Contacts of the strand formed by residues 561 - 573 (chain A) in PDB entry 4OMC
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 561 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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460A ASP* 3.3 10.3 + - - +
461A ILE* 3.0 25.9 + - - +
462A GLY 4.8 1.2 - - - +
494A SER* 3.1 19.5 - - - -
495A TYR* 3.7 7.5 - - - -
560A TYR* 1.3 80.6 - - - +
562A THR* 1.3 66.1 + - - -
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Residues in contact with THR 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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458A PRO* 3.8 27.4 - - + -
459A LYS 3.4 15.5 - - - +
460A ASP* 4.4 6.8 + - - +
461A ILE* 3.9 5.6 - - - -
493A LEU* 3.1 3.1 - - - -
494A SER* 2.9 45.2 + - - -
561A GLY* 1.3 77.7 + - - -
563A LEU* 1.3 64.5 + - - +
564A THR* 3.6 12.0 + - + +
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Residues in contact with LEU 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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455A LEU* 3.6 24.5 - - + +
458A PRO* 3.5 1.2 - - - +
459A LYS* 2.7 38.2 + - + +
461A ILE* 3.9 7.2 - - + +
465A LEU* 4.0 26.0 - - + -
467A VAL* 4.5 8.3 - - + -
491A LEU* 4.4 9.4 - - + -
492A THR 3.4 16.6 - - - +
493A LEU* 3.8 21.5 - - + -
549A LEU* 4.2 21.3 - - + -
551A ILE* 4.3 7.0 - - + -
562A THR* 1.3 72.2 - - - +
564A THR* 1.3 58.2 + - - +
565A LYS 3.5 13.0 - - - +
566A PHE* 4.3 5.8 - - + -
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Residues in contact with THR 564 (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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455A LEU* 3.6 12.9 - - - +
457A GLU 5.6 0.2 - - - -
458A PRO* 4.4 18.0 - - + +
492A THR* 2.9 31.5 + - - +
493A LEU* 4.4 0.9 + - - -
494A SER* 5.6 1.8 - - - +
562A THR* 3.6 22.4 + - + +
563A LEU* 1.3 74.9 - - - +
565A LYS* 1.3 62.5 + - - +
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Residues in contact with LYS 565 (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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453A ASP* 4.0 12.1 - - - +
455A LEU* 3.6 8.8 - - + +
490A ARG* 3.3 18.3 + - - +
491A LEU* 3.3 5.7 - - - -
492A THR* 2.8 63.1 + - + +
530A ASP* 3.3 28.3 + - - -
563A LEU* 3.5 8.2 - - - +
564A THR* 1.3 81.9 - - - +
566A PHE* 1.3 63.5 + - - +
567A THR* 3.4 23.6 - - - +
233B ASP* 6.4 2.2 - - + -
269B LEU* 6.4 1.3 - - - -
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Residues in contact with PHE 566 (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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453A ASP* 3.7 1.9 + - - +
454A ILE* 2.9 60.7 + - + +
455A LEU* 4.0 17.4 + - + +
467A VAL* 4.2 14.6 - - + -
469A LYS* 5.8 1.3 - - + -
489A ALA* 4.0 22.0 - - + -
490A ARG 3.4 2.7 - - - -
491A LEU* 3.5 20.2 - - + -
505A LEU* 4.3 13.7 - - + -
547A TRP* 5.7 5.8 - - + -
548A VAL* 6.3 0.2 - - - -
549A LEU* 3.8 33.9 - - + -
563A LEU* 4.3 7.9 - - + -
565A LYS* 1.3 77.4 - - - +
567A THR* 1.3 72.5 + - - +
568A LEU* 4.2 13.9 - - + -
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Residues in contact with THR 567 (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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451A ILE* 3.7 27.6 - - + -
452A ILE 3.5 12.1 - - - +
453A ASP* 2.6 23.6 + - - +
488A GLN 3.6 0.5 - - - +
489A ALA* 3.6 1.4 - - - -
490A ARG* 2.8 50.7 + - - +
565A LYS* 3.4 19.5 - - - +
