Contacts of the strand formed by residues 574 - 583 (chain A) in PDB entry 3S3J
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 SER 574 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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400A ASP* 3.4 27.3 + - - +
567A LEU 3.8 0.6 - - - +
568A VAL* 3.6 2.8 - - - +
569A GLU* 2.9 44.0 + - - +
572A ILE* 4.2 18.5 + - - +
573A ASN* 1.3 74.8 - - - +
575A TYR* 1.3 65.0 + - - +
576A LEU* 4.7 11.1 - - - +
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Residues in contact with TYR 575 (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 LEU* 3.6 33.0 - - + -
315A TYR* 4.9 2.9 - + - -
316A PHE* 3.7 16.9 - + - -
331A ILE* 3.3 19.8 - - + +
399A ALA* 4.4 7.6 - - + -
400A ASP* 2.7 18.2 + - - +
401A VAL* 4.2 18.4 - - + -
402A VAL* 3.0 26.1 + - - +
420A LEU* 4.5 4.7 - - + -
566A LEU* 4.1 3.4 - - + -
567A LEU 3.4 4.5 - - - -
568A VAL* 3.6 37.7 - - + +
570A PRO* 6.0 0.2 - - - +
573A ASN* 2.8 45.3 + - - -
574A SER* 1.3 75.8 - - - +
576A LEU* 1.3 68.9 + - - +
577A LEU* 4.2 0.7 - - + -
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Residues in contact with LEU 576 (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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400A ASP* 6.5 0.2 - - - -
402A VAL* 3.6 6.3 - - + +
404A TRP* 4.0 15.3 - - + +
473A MET* 3.5 48.0 - - + +
474A ALA* 4.0 15.3 - - - -
475A MET* 3.1 11.9 - - + +
566A LEU* 3.2 3.5 - - - -
567A LEU* 2.8 62.6 + - + +
569A GLU* 6.5 0.7 - - + -
574A SER* 4.7 9.4 - - - -
575A TYR* 1.3 87.2 - - - +
577A LEU* 1.3 63.0 + - - +
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Residues in contact with LEU 577 (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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310A ASN* 3.3 25.1 - - - +
311A LEU* 5.1 5.8 - - + -
312A LEU* 3.8 17.3 - - + -
401A VAL* 4.0 7.6 - - + -
402A VAL 2.9 8.1 + - - +
403A ASP* 3.3 27.6 - - - +
404A TRP* 2.9 33.0 + - - -
417A ASN* 3.6 12.6 - - - +
475A MET* 4.3 0.2 - - - -
565A ALA 3.5 3.6 - - - +
566A LEU* 3.1 42.0 - - + -
575A TYR* 5.1 0.2 - - + -
576A LEU* 1.3 75.6 - - - +
578A ALA* 1.3 60.5 + - - +
579A GLU* 6.6 0.2 - - + -
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Residues in contact with ALA 578 (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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404A TRP 3.8 7.6 - - - +
475A MET* 3.2 46.6 - - + +
476A ARG* 4.0 9.4 - - - -
477A ILE* 3.9 12.9 - - + +
564A ARG* 3.5 1.9 - - - +
565A ALA 2.8 36.8 + - - +
577A LEU* 1.3 71.8 - - - +
579A GLU* 1.3 61.3 + - - +
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Residues in contact with GLU 579 (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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404A TRP 3.8 12.2 + - - +
405A ILE* 4.6 11.1 - - - +
477A ILE* 4.0 3.0 + - - +
562A LYS* 2.7 53.1 + - - +
563A VAL 3.3 3.6 - - - -
564A ARG* 3.3 24.2 - - + -
577A LEU* 4.4 0.4 - - + -
578A ALA* 1.3 74.4 - - - +
580A ARG* 1.3 67.2 + - - +
581A ASP* 4.3 0.7 + - - +
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Residues in contact with ARG 580 (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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476A ARG* 4.8 1.2 - - - +
477A ILE* 2.9 47.3 + - + +
478A ARG* 4.0 0.4 - - - +
479A VAL* 4.1 15.2 - - - +
483A MET* 4.8 4.6 - - - +
561A ILE 3.8 0.5 - - - +
562A LYS* 3.6 0.6 - - - -
563A VAL* 2.7 43.1 + - - +
579A GLU* 1.3 82.4 + - - +
581A ASP* 1.3 72.5 + - - +
582A LEU* 3.6 18.4 - - + +
705A SO4 3.2 36.5 + - - -
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Residues in contact with ASP 581 (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 VAL* 3.7 15.8 - - + +
560A LEU* 5.0 12.7 - - + +
561A ILE 3.4 2.9 - - - +
562A LYS* 3.0 49.6 + - - +
579A GLU* 5.0 0.2 - - - -
580A ARG* 1.3 80.7 + - - +
582A LEU* 1.3 69.6 + - - +
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Residues in contact with LEU 582 (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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477A ILE* 5.4 0.4 - - + -
479A VAL* 3.6 12.6 - - + -
483A MET* 3.5 37.5 - - + -
489A PHE* 4.6 4.7 - - + -
491A VAL* 3.6 22.2 - - + -
546A ILE* 6.1 0.4 - - + -
559A ASN 3.6 1.4 - - - +
560A LEU* 3.3 11.2 - - - +
561A ILE* 2.8 44.9 + - + +
563A VAL* 3.5 29.2 - - + -
580A ARG* 3.6 20.6 - - + +
581A ASP* 1.3 84.2 - - - +
583A TYR* 1.3 61.4 + - - +
584A LEU* 3.8 2.3 + - + +
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Residues in contact with TYR 583 (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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483A MET* 3.7 15.7 + - - +
516A TYR* 4.0 14.6 - - - -
558A SER 3.4 25.8 - - - -
559A ASN* 3.8 10.2 + - + -
560A LEU* 3.9 14.8 - - + -
582A LEU* 1.3 74.4 - - - +
584A LEU* 1.3 68.4 + - - +
585A GLU* 3.3 28.3 + - + +
586A ASN* 5.1 8.1 + - - -
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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