Contacts of the strand formed by residues 507 - 515 (chain A) in PDB entry 3Q0F
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 LEU 507 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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445A LYS 4.3 2.3 - - - +
446A ASP* 2.9 29.4 + - + +
447A GLN* 3.1 33.2 + - - +
499A GLU* 3.5 47.8 - - + +
500A GLU 3.4 11.9 - - - +
501A THR* 4.2 10.3 - - - +
506A LYS* 1.3 74.3 - - - +
508A VAL* 1.3 65.5 + - - +
509A PHE* 4.4 16.8 - - + -
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Residues in contact with VAL 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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429A THR* 3.5 31.6 - - + -
434A ASN 6.2 3.8 - - - -
447A GLN* 3.8 15.7 - - + +
499A GLU* 3.3 3.8 - - - -
500A GLU* 2.7 46.3 + - + +
502A GLY* 4.9 4.7 - - - +
504A HIS* 4.7 11.9 - - + +
506A LYS 4.1 9.0 - - - +
507A LEU* 1.3 79.9 - - - +
509A PHE* 1.3 69.4 + - - +
510A LYS* 4.4 9.2 - - - -
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Residues in contact with PHE 509 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
429A THR* 3.6 3.5 - - - -
430A GLY* 3.0 21.3 + - - -
447A GLN* 3.0 57.3 + - + +
448A GLN 3.6 11.9 - - - -
449A LEU* 3.8 27.8 - - + -
453A ASN* 3.6 14.6 - - + -
497A TYR* 4.2 21.8 - + + -
498A TRP 3.5 2.0 - - - +
499A GLU* 3.8 29.6 - - + -
507A LEU* 4.4 10.8 - - + -
508A VAL* 1.3 82.1 - - - +
510A LYS* 1.3 62.5 + - - +
511A PHE* 3.8 21.8 - + + -
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Residues in contact with LYS 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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417A ASN* 2.9 30.1 + - - +
418A ASP* 4.8 1.2 - - - +
419A VAL* 5.9 2.4 - - - +
427A ILE* 4.1 17.1 - - + +
428A TYR 3.5 2.0 - - - -
429A THR* 2.9 21.0 + - - +
497A TYR* 3.1 6.9 - - - +
498A TRP* 2.9 57.4 + - + +
500A GLU* 3.5 43.3 - - + +
508A VAL* 4.4 7.8 - - - +
509A PHE* 1.3 83.4 - - - +
511A PHE* 1.3 63.9 + - - +
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Residues in contact with PHE 511 (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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426A LEU 3.4 1.9 - - - +
427A ILE* 3.4 6.0 - - - -
428A TYR* 2.7 49.8 + - + +
430A GLY* 3.8 17.9 - - - -
449A LEU* 5.3 1.6 - - + -
453A ASN* 3.6 27.1 - - + -
456A LEU* 3.7 39.7 - - + -
457A LYS* 3.9 9.0 - - + -
494A VAL* 4.4 10.8 - - + -
496A GLU 3.5 2.9 - - - +
497A TYR* 3.5 28.5 - + + -
498A TRP* 5.0 0.2 - - - -
509A PHE* 3.8 29.2 - + + -
510A LYS* 1.3 73.2 - - - +
512A LYS* 1.3 60.7 + - - +
513A LEU* 3.5 18.7 - - + +
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Residues in contact with LYS 512 (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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425A VAL* 4.1 16.4 - - + -
426A LEU 3.7 3.6 - - - -
427A ILE* 4.1 16.6 - - + -
494A VAL* 3.7 2.4 - - - -
495A GLU* 2.8 56.3 + - + +
496A GLU* 2.9 45.6 + - + +
498A TRP* 4.0 12.7 - - + -
510A LYS 4.2 0.6 + - - -
511A PHE* 1.3 71.2 - - - +
513A LEU* 1.3 61.9 + - - +
514A ARG* 4.5 13.1 - - - +
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Residues in contact with LEU 513 (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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410A ILE* 3.7 25.8 - - + -
424A ASP 3.8 0.3 - - - +
425A VAL* 3.4 5.5 - - - +
426A LEU* 2.8 40.9 + - + +
428A TYR* 4.1 14.4 - - + -
456A LEU* 4.8 3.8 - - + -
466A VAL* 4.5 10.8 - - + -
468A VAL* 4.6 0.9 - - + -
492A TYR* 4.0 29.0 - - + -
493A LEU 3.2 9.2 - - - +
494A VAL* 3.9 24.5 - - + -
511A PHE* 3.5 31.6 - - + +
512A LYS* 1.3 78.3 - - - +
514A ARG* 1.3 61.1 + - - +
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Residues in contact with ARG 514 (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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424A ASP* 2.6 50.5 + - - +
425A VAL* 3.6 20.5 - - + +
492A TYR* 3.4 4.7 - - - -
493A LEU* 2.9 33.8 + - + +
495A GLU* 3.2 41.6 + - + +
512A LYS* 4.3 9.3 + - - +
513A LEU* 1.3 73.3 - - - +
515A ARG* 1.3 73.5 + - - +
516A ILE* 3.4 1.4 + - - +
517A PRO* 6.3 1.8 - - - -
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Residues in contact with ARG 515 (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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372A VAL* 3.6 20.6 - - - +
423A SER 5.7 1.1 - - - -
424A ASP* 2.7 32.1 + - + +
489A ASP* 2.9 41.3 + - - -
491A LEU 3.7 5.6 - - - +
492A TYR* 3.3 35.0 + - + -
514A ARG* 1.3 80.1 - - - +
516A ILE* 1.3 69.2 + - - +
517A PRO* 3.3 9.2 - - - +
519A GLN* 3.7 24.6 + - - +
520A PRO 2.8 30.5 + - - -
521A GLU* 4.4 5.6 - - - +
522A LEU* 4.6 3.2 - - - +
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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