Contacts of the strand formed by residues 405 - 411 (chain C) in PDB entry 4QYJ
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 VAL 405 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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293C ILE* 3.7 15.3 - - - +
305C SER* 4.2 10.4 - - - +
352C VAL* 4.7 1.6 - - + -
355C HIS 5.8 0.4 - - - -
356C ILE* 3.9 30.3 - - + +
381C VAL* 5.7 0.2 - - + -
384C THR* 3.4 7.2 - - - +
386C PHE* 4.2 28.0 - - + -
396C LEU* 4.5 20.0 - - + +
401C VAL* 4.0 32.3 - - + +
403C GLY 2.9 7.5 + - - +
404C PRO* 1.3 85.7 - - + +
406C LEU* 1.3 62.0 + - - +
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Residues in contact with LEU 406 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274C VAL* 5.9 0.2 - - + -
289C ALA* 4.8 3.6 - - + -
293C ILE* 4.1 22.7 - - + -
294C PHE* 5.0 1.1 - - + -
304C GLY 3.5 21.5 - - - +
305C SER 3.4 19.5 - - - +
307C LEU* 3.8 27.1 - - + +
321C LEU* 4.0 30.5 - - + -
384C THR 3.0 10.7 + - - +
385C ILE* 4.2 14.8 - - + -
386C PHE* 2.7 36.0 + - - +
396C LEU* 5.7 0.7 - - - -
405C VAL* 1.3 77.4 - - - +
407C VAL* 1.3 60.3 + - - +
408C ALA 4.7 0.2 - - - +
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Residues in contact with VAL 407 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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305C SER 3.3 14.4 + - - +
306C ARG* 3.7 6.5 - - + -
307C LEU* 2.8 25.6 + - - +
386C PHE* 3.2 13.0 - - + +
388C ASN* 3.6 26.7 - - + -
394C ILE* 4.1 16.2 - - + -
396C LEU* 4.7 18.5 - - + +
397C LEU* 3.2 35.4 - - + -
405C VAL 4.4 0.2 + - - -
406C LEU* 1.3 73.3 - - - +
408C ALA* 1.3 61.4 + - - +
409C THR* 4.0 2.7 + - - +
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Residues in contact with ALA 408 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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307C LEU* 3.2 23.1 - - + -
314C TYR* 2.5 27.8 + - + +
318C ILE* 3.9 27.4 - - + -
367C ILE* 6.0 0.2 - - + -
385C ILE* 4.8 9.0 - - + -
386C PHE 2.8 14.5 + - - +
387C ALA* 4.7 2.0 - - - -
388C ASN 3.1 13.2 + - - -
406C LEU* 5.0 0.4 - - + -
407C VAL* 1.3 72.7 - - - +
409C THR* 1.3 57.3 + - - +
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Residues in contact with THR 409 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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307C LEU 2.7 12.5 + - - +
308C TYR* 3.3 27.1 - - + -
309C VAL 3.2 21.0 + - - -
314C TYR* 3.7 4.1 - - - -
388C ASN* 3.6 33.3 + - - +
391C LYS* 4.4 15.3 - - + -
397C LEU* 4.2 12.8 - - - +
407C VAL* 4.3 1.4 + - - +
408C ALA* 1.3 75.0 - - - +
410C PRO* 1.3 78.2 - - + +
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Residues in contact with PRO 410 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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308C TYR* 4.9 2.5 - - - -
309C VAL 3.3 9.0 - - - +
311C GLU* 4.8 9.2 - - + +
314C TYR* 3.7 39.5 - - + +
388C ASN 4.0 8.7 - - - +
389C ARG* 4.3 9.2 - - + -
390C GLU 5.1 2.9 - - - +
391C LYS* 5.5 5.1 - - + +
409C THR* 1.3 102.0 - - + +
411C PHE* 1.3 65.4 + - - +
416C GLU* 4.4 3.6 - - - +
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Residues in contact with PHE 411 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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275C ILE* 4.2 3.8 - - + -
276C VAL 3.9 15.3 - - - -
277C LEU* 4.2 17.0 - - + -
308C TYR* 3.9 13.2 - - + -
309C VAL 3.3 23.5 + - - -
310C HIS* 3.2 35.3 - + + -
311C GLU* 3.1 23.2 + - - +
410C PRO* 1.3 79.4 - - - +
412C SER* 1.3 60.3 + - - +
413C ASP 3.3 26.0 - - - -
414C ILE* 4.5 4.5 - - + -
416C GLU* 3.7 19.5 - - + +
417C VAL* 3.8 37.7 - - + -
420C GLU* 6.4 0.2 - - + -
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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