Contacts of the strand formed by residues 546 - 560 (chain A) in PDB entry 4X61
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 546 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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220A ARG* 3.3 14.4 + - - +
476A SER* 3.3 23.2 + - - -
510A HIS* 4.5 4.2 + - - -
512A LEU* 3.3 33.6 - - + +
542A VAL* 4.3 4.9 - - + -
544A VAL* 4.0 10.3 - - + +
545A ASN* 1.3 78.2 - - - +
547A VAL* 1.3 75.5 + - - +
591A THR* 3.8 4.5 - - - +
592A VAL* 2.8 47.7 + - + +
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Residues in contact with VAL 547 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186A TRP* 3.6 18.7 - - + -
190A HIS* 3.5 32.3 - - + +
193A ARG* 5.7 0.9 - - - +
198A TYR* 4.7 0.9 - - - +
220A ARG* 4.6 0.4 - - - +
476A SER* 2.6 29.4 + - - +
478A SER* 5.6 0.2 - - - +
546A THR* 1.3 87.3 + - - +
548A LEU* 1.3 59.6 + - - +
549A HIS* 3.2 34.4 + - + +
589A PRO* 3.6 20.6 - - + -
590A ILE 3.6 8.3 - - - +
591A THR* 4.4 13.9 - - + +
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Residues in contact with LEU 548 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
474A PRO* 3.7 22.7 - - + -
475A ILE 3.6 10.8 - - - +
512A LEU* 4.2 4.7 - - + -
547A VAL* 1.3 70.9 - - - +
549A HIS* 1.3 58.5 + - - +
550A GLY 3.4 27.1 - - - +
551A PHE* 4.2 12.3 - - + -
586A ILE* 3.5 20.9 - - + +
589A PRO* 3.3 8.7 - - - +
590A ILE* 2.7 47.8 + - + +
592A VAL* 4.1 11.9 - - + +
598A ILE* 4.1 27.8 - - + -
617A VAL* 4.3 9.6 - - + -
620A PRO* 6.0 0.4 - - + -
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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
----------------------------------------------------------
198A TYR* 4.2 6.7 + - - -
475A ILE* 3.1 12.4 + - + +
476A SER* 3.9 3.6 - - - -
477A SER* 2.9 36.4 + - - +
478A SER* 3.2 34.0 + - - -
481A TYR* 3.5 36.1 - + + +
547A VAL* 3.2 38.1 + - + +
548A LEU* 1.3 71.7 - - - +
550A GLY* 1.3 58.0 + - - +
583A LEU* 5.1 2.1 - - - +
585A PRO* 3.8 6.2 - - - +
586A ILE* 3.5 25.1 + - - +
589A PRO* 3.8 19.0 - - + +
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Residues in contact with GLY 550 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
475A ILE* 2.9 33.1 + - - +
548A LEU* 3.4 12.8 - - - +
549A HIS* 1.3 80.1 - - - +
551A PHE* 1.3 71.2 + - - -
583A LEU* 4.5 2.7 - - - -
584A PHE 3.2 13.5 - - - -
585A PRO* 4.2 2.0 - - - -
586A ILE* 4.1 5.3 - - - +
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Residues in contact with PHE 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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472A LEU* 3.9 19.7 - - + -
473A ALA 3.3 6.7 - - - +
474A PRO* 3.7 29.8 - - + -
540A PHE* 4.1 9.9 - + - -
548A LEU* 4.2 11.0 - - + -
550A GLY* 1.3 82.2 - - - -
552A ALA* 1.3 62.7 + - - +
553A GLY 3.8 0.3 + - - -
583A LEU* 3.6 6.0 - - - +
584A PHE* 2.9 43.6 + - + +
586A ILE* 4.6 7.2 - - + -
598A ILE* 3.8 19.5 - - + -
600A VAL* 3.5 48.9 - - + -
602A PHE* 4.7 6.1 - + + -
615A TRP* 5.6 1.8 - + - -
617A VAL* 3.8 18.8 - - + -
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Residues in contact with ALA 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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471A PHE 3.5 0.3 - - - +
472A LEU* 3.2 9.3 - - - +
473A ALA* 2.8 37.5 + - + +
475A ILE* 3.9 15.6 - - + +
506A LEU* 3.6 29.4 - - + -
551A PHE* 1.3 72.1 - - - +
553A GLY* 1.3 59.9 + - - +
554A TYR* 3.8 21.3 - - + +
582A ILE 3.4 5.6 - - - -
583A LEU* 4.8 2.0 - - - +
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Residues in contact with GLY 553 (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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439A SER 4.1 2.7 - - - +
440A PHE* 3.7 13.0 - - - -
471A PHE 3.3 6.7 - - - -
472A LEU* 4.5 0.7 - - - -
552A ALA* 1.3 72.8 - - - +
