Contacts of the strand formed by residues 438 - 445 (chain F) in PDB entry 6Q2N
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 438 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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364F ILE* 4.7 7.2 - - + -
402F LEU* 5.3 8.7 - - + -
427F VAL* 4.6 16.2 - - + -
433F PHE* 5.7 11.4 - - + -
436F ILE* 3.3 30.0 + - + +
437F ASN* 1.3 68.5 - - - +
439F GLN* 1.3 59.2 + - - +
440F TYR* 3.8 22.4 - - + -
456F THR* 3.2 26.9 + - - +
461F THR* 4.7 13.5 - - - +
487F ALA* 4.9 6.1 - - + -
488F THR 3.3 19.3 - - - +
489F ASP* 4.4 5.6 - - + +
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Residues in contact with GLN 439 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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437F ASN* 3.5 19.2 - - + +
438F VAL* 1.3 74.8 - - - +
440F TYR* 1.3 65.9 + - - +
441F LYS* 5.7 4.1 - - + +
456F THR* 3.5 6.3 - - - -
488F THR* 2.8 44.1 + - - +
489F ASP 5.3 1.1 - - - +
490F GLN* 2.8 44.2 + - - +
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Residues in contact with TYR 440 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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404F LEU* 5.6 1.1 - - + -
425F VAL* 3.6 24.0 + - + +
427F VAL* 3.3 24.3 + - + +
438F VAL* 3.8 23.8 - - + -
439F GLN* 1.3 79.7 - - - +
441F LYS* 1.3 70.5 + - - +
454F VAL* 3.7 44.3 - - + +
455F VAL* 5.2 2.1 - - - -
456F THR* 2.9 24.2 + - - +
461F THR 3.1 20.7 + - - -
462F SER* 3.8 5.0 - - - -
463F GLY* 3.3 27.6 - - - -
485F VAL* 5.4 8.1 - - + -
486F VAL 3.8 2.0 - - - +
487F ALA* 4.4 16.2 - - + -
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Residues in contact with LYS 441 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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439F GLN* 3.9 5.1 + - + +
440F TYR* 1.3 83.4 - - - +
442F LEU* 1.3 60.0 + - - +
443F HIS* 3.8 16.7 + - + +
454F VAL* 6.1 0.7 - - - -
485F VAL* 3.7 3.6 - - - +
486F VAL* 2.7 55.7 + - + +
488F THR* 4.1 23.8 - - + +
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Residues in contact with LEU 442 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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440F TYR 4.3 0.8 + - - -
441F LYS* 1.3 73.9 - - - +
443F HIS* 1.3 62.5 + - - +
444F SER* 3.9 3.3 + - - -
452F LEU* 4.0 7.9 - - + +
453F GLY* 3.9 28.0 - - - +
454F VAL* 4.5 23.3 + - + +
483F TYR* 3.6 51.4 - - + -
484F MET 4.5 0.2 - - - -
485F VAL* 3.7 25.6 - - + -
500F LEU* 5.9 0.7 - - + -
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Residues in contact with HIS 443 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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441F LYS* 3.8 17.1 + - + +
442F LEU* 1.3 76.3 + - - +
444F SER* 1.3 59.9 + - - +
483F TYR* 3.7 2.6 - - - +
484F MET* 2.9 46.2 + - + +
486F VAL* 3.5 32.0 - - + +
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Residues in contact with SER 444 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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442F LEU* 3.9 4.4 + - - -
443F HIS* 1.3 77.3 + - - +
445F SER* 1.3 71.9 + - - +
449F CYS 4.6 5.2 + - - -
481F LEU* 5.8 0.7 - - - +
482F HIS 3.9 4.3 + - - -
483F TYR* 3.2 35.6 + - - -
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Residues in contact with SER 445 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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444F SER* 1.3 83.9 + - - +
449F CYS 5.9 0.3 + - - -
481F LEU* 4.2 17.8 - - - +
482F HIS* 3.1 39.3 + - - +
484F MET* 5.5 5.5 + - - +
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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