Contacts of the helix formed by residues 549 - 564 (chain C) in PDB entry 1XMI
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 549 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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547C THR 4.1 0.6 + - - -
548C LEU* 1.3 77.0 - - - +
550C GLY* 1.3 59.7 + - - +
551C GLY 3.7 3.0 + - - -
552C GLN* 3.1 38.1 + - - +
553C ARG* 3.0 28.9 + - - +
660C SER* 5.7 0.2 - - - -
663C THR* 4.4 23.0 - - - +
664C GLU* 4.1 6.1 + - - -
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Residues in contact with GLY 550 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
495C SER* 5.3 0.5 + - - -
549C SER* 1.3 73.4 - - - +
551C GLY* 1.3 55.7 + - - +
553C ARG* 3.4 23.1 + - - +
554C ALA* 3.0 29.3 + - - +
577C TYR* 4.1 14.5 - - - +
660C SER* 3.5 21.2 + - - +
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Residues in contact with GLY 551 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
549C SER* 3.3 3.0 + - - -
550C GLY* 1.3 73.0 - - - +
552C GLN* 1.3 60.4 + - - +
554C ALA* 3.5 2.6 + - - +
555C ARG* 3.1 40.6 + - - +
578C LEU* 3.7 18.7 - - - +
660C SER* 3.2 10.5 + - - +
664C GLU* 3.4 19.6 + - - +
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Residues in contact with GLN 552 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
526C LEU* 4.5 1.7 - - + +
529C ASP* 3.0 31.7 + - + +
533C PHE* 4.3 15.5 - - - -
547C THR 4.9 0.7 - - - +
548C LEU* 3.7 22.9 - - + +
549C SER* 3.1 38.9 + - - +
551C GLY* 1.3 74.5 - - - +
553C ARG* 1.3 58.9 + - - +
555C ARG* 3.2 24.3 + - - +
556C ILE* 3.0 38.6 + - + +
667C ARG* 6.0 0.6 - - - +
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Residues in contact with ARG 553 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
495C SER* 3.7 20.1 - - - -
497C ILE* 3.8 34.2 - - + +
544C GLY 4.4 9.2 - - - -
545C GLY* 3.5 27.9 - - - -
546C ILE 4.2 1.4 - - - +
548C LEU* 2.8 38.8 + - + +
549C SER* 3.0 15.1 + - - +
550C GLY* 3.6 23.1 - - - +
552C GLN* 1.3 75.6 - - - +
554C ALA* 1.3 57.2 + - - +
556C ILE* 3.5 1.9 + - - +
557C SER* 3.0 32.1 + - - -
577C TYR* 6.1 2.0 - - - -
656C GLU* 5.1 8.9 + - - -
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Residues in contact with ALA 554 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
491C CYS* 5.5 0.9 - - - -
495C SER* 3.5 16.5 + - - +
550C GLY 3.0 17.6 + - - +
551C GLY 3.6 5.6 - - - +
553C ARG* 1.3 77.6 - - - +
555C ARG* 1.3 57.2 + - - +
557C SER* 3.9 1.6 - - - -
558C LEU* 3.1 28.9 + - - +
574C PRO* 4.0 20.0 - - - +
577C TYR* 4.6 10.5 - - + -
578C LEU* 3.9 18.4 - - + -
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Residues in contact with ARG 555 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
524C CYS* 3.0 31.4 - - + +
525C GLN* 3.4 19.0 + - - -
526C LEU* 3.7 11.7 - - + +
529C ASP* 3.5 16.3 + - - -
551C GLY* 3.1 27.5 + - - +
552C GLN* 3.2 30.9 + - - +
554C ALA* 1.3 75.7 - - - +
556C ILE* 1.3 59.6 + - - +
558C LEU* 3.6 7.0 + - - +
559C ALA* 3.0 28.4 + - - +
578C LEU* 4.1 10.6 - - + +
582C THR* 4.5 2.9 - - - +
586C ILE* 3.8 21.8 - - + -
664C GLU* 2.6 37.3 + - - -
667C ARG* 3.9 17.8 - - - +
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Residues in contact with ILE 556 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
497C ILE* 3.9 16.4 - - + -
502C ILE* 4.2 25.1 - - + +
505C ASN* 4.1 23.6 - - + -
506C ILE* 4.3 8.6 - - + +
526C LEU* 3.8 26.2 - - + -
541C LEU* 4.7 1.3 - - + -
548C LEU* 3.9 35.0 - - + -
552C GLN* 3.0 23.3 + - + +
553C ARG 4.0 3.1 - - - +
555C ARG* 1.3 73.0 - - - +
557C SER* 1.3 61.5 + - - +
559C ALA* 3.1 3.3 + - - +
560C ARG* 2.9 32.4 + - - +
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Residues in contact with SER 557 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
491C CYS* 3.7 16.8 - - - -
492C SER 4.8 2.4 + - - -
494C PHE 4.4 3.6 + - - -
495C SER* 3.9 27.5 + - - -
496C TRP 4.3 4.8 + - - -
497C ILE* 5.1 0.2 - - - +
553C ARG 3.0 19.5 + - - -
554C ALA 3.9 3.6 - - - -
