Contacts of the helix formed by residues 538 - 550 (chain A) in PDB entry 5IYB
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 VAL 538 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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486A LEU* 4.3 17.9 - - + +
487A SER* 4.5 7.2 - - - -
489A THR* 4.3 17.5 - - + -
490A THR* 4.0 16.8 - - + +
536A GLY* 3.4 15.3 - - - +
537A ILE* 1.3 82.8 - - - +
539A GLN* 1.3 84.9 + - + +
541A THR* 3.4 9.9 + - - -
542A LEU* 3.1 16.8 + - + -
647A THR* 5.9 2.7 - - + -
790B GLN* 4.2 1.7 + - - -
282U ASP* 5.9 0.9 - - - +
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Residues in contact with GLN 539 (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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486A LEU* 4.2 14.1 - - + -
489A THR* 6.1 1.1 - - + -
538A VAL* 1.3 82.7 - - + +
540A ASP* 1.3 67.3 + - - +
542A LEU* 2.9 15.7 + - - +
543A THR* 3.1 9.7 + - - -
774A ALA* 4.1 7.3 + - - +
775A LYS* 3.6 31.2 - - - +
790B GLN* 3.5 17.5 - - + +
791B GLU* 2.6 53.2 + - + +
792B ASP* 5.5 0.4 + - - -
970B HIS* 3.6 29.9 + - + +
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Residues in contact with ASP 540 (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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539A GLN* 1.3 76.8 - - - +
541A THR* 1.3 56.3 + - - +
543A THR* 3.0 0.7 + - - -
544A ALA* 2.5 39.6 + - - +
677A ASN* 5.2 2.2 - - - +
680A LEU* 3.8 13.3 - - + +
685A HIS* 4.1 1.0 - - - -
784B SER* 2.7 39.0 + - - +
787B GLY* 4.3 2.1 - - - -
789B ASN* 4.3 0.7 - - - +
790B GLN* 3.0 19.5 + - - +
968B ASN* 2.6 29.1 + - - -
970B HIS* 3.1 24.2 + - - -
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Residues in contact with THR 541 (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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486A LEU* 5.6 1.2 - - - +
537A ILE* 3.6 21.9 - - + +
538A VAL 3.7 4.4 + - - -
539A GLN 3.4 0.2 - - - -
540A ASP* 1.3 78.4 - - - +
542A LEU* 1.3 58.9 + - - +
544A ALA* 4.4 0.7 - - - -
545A VAL* 3.1 29.0 + - + +
672A ILE* 4.4 3.4 - - + +
673A GLN* 3.8 36.1 - - + +
676A ILE* 3.8 21.5 - - + -
677A ASN* 3.2 21.9 + - - +
680A LEU* 5.7 0.2 - - - -
790B GLN* 3.3 10.9 + - - +
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Residues in contact with LEU 542 (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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537A ILE* 3.2 31.1 - - + +
538A VAL* 3.1 19.4 + - + -
539A GLN 2.9 11.4 + - - +
541A THR* 1.3 75.6 - - - +
543A THR* 1.3 60.3 + - - +
545A VAL* 3.0 25.4 - - + +
546A ARG* 3.9 1.6 + - - +
640A LEU 5.2 0.3 - - - +
641A CYS* 3.8 24.4 - - - +
642A LYS* 4.9 10.1 - - + -
645A LEU* 4.4 4.7 - - + -
646A GLY* 5.4 0.4 - - - +
772A SER* 3.6 16.9 - - - +
773A GLY 3.5 33.4 - - - +
774A ALA* 3.7 6.7 - - + +
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Residues in contact with THR 543 (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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539A GLN 3.1 3.6 + - - -
540A ASP 3.0 4.3 + - - -
542A LEU* 1.3 73.7 - - - +
544A ALA* 1.3 66.9 + - - +
546A ARG* 3.2 18.7 - - + +
547A LYS* 3.5 11.4 + - + +
680A LEU* 6.4 0.2 - - + -
685A HIS* 4.1 30.7 - - + +
768A SER* 3.9 23.1 - - - +
769A MET* 4.0 3.6 - - - +
772A SER* 3.4 8.5 + - - -
774A ALA* 3.1 14.6 - - - +
970B HIS* 2.9 30.8 + - - -
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Residues in contact with ALA 544 (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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540A ASP 2.5 22.0 + - - +
