -
478A VAL* 3.6 32.3 - - + -
479A SER* 3.8 10.5 - - - -
495A LEU* 3.9 10.0 - - + +
554A ASP 2.8 16.9 + - - +
555A VAL 3.1 10.7 + - - +
557A SER* 1.3 73.4 - - - +
559A GLY* 1.4 54.6 + - - +
561A LEU* 3.1 10.6 + - + +
562A MET* 2.9 58.2 + - + +
608A CYS* 4.1 6.3 - - - -
619A PHE* 3.8 19.3 - + + -
622A VAL* 3.5 30.1 - - + -
626A LEU* 3.6 13.7 - - + -
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Residues in contact with GLY 559 (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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555A VAL 3.1 6.5 + - - -
556A TRP 2.9 7.2 + - - -
558A PHE* 1.4 74.0 - - - +
560A VAL* 1.3 62.1 + - - +
562A MET* 3.4 10.7 + - - +
563A TRP 3.1 17.5 + - - -
605A MET* 3.8 4.9 - - - +
608A CYS* 3.7 19.7 - - - -
609A TRP* 3.3 26.5 - - - -
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Residues in contact with VAL 560 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
537A LYS 3.8 19.1 - - - +
538A TRP* 3.5 28.7 - - + +
556A TRP* 3.6 23.1 - - + +
557A SER 3.2 6.3 + - - +
559A GLY* 1.3 76.6 - - - +
561A LEU* 1.3 56.7 + - - +
563A TRP* 3.2 4.1 + - - +
564A GLU* 2.9 27.5 + - - +
572A PRO* 3.7 28.5 - - + -
573A TYR* 4.7 7.2 - - - +
591A MET* 4.3 3.1 - - + -
609A TRP* 3.1 23.1 - - + +
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Residues in contact with LEU 561 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
456A LEU* 4.4 20.6 - - + -
475A VAL* 4.7 10.3 - - + -
478A VAL* 4.0 15.9 - - + -
495A LEU* 3.5 39.3 - - + +
496A ALA 3.8 5.8 - - - -
497A ALA* 3.5 18.3 - - - +
500A VAL* 3.7 18.6 - - + -
538A TRP* 4.4 0.2 - - - -
557A SER 2.9 13.4 + - - +
558A PHE* 3.1 13.6 + - + +
560A VAL* 1.3 76.0 - - - +
562A MET* 1.3 55.9 + - - +
564A GLU* 3.2 14.5 + - - +
565A ALA* 2.8 29.3 + - - +
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Residues in contact with MET 562 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
475A VAL* 4.3 10.8 - - + -
558A PHE* 2.9 47.4 + - + +
559A GLY* 3.4 10.1 - - - +
561A LEU* 1.3 77.1 - - - +
563A TRP* 1.3 59.8 + - - +
565A ALA* 3.1 6.2 + - - -
566A PHE* 2.8 45.9 + - + -
601A MET* 3.9 35.2 - - - +
604A LEU* 3.6 32.1 - - + -
605A MET* 4.0 19.1 - - + -
608A CYS* 4.7 0.7 - - - -
626A LEU* 4.1 8.1 - - + -
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Residues in contact with TRP 563 (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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559A GLY 3.1 10.0 + - - +
560A VAL 3.2 8.3 + - - +
562A MET* 1.3 78.2 - - - +
564A GLU* 1.3 58.1 + - - +
566A PHE 3.9 0.2 - - - -
567A SER* 2.6 58.9 + - - -
570A GLN* 3.6 19.7 - - + -
571A LYS 3.5 26.0 - - - -
572A PRO* 3.7 13.0 - - + -
573A TYR 5.2 0.9 - - - -
591A MET* 3.6 38.0 - - + +
592A GLY 2.8 29.0 + - - -
594A PRO* 3.6 16.8 - - + +
605A MET* 3.7 20.9 - - - -
609A TRP* 4.0 9.9 - + + -
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Residues in contact with GLU 564 (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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457A ASN* 4.8 7.6 + - - +
497A ALA* 2.9 37.2 + - + +
498A ARG 4.7 2.6 + - - -
538A TRP* 2.6 46.9 + - - +
560A VAL 2.9 19.1 + - - +
561A LEU* 3.3 12.2 - - - +
563A TRP* 1.3 79.4 - - + +
565A ALA* 1.3 61.9 + - - +
567A SER 3.3 2.8 + - - -
568A TYR 3.2 4.9 + - - -
569A GLY* 2.9 28.8 + - - -
570A GLN 3.8 18.7 - - - +
571A LYS* 5.0 1.2 - - - -
572A PRO* 4.1 12.4 - - + +
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Residues in contact with ALA 565 (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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456A LEU* 4.3 15.0 - - + -
460A LEU* 3.4 27.4 - - + +
471A ILE* 3.8 18.0 - - + +
475A VAL* 3.7 26.0 - - + -
497A ALA* 5.0 0.9 - - - +
561A LEU 2.8 16.5 + - - +
562A MET 3.1 7.4 + - - +
564A GLU* 1.3 72.6 - - - +
566A PHE* 1.3 57.2 + - - +
568A TYR* 3.0 16.5 + - - -
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Residues in contact with PHE 566 (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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468A ASP* 3.3 27.1 - - - -
471A ILE* 3.8 27.6 - - + -
472A ILE* 3.6 28.5 - - + -
475A VAL* 4.4 9.0 - - + -
562A MET* 2.8 41.4 + - + +
565A ALA* 1.3 72.1 - - + +
567A SER* 1.3 56.0 + - - +
568A TYR* 3.3 18.5 - - - -
594A PRO* 3.7 17.0 - - + +
595A ALA 4.2 7.3 - - - +
596A GLY 5.9 0.2 - - - -
597A CYS* 3.7 27.2 - - + +
598A PRO* 3.9 7.9 - - + -
601A MET* 3.7 26.9 - - + -
605A MET* 3.9 11.2 - - + -
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Residues in contact with SER 567 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
464A ARG* 5.4 0.6 + - - -
563A TRP* 2.6 52.1 + - - -
564A GLU 3.8 3.1 - - - -
565A ALA 3.2 0.2 - - - -
566A PHE* 1.3 74.1 - - - +
568A TYR* 1.3 71.3 + - - +
569A GLY 3.3 1.7 + - - -
570A GLN* 3.4 17.0 + - - +
594A PRO* 3.2 21.9 - - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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