556C ILE* 1.3 78.9 - - - +
558C LEU* 1.3 58.5 + - - +
560C ARG* 3.6 26.5 + - - +
561C ALA* 3.4 19.8 + - - +
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Residues in contact with LEU 558 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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491C CYS* 3.9 15.4 - - - -
524C CYS* 4.0 10.3 - - + -
554C ALA 3.1 18.7 + - - +
555C ARG* 3.8 6.3 - - - +
557C SER* 1.3 73.8 + - - +
559C ALA* 1.3 60.6 + - - +
561C ALA* 3.1 3.1 + - - +
562C VAL* 3.0 36.6 + - + +
571C LEU* 4.0 27.6 - - + -
574C PRO* 4.3 13.9 - - + +
575C PHE* 3.9 15.5 - - + -
586C ILE* 3.6 32.1 - - + -
590C CYS* 4.0 15.5 - - - -
591C VAL* 5.5 2.5 - - + -
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Residues in contact with ALA 559 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
506C ILE* 4.0 13.5 - - + -
520C VAL* 3.5 25.7 - - + +
521C ILE* 5.5 0.2 - - + -
524C CYS* 3.8 8.7 - - - -
526C LEU* 3.7 18.8 - - + -
555C ARG 3.0 19.3 + - - +
556C ILE 3.1 5.6 + - - +
558C LEU* 1.3 76.1 - - - +
560C ARG* 1.3 52.8 + - - +
562C VAL* 3.4 0.6 + - - +
563C TYR* 2.8 37.2 + - - +
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Residues in contact with ARG 560 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
496C TRP* 2.7 61.8 + - - +
497C ILE* 4.1 0.6 - - - +
498C MET* 4.2 5.6 - - - +
505C ASN* 2.7 54.4 + - - +
506C ILE* 3.5 17.6 - - - +
508C ALA* 4.1 16.7 - - + +
556C ILE* 2.9 19.8 + - - +
557C SER* 3.7 21.7 + - - +
558C LEU 3.3 0.2 - - - -
559C ALA* 1.3 77.2 - - - +
561C ALA* 1.3 61.2 + - - +
562C VAL 3.4 0.3 + - - -
563C TYR* 3.5 8.0 + - - +
564C LYS* 3.5 13.9 + - - +
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Residues in contact with ALA 561 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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489C SER* 2.5 36.7 + - - +
490C PHE 4.0 11.0 - - - +
491C CYS* 3.7 30.7 - - + +
557C SER 3.4 5.2 + - - +
558C LEU* 3.1 9.5 + - - +
560C ARG* 1.3 80.6 - - - +
562C VAL* 1.3 60.0 + - - +
564C LYS 3.8 4.0 + - - -
569C TYR* 3.4 7.8 - - + -
571C LEU* 4.8 8.3 - - + -
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Residues in contact with VAL 562 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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516C ARG* 3.9 6.9 + - - -
520C VAL* 3.9 10.1 - - + +
524C CYS* 5.2 0.2 - - - -
558C LEU* 3.0 27.6 + - + +
559C ALA* 4.0 4.0 - - - +
561C ALA* 1.3 78.3 - - + +
563C TYR* 1.3 65.8 + - - +
564C LYS 3.2 7.9 + - - +
569C TYR* 4.1 8.9 + - - -
571C LEU* 5.0 1.8 - - + -
590C CYS* 3.5 24.2 - - - -
594C LEU* 3.2 35.9 - - + -
595C MET* 3.5 27.1 - - + -
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Residues in contact with TYR 563 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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506C ILE* 4.0 24.0 - - + +
507C ILE* 3.3 31.7 - - + +
510C VAL* 3.7 17.8 - - + +
511C SER 2.8 28.1 + - - -
512C TYR* 3.4 2.6 - - - -
513C ASP* 2.8 22.9 + - - +
516C ARG* 2.6 52.3 + - + +
517C TYR* 3.6 35.0 - - + -
520C VAL* 3.9 10.3 - - + +
559C ALA 2.8 18.3 + - - +
560C ARG 3.9 4.5 - - - +
561C ALA 3.5 0.2 - - - -
562C VAL* 1.3 77.1 - - - +
564C LYS* 1.3 59.7 + - - +
565C ASP 3.4 0.5 + - - -
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Residues in contact with LYS 564 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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487C ARG* 4.6 14.4 - - - +
488C ILE 3.0 22.9 + - - +
489C SER* 3.9 21.3 - - - +
510C VAL* 5.0 19.3 - - + -
516C ARG* 3.4 0.5 + - - -
560C ARG 3.5 9.9 + - - +
561C ALA 3.8 11.2 - - - +
562C VAL 3.2 2.2 - - - +
563C TYR* 1.3 83.5 - - - +
565C ASP* 1.3 66.4 + - - +
566C ALA* 3.3 5.5 + - + -
569C TYR* 2.7 32.6 + - - -
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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
------------------------------------------------------------
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