554A TYR* 1.3 69.7 + - - -
581A PRO* 3.5 7.4 - - - +
582A ILE* 2.8 51.3 + - - +
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Residues in contact with TYR 554 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
439A SER 3.4 9.2 - - - +
440A PHE* 4.0 1.4 - - - -
470A SER* 3.4 5.7 - - - -
471A PHE* 2.7 47.1 + - + +
473A ALA* 4.6 2.9 - - + -
505A ARG* 5.4 2.4 + - - -
506A LEU* 4.0 7.4 - - - +
509A PHE* 4.4 7.1 - - - -
511A GLN* 3.3 25.5 + - - -
515A PRO* 4.5 11.0 - - + -
552A ALA* 3.8 30.9 - - + +
553A GLY* 1.3 77.9 - - - -
555A PHE* 1.3 63.9 + - - +
567A ILE* 3.3 23.3 - - + -
568A ARG* 3.8 15.3 - - - +
569A PRO* 3.6 32.0 - - + +
581A PRO* 3.7 27.1 - - + -
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Residues in contact with PHE 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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437A LEU* 4.1 11.2 - - + -
438A GLY 3.3 16.2 - - - -
439A SER 3.2 18.4 - - - -
441A ALA* 3.5 28.9 - - + +
468A TYR* 5.1 0.2 - - + -
469A THR 3.2 12.1 - - - +
471A PHE* 4.5 2.9 - - - -
554A TYR* 1.3 77.8 - - - +
556A GLU* 1.3 73.7 + - - +
557A THR* 4.0 23.6 - - + -
565A LEU* 4.8 5.2 - - + -
566A SER* 3.6 0.9 - - - -
567A ILE* 3.0 44.9 + - + +
568A ARG 3.7 3.6 + - - -
576A MET* 5.4 1.6 - - + -
579A TRP* 3.5 50.7 - + + -
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Residues in contact with GLU 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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468A TYR* 3.2 4.9 - - - +
469A THR* 2.8 35.0 + - - +
471A PHE* 3.4 25.0 - - + -
555A PHE* 1.3 78.1 - - - +
557A THR* 1.3 61.6 + - - +
565A LEU 3.5 6.1 - - - +
566A SER* 3.4 20.4 - - - +
568A ARG* 2.7 30.1 + - - -
571A THR* 2.6 26.0 + - - +
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Residues in contact with THR 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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437A LEU* 4.0 21.2 - - + +
465A PRO* 3.5 16.8 - - - +
467A GLU 2.7 19.8 + - - -
468A TYR* 3.4 13.3 - - - +
555A PHE* 4.0 6.5 - - + -
556A GLU* 1.3 77.1 - - - +
558A VAL* 1.3 60.9 + - - +
559A LEU* 4.3 7.2 - - + -
564A THR* 3.3 9.0 - - - -
565A LEU* 2.8 66.5 + - + +
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Residues in contact with VAL 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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465A PRO* 3.2 4.5 - - - +
466A GLY* 2.8 32.6 + - - +
467A GLU* 2.8 43.1 + - + +
557A THR* 1.3 72.8 - - - +
559A LEU* 1.3 53.8 + - - +
560A TYR* 4.1 1.6 - - - +
561A GLN* 3.4 37.0 - - - +
563A ILE 4.4 0.9 - - - +
564A THR* 3.8 17.0 - - + -
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Residues in contact with LEU 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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336A GLN* 3.7 39.5 - - + +
337A TYR* 3.6 46.2 - - + +
340A ALA* 3.7 10.5 - - + -
463A SER 4.0 1.4 - - - +
464A ILE* 3.6 17.9 - - + +
465A PRO* 3.6 17.0 - - + +
466A GLY* 3.3 18.2 + - - -
557A THR* 3.8 7.4 + - + -
558A VAL* 1.3 71.4 - - - +
560A TYR* 1.3 64.4 + - - +
563A ILE* 3.0 20.4 + - + +
564A THR* 4.7 1.6 - - - +
565A LEU* 3.8 20.6 - - + -
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Residues in contact with TYR 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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340A ALA* 3.6 33.6 - - + +
343A LYS* 3.7 15.9 - - + -
344A CYS* 3.4 34.8 - - + -
347A ASP* 3.2 25.7 + - - +
348A ARG* 5.7 1.0 - - - +
462A VAL* 3.9 27.9 - - + +
464A ILE* 4.5 2.9 - - + -
558A VAL* 4.2 2.0 - - - -
559A LEU* 1.3 84.1 - - - +
561A GLN* 1.3 91.5 + - + +
562A ASP 3.0 0.7 + - - -
563A ILE* 2.7 36.1 + - - +
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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