Contacts of the strand formed by residues 556 - 563 (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 GLY 556 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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355A GLN* 3.0 12.6 + - - +
549A HIS* 4.2 0.9 - - - -
550A SER 3.1 13.0 - - - -
551A GLY* 4.0 2.9 - - - -
555A GLY* 1.3 74.6 - - - -
557A HIS* 1.3 59.4 + - - +
74B ARG 3.4 3.2 + - - -
75B GLY* 3.7 2.5 - - - -
76B NEH 2.8 27.4 + - - +
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Residues in contact with HIS 557 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271A ASN* 5.7 2.7 - - - -
276A CYS* 3.7 10.8 - - + -
548A ASN 3.6 2.9 - - - +
549A HIS* 3.7 2.2 + - - -
550A SER* 2.8 39.2 + - - +
556A GLY* 1.3 75.1 + - - -
558A TYR* 1.3 82.2 + - - +
559A THR* 4.2 8.1 + - + +
574A ASN* 2.9 31.3 + - - -
575A ASP* 3.4 21.4 + - - -
75B GLY* 4.3 0.6 - - - -
76B NEH 3.5 13.0 - - + +
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Residues in contact with TYR 558 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276A CYS* 3.2 33.3 - - - +
277A PHE* 3.6 21.8 - - + -
280A SER* 3.8 5.6 - - - -
356A GLN 3.4 20.9 - - - -
358A ALA* 3.2 29.3 + - + -
547A SER* 3.5 16.6 - - - -
548A ASN 3.2 19.3 - - - -
549A HIS* 3.5 25.4 - + + -
557A HIS* 1.3 90.1 + - - +
559A THR* 1.3 62.4 + - - +
573A PHE 4.9 0.5 - - - +
574A ASN* 4.4 2.4 - - - +
575A ASP* 5.1 2.3 + - - +
592A TYR* 3.6 20.4 - + - -
73B LEU* 2.5 26.2 + - - +
75B GLY* 3.9 10.5 - - - -
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Residues in contact with THR 559 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280A SER* 2.7 23.4 + - - +
548A ASN* 2.8 48.3 + - + +
557A HIS* 4.3 7.6 - - + +
558A TYR* 1.3 77.9 - - - +
560A ALA* 1.3 58.8 + - - +
561A TYR* 4.0 7.4 + - - -
572A THR* 4.7 7.9 - - + -
573A PHE 3.5 12.3 - - - -
574A ASN* 3.8 28.7 - - + +
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Residues in contact with ALA 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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280A SER* 3.7 29.1 - - - +
283A GLN* 4.2 7.4 - - + -
284A CYS* 4.1 2.5 - - - -
546A VAL 3.2 9.4 - - - +
548A ASN* 4.2 0.2 - - - -
559A THR* 1.3 76.9 - - - +
561A TYR* 1.3 68.8 + - - +
562A CYS* 3.8 19.1 - - - -
571A HIS 3.7 0.3 - - - +
573A PHE* 2.7 40.4 + - + +
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Residues in contact with TYR 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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545A ALA* 3.1 4.5 - - - -
546A VAL* 2.9 36.8 + - + +
548A ASN* 3.4 30.6 + - - +
559A THR* 4.0 6.5 + - + -
560A ALA* 1.3 78.5 - - - +
562A CYS* 1.3 61.9 + - - +
570A TRP* 3.6 15.4 - - + -
571A HIS 3.3 3.1 - - - -
572A THR* 3.4 36.8 - - + -
581A MET* 3.5 16.8 - - + -
585A GLN 3.6 12.4 + - - -
586A VAL* 3.4 37.0 - - + -
588A THR* 4.3 13.8 + - + +
590A ASP* 6.1 0.2 - - - +
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Residues in contact with CYS 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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283A GLN 3.7 24.7 - - - -
284A CYS 4.1 1.3 - - - -
287A ASN* 3.5 26.9 - - + +
544A TYR 3.4 4.9 - - - +
545A ALA* 4.2 7.4 - - - -
560A ALA* 3.8 22.0 - - - -
561A TYR* 1.3 81.6 - - - +
563A ARG* 1.3 60.1 + - - +
564A SER 3.7 0.7 + - - -
569A GLU 3.5 2.1 - - - +
570A TRP* 3.3 7.3 - - - -
571A HIS* 3.0 32.5 + - - +
573A PHE* 3.6 17.6 - - + -
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Residues in contact with ARG 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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287A ASN* 4.0 11.3 - - - +
524A ARG* 5.2 12.3 - - - +
542A ASN* 4.6 8.9 - - - +
543A LEU 3.3 23.4 + - - -
544A TYR* 2.8 27.6 + - - +
562A CYS* 1.3 71.4 - - - +
564A SER* 1.3 71.8 + - - +
565A PRO* 3.2 8.5 - - - +
566A GLY* 4.7 9.7 - - - +
567A THR 4.9 0.2 - - - +
568A GLY* 3.6 44.5 - - - +
569A GLU 3.4 2.7 - - - +
570A TRP* 3.4 32.9 - - + +
597A GLU* 2.8 31.1 + - - +
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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