566A PHE* 1.3 75.1 - - - +
568A LEU* 1.3 65.4 + - - +
569A VAL* 3.7 4.4 + - + -
234B ALA* 4.7 1.8 - - + +
269B LEU* 4.2 14.0 - - + +
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Residues in contact with LEU 568 (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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450A CYS 3.7 2.4 - - - +
451A ILE* 3.7 0.7 - - - -
452A ILE* 2.8 58.1 + - + +
454A ILE* 4.1 13.2 - - + +
471A VAL* 4.5 5.6 - - + -
487A ALA* 5.1 1.3 - - + -
488A GLN 3.5 15.9 - - - +
505A LEU* 4.5 20.9 - - + -
547A TRP* 3.7 45.3 - - + +
566A PHE* 4.1 15.9 + - + -
567A THR* 1.3 72.0 - - - +
569A VAL* 1.3 61.1 + - - +
570A LEU* 3.8 21.5 - - + -
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Residues in contact with VAL 569 (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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449A LYS* 3.7 35.7 - - + -
450A CYS 3.6 4.0 - - - +
451A ILE* 4.6 6.1 - - + -
486A HIS 4.2 0.2 - - - +
487A ALA* 3.3 5.9 - - - +
488A GLN* 2.9 50.2 + - - +
490A ARG* 3.9 31.9 - - + -
567A THR* 4.2 10.8 - - + -
568A LEU* 1.3 77.7 - - - +
570A LEU* 1.3 63.5 + - - +
571A TYR* 3.8 17.5 + - + -
269B LEU* 4.4 8.3 - - + -
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Residues in contact with LEU 570 (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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449A LYS* 3.3 4.5 - - - +
450A CYS* 2.8 44.4 + - + +
452A ILE* 3.8 26.7 - - + -
471A VAL* 5.0 0.9 - - + -
473A ALA* 4.1 17.7 - - + -
481A ILE* 3.3 11.4 - - + +
484A LEU* 3.8 24.5 - - + -
486A HIS 4.1 0.2 - - - -
487A ALA* 4.4 4.3 - - + -
543A PRO* 3.9 21.1 - - + +
547A TRP* 3.9 18.8 - - + -
568A LEU* 3.8 23.6 - - + -
569A VAL* 1.3 77.1 - - - +
571A TYR* 1.3 61.2 + - - +
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Residues in contact with TYR 571 (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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312A ILE* 3.8 22.5 - - + +
447A GLN* 3.6 28.9 - - + +
448A ARG 3.2 6.3 - - - +
449A LYS* 3.3 40.4 + - + -
481A ILE* 3.6 2.9 - - - -
484A LEU* 3.4 9.4 - - - +
485A GLU* 2.8 25.2 + - + -
486A HIS* 3.1 37.8 + - + +
487A ALA 4.9 0.2 - - - -
488A GLN* 3.4 37.2 + - + -
569A VAL* 3.8 9.2 - - + -
570A LEU* 1.3 75.7 - - - +
572A GLY* 1.3 58.9 + - - +
604A FMT 3.7 24.5 - - - -
272B GLU* 4.1 4.2 + - - -
276B ARG* 4.2 2.7 - - - -
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Residues in contact with GLY 572 (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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447A GLN* 3.8 1.9 - - - +
448A ARG* 2.8 40.6 + - - +
481A ILE* 3.5 11.3 - - - +
483A ARG 3.4 11.2 - - - -
485A GLU* 4.0 17.7 + - - +
571A TYR* 1.3 76.5 - - - +
573A THR* 1.3 66.9 + - - +
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Residues in contact with THR 573 (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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391A ARG* 3.3 27.4 - - - +
395A HIS* 6.3 0.4 - - + -
444A VAL* 5.1 2.5 - - + -
445A ALA* 3.7 26.0 - - + +
446A PRO 3.8 4.3 - - - +
448A ARG* 4.5 6.7 - - - +
480A HIS 4.4 4.3 - - - -
481A ILE* 3.6 1.4 - - - +
482A THR 3.0 8.0 + - - -
483A ARG* 3.0 51.1 + - - +
485A GLU* 4.0 5.6 - - - +
572A GLY* 1.3 80.0 - - - +
574A ALA* 1.3 70.0 + - - +
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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