Contacts of the strand formed by residues 499 - 510 (chain A) in PDB entry 3SMQ
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 GLN 499 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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420A VAL 3.6 0.5 - - - +
421A VAL* 3.3 5.9 - - - +
422A GLU 2.9 32.6 + - - +
423A VAL* 3.6 9.1 - - - +
424A LEU* 2.8 49.7 + - + +
469A ALA* 5.1 1.8 - - + -
470A GLY 3.8 11.7 - - - +
471A TYR* 4.3 3.1 - - + +
488A THR 2.9 25.2 + - - +
489A GLY* 3.4 13.4 + - - -
490A PRO* 3.5 30.4 - - + +
492A SER 5.2 1.8 + - - -
494A LYS* 5.5 5.3 - - - +
495A THR 5.9 0.4 - - - +
497A TRP 4.0 2.7 - - - -
498A LYS* 1.3 86.8 + - - +
500A THR* 1.3 64.0 + - - +
501A VAL* 4.1 0.6 + - - +
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Residues in contact with THR 500 (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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350A TYR* 4.1 8.7 - - - +
351A PHE* 3.4 38.7 + - + +
419A ALA* 4.1 11.2 - - + -
420A VAL 3.3 7.4 - - - +
421A VAL* 4.2 7.4 - - + +
468A ILE 4.0 0.3 - - - +
469A ALA* 3.2 4.9 - - - +
470A GLY 2.7 41.3 + - - -
497A TRP 5.1 1.0 + - - -
499A GLN* 1.3 74.4 + - - +
501A VAL* 1.3 63.9 + - - +
502A PHE* 3.6 30.3 - - + -
547A LEU* 5.4 4.7 - - + -
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Residues in contact with VAL 501 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A TDU 4.0 21.3 - - + -
387A VAL* 5.4 0.4 - - + -
419A ALA* 3.4 6.8 - - - -
420A VAL* 2.7 57.4 + - + +
422A GLU* 4.6 4.3 - - + +
424A LEU* 3.8 32.5 - - + -
467A ALA* 3.7 25.4 - - + -
468A ILE 3.7 4.9 - - - +
469A ALA* 4.5 2.2 - - + +
499A GLN 4.4 5.4 - - - +
500A THR* 1.3 79.7 - - - +
502A PHE* 1.3 65.3 + - - +
503A LEU* 3.9 11.5 + - + +
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Residues in contact with PHE 502 (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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351A PHE* 4.2 26.5 - + - -
384A LEU* 4.5 5.6 - - + -
419A ALA* 3.8 23.1 - - + -
467A ALA* 3.4 2.2 - - - -
468A ILE* 2.8 52.8 + - + +
470A GLY 4.4 4.0 - - - -
500A THR* 3.6 25.6 - - + -
501A VAL* 1.3 70.3 - - - +
503A LEU* 1.3 64.9 + - - +
504A LEU* 3.6 2.1 + - - +
534A VAL* 4.1 35.7 - - + -
536A LEU* 3.8 28.0 - - + -
545A TYR* 3.7 36.1 + + + -
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Residues in contact with LEU 503 (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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1A TDU 3.9 40.2 - - + +
393A HIS* 4.9 0.9 - - + -
396A ARG* 3.7 41.5 - - + +
397A ILE* 4.4 14.6 - - + -
415A VAL* 5.8 3.6 - - + +
416A ILE* 3.9 21.8 + - + +
418A GLU 4.8 5.1 + - - +
420A VAL* 4.1 18.6 - - + -
466A THR 4.1 4.9 - - - +
467A ALA* 4.1 1.6 - - - -
501A VAL* 4.2 12.3 - - + +
502A PHE* 1.3 72.6 - - - +
504A LEU* 1.3 58.8 + - - +
505A GLU 3.8 1.6 + - - -
545A TYR* 2.6 32.6 + - - -
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Residues in contact with LEU 504 (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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393A HIS* 2.7 32.7 + - - -
416A ILE* 3.9 2.2 - - - +
465A CYS* 3.8 28.0 - - - +
466A THR 3.0 19.2 + - - +
467A ALA* 4.0 6.1 - - - +
468A ILE* 4.5 9.4 - - + -
502A PHE 4.5 1.6 - - - +
503A LEU* 1.3 74.0 - - - +
505A GLU* 1.3 58.3 + - - +
506A LYS 4.3 12.6 - - - +
507A PRO* 4.0 1.6 - - - +
508A PHE* 3.6 32.3 - - + -
536A LEU* 5.4 5.8 - - + -
538A LEU* 4.2 19.1 - - + -
545A TYR* 4.0 14.1 - - - +
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Residues in contact with GLU 505 (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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393A HIS* 4.2 6.8 + - - -
397A ILE* 4.9 6.9 - - + +
412A LYS* 5.7 4.6 - - + +
413A LYS* 2.6 42.1 + - - +
416A ILE* 3.7 33.6 - - + +
503A LEU 3.8 1.4 + - - -
504A LEU* 1.3 73.3 - - - +
506A LYS* 1.3 60.1 + - + +
507A PRO* 3.5 7.4 - - - +
543A GLN* 4.2 14.6 - - + +
545A TYR* 5.0 1.0 + - - -
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Residues in contact with LYS 506 (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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504A LEU* 4.3 6.9 - - - +
505A GLU* 1.3 81.8 - - + +
507A PRO* 1.4 77.4 - - + +
508A PHE* 3.6 14.4 + - + +
539A ASN* 4.5 21.3 + - - +
541A SER* 4.6 17.1 + - - +
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Residues in contact with PRO 507 (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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393A HIS* 3.4 40.4 - - + +
464A MET* 3.6 25.0 - - + +
465A CYS 3.1 17.0 - - - +
466A THR* 4.0 9.0 - - + -
504A LEU* 4.0 3.8 - - + +
505A GLU 3.5 9.6 - - - +
506A LYS* 1.4 95.9 - - + +
508A PHE* 1.3 59.5 + - + +
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Residues in contact with PHE 508 (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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464A MET* 3.4 7.8 - - - -
465A CYS* 2.8 35.0 + - + +
504A LEU* 3.6 26.7 - - + -
506A LYS* 3.8 11.2 - - + +
507A PRO* 1.3 75.0 - - - +
509A SER* 1.3 73.1 + - - +
510A VAL* 3.5 20.2 - - + -
514A GLU* 5.2 0.9 - - - -
516A LEU* 3.7 23.8 - - + -
538A LEU* 3.7 24.2 - - + -
539A ASN* 3.4 48.7 - - + +
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Residues in contact with SER 509 (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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463A SER 3.4 9.6 - - - -
464A MET* 3.7 21.4 - - - +
508A PHE* 1.3 82.7 - - - +
510A VAL* 1.3 65.4 + - - +
511A LYS* 5.9 0.9 - - - +
514A GLU* 4.6 2.1 - - - +
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Residues in contact with VAL 510 (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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430A ILE* 3.7 28.5 - - + -
459A ILE* 3.7 28.7 - - + -
461A ARG 3.9 3.6 - - - +
462A THR* 3.4 6.2 - - - +
463A SER 2.8 39.7 + - - +
465A CYS* 4.2 7.4 - - + -
508A PHE* 3.5 29.2 - - + +
509A SER* 1.3 79.9 - - - +
511A LYS* 1.3 63.3 + - - +
514A GLU* 3.5 18.8 - - - +
516A LEU* 4.4 2.9 - - + -
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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