Contacts of the helix formed by residues 551 - 563 (chain A) in PDB entry 2XBB
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 THR 551 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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548A ARG* 2.7 24.1 + - - +
550A ALA* 1.3 90.5 - - + +
552A VAL* 1.3 58.6 + - - +
553A LEU* 3.2 4.2 + - - -
554A GLU* 3.4 3.1 + - - +
555A ASP* 2.6 53.7 + - - -
40C GLN* 6.4 0.4 - - - +
74C ARG* 4.0 23.8 - - - +
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Residues in contact with VAL 552 (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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547A LEU* 4.8 5.2 - - + -
548A ARG 2.9 6.0 + - - +
549A ARG* 3.4 28.5 - - + +
550A ALA 5.3 0.2 - - - -
551A THR* 1.3 75.5 - - - +
553A LEU* 1.3 55.9 + - - +
555A ASP* 4.4 3.8 - - - -
556A SER* 2.6 43.4 + - - +
577A PHE* 3.4 33.9 - - + -
592A TRP* 5.0 2.0 - - + -
595A LEU* 4.4 23.8 - - + +
596A ILE* 4.0 5.8 - - + -
599A GLU* 4.1 21.5 - - + -
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Residues in contact with LEU 553 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
551A THR* 3.2 1.5 - - - -
552A VAL* 1.3 81.3 - - - +
554A GLU* 1.3 69.4 + - + +
556A SER* 3.8 0.9 - - - -
557A TYR* 2.8 31.9 + - - +
596A ILE* 3.7 18.8 - - + -
599A GLU* 4.0 24.7 - - + +
600A MET* 4.3 12.8 - - + +
605A TYR* 3.5 42.0 - - + +
607A LEU* 6.4 1.8 - - + -
634A TYR* 4.9 9.2 - - + -
637A PHE* 4.2 15.6 - - + -
73C LEU* 4.1 16.6 - - + -
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Residues in contact with GLU 554 (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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551A THR* 3.4 6.1 + - - +
553A LEU* 1.3 88.5 - - + +
555A ASP* 1.3 63.8 + - - +
557A TYR* 4.1 7.2 - - - -
558A ARG* 3.1 47.7 + - - +
605A TYR* 5.7 0.7 - - - -
634A TYR* 2.8 28.6 + - - -
72C ARG 4.3 2.9 - - - +
73C LEU* 3.9 10.2 - - - +
74C ARG* 3.1 67.6 + - - +
75C GLY 4.5 0.9 + - - +
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Residues in contact with ASP 555 (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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546A LYS 4.9 2.9 - - - +
547A LEU* 3.9 21.9 - - + +
548A ARG* 3.1 46.5 + - - +
551A THR* 2.6 43.4 + - - +
552A VAL* 4.0 2.7 - - - +
554A GLU* 1.3 77.0 - - - +
556A SER* 1.3 63.1 + - - +
558A ARG* 4.2 11.1 + - - +
559A ARG* 3.2 24.9 + - - +
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Residues in contact with SER 556 (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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545A MET* 4.1 9.6 - - - -
547A LEU* 3.4 9.9 - - - +
552A VAL 2.6 29.1 + - - -
555A ASP* 1.3 70.3 - - - +
557A TYR* 1.3 64.8 + - - +
560A ILE* 3.0 30.5 + - - +
592A TRP* 2.8 37.4 + - - -
596A ILE* 3.8 13.2 - - - +
637A PHE* 3.7 8.3 - - - -
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Residues in contact with TYR 557 (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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553A LEU 2.8 18.8 + - - +
554A GLU* 3.9 7.2 - - - +
556A SER* 1.3 76.5 - - - +
558A ARG* 1.3 71.7 + - + +
561A MET* 2.8 64.5 + - + +
633A SER* 2.8 31.4 + - - -
634A TYR* 3.3 58.6 - + + -
637A PHE* 3.6 21.5 - + + -
75C GLY* 3.9 18.9 - - - -
76C GLY 4.0 14.9 + - - -
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Residues in contact with ARG 558 (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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548A ARG* 5.7 1.2 - - - +
554A GLU* 3.1 41.8 + - - +
555A ASP* 4.3 12.2 + - - +
557A TYR* 1.3 91.5 - - + +
559A ARG* 1.3 63.5 + - - +
561A MET* 3.9 1.3 - - - -
562A GLY* 2.9 22.5 + - - -
74C ARG* 4.0 23.8 - - - +
75C GLY 4.7 6.2 + - - +
76C GLY 5.9 1.1 - - - +
20D SER* 5.2 13.3 - - - -
55D THR* 4.3 13.1 + - - +
57D SER* 3.4 21.2 + - - -
58D ASP* 2.7 29.9 + - - -
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Residues in contact with ARG 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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543A PHE* 3.4 31.1 - - + -
544A GLU* 2.9 33.8 + - - +
545A MET* 4.1 30.3 - - + +
546A LYS 5.7 1.8 - - - +
547A LEU* 5.0 3.1 - - + -
555A ASP 3.2 17.7 + - - +
556A SER 4.0 2.7 - - - +
558A ARG* 1.3 80.5 - - - +
560A ILE* 1.3 63.1 + - - +
562A GLY* 3.3 5.3 + - - -
563A VAL* 3.3 24.4 - - - +
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Residues in contact with ILE 560 (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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543A PHE* 4.3 11.4 - - + -
545A MET* 3.9 14.6 - - + -
556A SER 3.0 15.2 + - - +
559A ARG* 1.3 71.3 - - - +
561A MET* 1.3 79.0 + - + +
562A GLY 3.0 4.7 - - - -
563A VAL* 3.1 16.7 - - - +
569A LEU* 4.1 11.0 - - + -
592A TRP* 3.6 37.5 - - + -
637A PHE* 4.0 17.0 - - + -
640A ARG* 3.0 36.1 + - + -
641A VAL* 4.2 2.7 - - + -
644A MET* 3.7 16.4 - - + -
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Residues in contact with MET 561 (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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557A TYR* 2.8 58.8 + - + +
558A ARG* 3.9 1.3 - - - +
560A ILE* 1.3 82.5 - - + +
562A GLY* 1.3 59.8 + - - +
563A VAL 3.3 4.4 + - - +
564A LYS* 6.0 1.2 - - - +
633A SER* 3.8 13.5 - - - +
636A LYS* 4.4 11.9 - - - +
637A PHE* 3.6 29.8 - - + +
640A ARG* 3.3 39.2 + - + +
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Residues in contact with GLY 562 (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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558A ARG 2.9 19.6 + - - -
559A ARG* 3.3 4.7 + - - -
560A ILE 3.0 0.6 - - - -
561A MET* 1.3 79.7 - - - +
563A VAL* 1.3 60.5 + - - +
564A LYS* 3.6 7.2 + - - +
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Residues in contact with VAL 563 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
543A PHE* 4.2 12.6 - - + -
559A ARG* 3.3 28.0 - - - +
560A ILE* 3.1 18.8 + - - +
561A MET 4.2 3.1 - - - +
562A GLY* 1.3 75.0 - - - +
564A LYS* 1.3 59.8 + - - +
565A ARG 3.0 30.5 - - - +
566A ALA* 4.3 3.1 - - - +
568A PHE* 4.4 15.5 - - + -
569A LEU* 4.2 6.7 - - + -
640A ARG* 2.9 26.0 + - - +
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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