541A THR* 4.4 0.2 - - - -
543A THR* 1.3 75.9 - - - +
545A VAL* 1.3 56.1 + - - +
547A LYS* 3.7 7.3 + - - +
548A PHE* 3.0 27.5 + - - +
676A ILE* 3.6 18.4 - - + +
679A TRP* 4.1 5.3 - - + -
680A LEU* 3.6 41.5 - - + +
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Residues in contact with VAL 545 (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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541A THR* 3.1 17.6 + - + +
542A LEU* 3.0 24.0 - - + +
544A ALA* 1.3 75.0 - - - +
546A ARG* 1.3 60.1 + - - +
548A PHE* 3.1 3.5 + - - +
549A THR* 2.8 31.6 + - + +
592A PHE* 4.0 14.4 - - + -
640A LEU* 3.8 31.6 - - + +
645A LEU* 3.5 25.8 - - + -
672A ILE* 5.1 1.1 - - + -
676A ILE* 3.6 19.8 - - + +
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Residues in contact with ARG 546 (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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542A LEU 4.0 0.7 - - - +
543A THR 3.2 14.4 - - - +
545A VAL* 1.3 79.8 - - - +
547A LYS* 1.3 73.1 + - - +
549A THR* 3.1 19.0 + - - -
550A LYS* 3.2 54.0 + - - +
639A ILE* 3.8 24.2 - - + +
640A LEU 2.9 28.0 - - - +
641A CYS* 5.3 0.2 - - + -
762A GLU* 4.5 12.7 + - - -
767A LYS 5.6 0.2 - - - -
768A SER* 3.8 33.1 + - - +
771A VAL* 4.4 14.2 - - - +
772A SER* 3.5 35.0 - - - +
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Residues in contact with LYS 547 (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 THR* 3.7 22.0 - - + +
544A ALA* 3.8 7.4 - - - +
546A ARG* 1.3 87.8 - - + +
548A PHE* 1.3 60.6 + - - +
550A LYS* 3.7 22.8 + - + +
553A VAL* 3.6 17.8 - - - +
679A TRP* 4.5 9.9 - - + -
680A LEU* 5.5 2.7 - - + -
683A GLU* 3.4 30.8 + - + +
684A GLY 2.7 28.9 + - - -
685A HIS* 4.4 13.2 + - + +
765A ASN* 5.1 3.0 + - - -
768A SER* 5.0 12.3 - - - +
1039B SER* 3.8 13.0 + - - -
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Residues in contact with PHE 548 (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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544A ALA 3.0 19.9 + - - +
545A VAL* 3.1 7.8 + - - +
547A LYS* 1.3 79.8 - - - +
549A THR* 1.3 67.4 + - + +
550A LYS 3.3 2.8 + - - +
553A VAL* 4.3 4.9 - - + +
555A LEU* 4.1 13.9 - - + -
563A LEU* 4.0 18.4 - - + -
588A GLY* 3.5 41.5 - - - -
591A ILE* 4.4 9.9 - - + -
592A PHE* 4.4 12.8 - - + -
675A VAL* 6.0 2.7 - - + -
676A ILE* 3.4 25.1 - - + -
679A TRP* 3.1 57.9 - + + -
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Residues in contact with THR 549 (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 VAL* 2.8 24.1 + - + +
546A ARG 3.1 10.2 + - - -
548A PHE* 1.3 74.4 - - + +
550A LYS* 1.3 55.6 + - - +
588A GLY 4.7 0.2 - - - -
589A LYS* 2.8 42.6 + - - +
592A PHE* 4.4 14.1 - - + -
635A LEU* 3.8 18.6 - - + -
639A ILE* 3.2 6.4 - - - -
640A LEU* 2.8 51.8 + - + -
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Residues in contact with LYS 550 (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 ARG* 3.2 44.1 + - - +
547A LYS* 3.7 20.4 - - + +
548A PHE 3.3 1.3 - - - +
549A THR* 1.3 77.1 - - - +
551A ARG* 1.3 59.2 + - - +
552A ASP* 2.9 38.0 + - - +
553A VAL* 3.1 18.9 + - - +
588A GLY 5.0 2.3 + - - -
589A LYS* 5.5 0.2 - - - +
639A ILE* 3.5 14.1 - - + -
762A GLU* 3.6 28.9 + - - +
22H PHE* 5.4 15.3 - - - -
23H ASP* 5.9 0.4 + - - -
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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