Contacts of the strand formed by residues 507 - 515 (chain X) 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 X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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445X LYS 4.3 2.1 - - - +
446X ASP* 2.9 30.4 + - + +
447X GLN* 3.1 34.7 + - - +
499X GLU* 3.5 47.6 - - + +
500X GLU 3.4 12.8 - - - +
501X THR* 4.2 10.3 - - - +
505X GLY 4.1 0.4 + - - +
506X LYS* 1.3 72.1 - - - +
508X VAL* 1.3 63.2 + - - +
509X PHE* 4.4 15.5 - - + -
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Residues in contact with VAL 508 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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429X THR* 3.4 31.6 - - + -
434X ASN 6.2 3.8 - - - -
447X GLN* 3.7 15.5 - - + +
499X GLU* 3.2 3.4 - - - -
500X GLU* 2.7 47.4 + - + +
502X GLY* 4.9 4.7 - - - +
504X HIS* 4.7 11.9 - - + +
506X LYS* 4.1 9.6 - - + +
507X LEU* 1.3 81.0 - - - +
509X PHE* 1.3 68.6 + - - +
510X LYS* 4.4 9.6 - - - -
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Residues in contact with PHE 509 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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429X THR* 3.5 5.0 - - - -
430X GLY* 2.9 22.0 + - - -
447X GLN* 2.9 47.6 + - + +
448X GLN 3.6 24.5 - - - -
449X LEU* 3.8 28.5 - - + -
453X ASN* 3.6 15.3 - - + -
497X TYR* 4.2 20.6 - + + -
498X TRP 3.5 2.0 - - - +
499X GLU* 3.8 30.3 - - + -
507X LEU* 4.4 10.3 - - + -
508X VAL* 1.3 79.7 - - - +
510X LYS* 1.3 62.1 + - - +
511X PHE* 3.8 22.7 - + + -
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Residues in contact with LYS 510 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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417X ASN* 3.6 21.8 + - - +
418X ASP* 5.2 0.2 - - - +
419X VAL* 5.6 2.4 - - - +
427X ILE* 4.0 17.3 - - + +
428X TYR 3.4 2.0 - - - -
429X THR* 2.9 32.5 + - - +
497X TYR* 3.1 7.1 - - - +
498X TRP* 2.9 56.9 + - + +
500X GLU* 3.5 43.1 - - + +
508X VAL* 4.4 8.0 - - - +
509X PHE* 1.3 81.0 - - - +
511X PHE* 1.3 63.3 + - - +
512X LYS 4.2 0.2 - - - -
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Residues in contact with PHE 511 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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426X LEU 3.5 2.1 - - - +
427X ILE* 3.4 6.3 - - - -
428X TYR* 2.7 48.7 + - + +
430X GLY* 3.8 17.5 - - - -
449X LEU* 5.2 1.6 - - + -
453X ASN* 3.6 27.6 - - + -
456X LEU* 3.6 39.3 - - + -
457X LYS* 3.9 8.7 - - + -
494X VAL* 4.4 11.0 - - + -
496X GLU 3.5 3.6 - - - +
497X TYR* 3.4 28.7 - + + -
498X TRP* 5.0 0.2 - - - -
509X PHE* 3.8 30.1 - + + -
510X LYS* 1.3 72.8 - - - +
512X LYS* 1.3 59.9 + - - +
513X LEU* 3.5 17.2 - - + +
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Residues in contact with LYS 512 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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425X VAL* 4.1 16.4 - - + -
426X LEU 3.7 3.4 - - - -
427X ILE* 4.1 17.3 - - + -
494X VAL* 3.7 2.3 - - - -
495X GLU* 2.8 55.8 + - + +
496X GLU* 2.9 46.3 + - + +
498X TRP* 4.0 12.9 - - + -
510X LYS 4.2 0.6 + - - -
511X PHE* 1.3 70.5 - - - +
513X LEU* 1.3 63.3 + - - +
514X ARG* 4.4 12.9 - - - +
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Residues in contact with LEU 513 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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410X ILE* 3.8 23.8 - - + -
424X ASP 3.8 0.3 - - - +
425X VAL* 3.5 5.4 - - - +
426X LEU* 2.9 40.8 + - + +
428X TYR* 4.1 14.4 - - + -
456X LEU* 4.7 4.9 - - + -
466X VAL* 4.5 12.1 - - + -
468X VAL* 4.6 1.1 - - + -
492X TYR* 4.1 26.6 - - + -
493X LEU 3.2 5.8 - - - +
494X VAL* 3.9 29.2 - - + -
495X GLU* 4.9 0.2 - - - -
511X PHE* 3.5 31.2 - - + +
512X LYS* 1.3 77.9 - - - +
514X ARG* 1.3 61.0 + - - +
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Residues in contact with ARG 514 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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424X ASP* 2.6 50.7 + - - +
425X VAL* 3.6 18.6 - - + +
492X TYR* 3.4 4.5 - - - -
493X LEU* 2.9 33.1 + - + +
495X GLU* 3.2 43.0 + - + +
512X LYS* 4.4 8.7 - - - +
513X LEU* 1.3 73.9 - - - +
515X ARG* 1.3 71.5 + - - +
516X ILE* 3.5 0.7 + - - -
517X PRO* 6.2 1.8 - - - -
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Residues in contact with ARG 515 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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372X VAL* 3.6 19.8 - - - +
423X SER 5.7 0.7 - - - -
424X ASP* 2.7 33.6 + - + +
489X ASP* 3.0 41.3 + - - -
491X LEU 3.7 1.1 - - - -
492X TYR* 3.3 30.1 + - + -
514X ARG* 1.3 80.5 - - - +
516X ILE* 1.3 70.1 + - - +
517X PRO* 3.3 9.2 - - - +
519X GLN* 3.7 30.9 + - - +
520X PRO 2.8 30.3 + - - -
521X GLU* 4.4 5.8 - - - +
522X LEU* 4.4 3.8 - - - +
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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