Contacts of the strand formed by residues 540 - 551 (chain A) in PDB entry 2IBI
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 540 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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525A ASP* 3.6 38.8 - - + +
526A LEU 3.2 5.4 - - - +
527A ASP* 3.7 27.8 - - + +
538A HIS* 3.8 33.0 + - + +
539A ALA* 1.3 79.0 - - - +
541A TYR* 1.3 66.2 + - - +
598A LEU* 3.6 9.7 - - - +
599A ALA* 2.9 35.0 + - + +
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Residues in contact with TYR 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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494A PHE* 3.4 29.2 - + - +
495A PRO* 2.7 34.8 + - - +
496A LYS 3.8 3.6 - - - -
498A LEU* 3.7 19.3 - - + -
524A ARG 3.8 0.7 - - - -
525A ASP 3.3 6.3 + - - -
526A LEU* 2.9 38.9 + - + +
528A LEU* 3.8 31.9 - - + -
539A ALA* 4.6 5.2 - - + -
540A VAL* 1.3 77.5 - - - +
542A ASN* 1.3 63.1 - - - +
596A TYR* 3.6 26.8 - - + -
597A GLU* 3.2 30.1 - - - +
598A LEU* 3.3 23.1 - - + +
599A ALA* 4.5 0.7 - - - -
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Residues in contact with ASN 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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523A LEU 3.6 6.5 - - - +
524A ARG* 3.2 41.4 - - - +
525A ASP* 3.0 26.5 + - - +
541A TYR* 1.3 76.5 - - - +
543A LEU* 1.3 68.6 + - - +
563A ARG* 4.6 9.1 - - - +
596A TYR* 3.3 3.9 - - - -
597A GLU* 2.7 42.0 + - + +
599A ALA* 3.2 28.0 - - - +
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Residues in contact with LEU 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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521A PHE* 3.7 19.1 - - + -
522A PRO 3.8 3.1 - - - +
523A LEU* 2.7 29.6 + - + +
542A ASN* 1.3 76.1 - - - +
544A TYR* 1.3 61.5 + - - +
545A ALA 3.7 13.5 - - - +
546A VAL* 3.7 22.0 - - + -
563A ARG* 3.3 19.6 + - - -
570A TRP* 3.8 20.1 - - + -
586A VAL* 4.0 6.7 - - + -
594A LEU* 3.9 9.0 - - + -
595A PHE 3.4 18.6 - - - +
596A TYR* 3.4 39.4 - - + +
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Residues in contact with TYR 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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284A CYS 3.7 8.5 - - - -
287A ASN* 3.5 22.9 - - + +
288A THR* 2.8 33.2 + - - +
415A PHE* 5.0 0.2 - - - -
497A ILE* 3.3 32.6 - - + +
543A LEU* 1.3 76.1 - - - +
545A ALA* 1.3 65.8 + - + +
562A CYS* 3.4 1.0 - - - +
563A ARG* 2.8 52.2 + - + +
570A TRP* 3.7 10.5 - - - -
595A PHE* 2.9 34.9 + - + +
596A TYR 3.6 21.1 - - - -
597A GLU* 3.7 26.9 - - + +
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Residues in contact with ALA 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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284A CYS* 3.8 29.8 - - + +
287A ASN* 5.5 0.2 - - + -
543A LEU* 3.7 2.3 - - - +
544A TYR* 1.3 95.9 - - + +
546A VAL* 1.3 68.0 + - - +
561A TYR 3.1 12.3 - - - +
562A CYS* 4.2 5.2 - - + -
570A TRP* 4.1 1.7 - - - -
594A LEU 3.6 0.2 - - - -
595A PHE* 2.7 40.4 + - + +
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Residues in contact with VAL 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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284A CYS* 4.1 3.8 - - - -
521A PHE* 4.1 11.0 - - + -
543A LEU* 3.7 25.1 - - + -
545A ALA* 1.3 80.0 - - - +
547A SER* 1.3 62.9 + - - +
548A ASN* 3.3 27.6 - - - +
560A ALA* 3.2 6.2 - - - +
561A TYR* 2.9 39.6 + - + +
570A TRP* 4.7 0.7 - - + -
586A VAL* 4.2 14.1 - - + +
591A ALA* 3.8 20.2 - - + -
593A LEU 3.2 12.6 - - - +
594A LEU* 4.0 5.2 - - + -
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Residues in contact with SER 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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280A SER* 3.0 21.5 + - - -
281A ILE* 4.5 5.2 - - - -
284A CYS* 4.1 12.7 - - - -
358A ALA* 4.2 5.9 - - - +
546A VAL* 1.3 74.1 - - - +
548A ASN* 1.3 58.8 + - - +
558A TYR* 3.5 19.1 - - - -
559A THR 3.5 4.0 - - - -
592A TYR* 2.9 26.0 + - - +
593A LEU* 2.8 35.3 + - - +
595A PHE* 4.4 0.6 - - - -
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Residues in contact with ASN 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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546A VAL* 3.3 24.2 - - - +
547A SER* 1.3 72.4 - - - +
549A HIS* 1.3 59.3 + - - +
550A SER* 6.4 0.2 - - - -
557A HIS 3.6 0.7 - - - +
558A TYR* 3.2 13.3 - - - -
559A THR* 2.8 54.6 + - + +
561A TYR* 3.4 38.5 + - + +
586A VAL 4.8 0.4 + - - -
588A THR* 3.8 10.9 + - - -
590A ASP* 3.3 14.6 - - + +
591A ALA* 3.5 14.8 - - - +
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Residues in contact with HIS 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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514A LYS* 3.1 34.0 + - - +
547A SER 4.2 1.0 + - - -
548A ASN* 1.3 73.2 - - - +
550A SER* 1.3 64.6 + - - +
551A GLY* 3.8 8.1 - - - -
552A THR 2.9 38.4 - - - -
555A GLY 4.2 1.2 + - - -
556A GLY* 4.2 0.2 - - - -
557A HIS 3.7 3.6 - - - -
558A TYR* 3.5 38.1 - + + -
590A ASP* 2.8 30.4 + - - +
592A TYR* 4.3 4.1 - - + +
73B LEU* 3.7 29.4 + - + +
74B ARG 2.6 26.7 + - - -
75B GLY* 4.1 3.4 - - - -
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Residues in contact with SER 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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514A LYS* 4.3 1.1 - - - +
548A ASN* 6.4 0.2 - - - -
549A HIS* 1.3 78.6 - - - +
551A GLY* 1.3 58.2 + - - +
556A GLY* 3.1 2.4 - - - -
557A HIS* 2.8 45.3 + - - +
590A ASP* 3.6 21.2 + - - -
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Residues in contact with GLY 551 (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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514A LYS* 3.5 17.8 + - - +
516A THR* 5.2 3.6 - - - +
549A HIS* 3.8 4.1 + - - -
550A SER* 1.3 77.4 + - - +
552A THR* 1.3 65.4 + - - +
555A GLY 3.5 8.1 - - - -
556A GLY* 4.0 2.2 - - - -
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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