Contacts of the strand formed by residues 419 - 424 (chain B) in PDB entry 6RKU
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 GLU 419 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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417B LEU 4.9 3.8 - - - +
418B SER* 1.3 78.2 - - - +
420B LEU* 1.3 59.3 + - - +
421B TYR* 3.1 15.2 + - + -
440B ASN* 3.2 14.6 + - - +
441B GLN* 2.9 34.0 + - - +
442B ALA* 2.9 31.6 + - - +
490B TYR* 4.3 3.3 - - - -
492B SER* 3.7 13.5 - - - +
494B ILE* 4.4 12.1 - - + -
757B PRO* 5.4 3.3 - - - +
760B ARG* 2.5 38.9 + - - -
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Residues in contact with LEU 420 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
407B LEU* 4.4 13.7 - - + -
419B GLU* 1.3 73.4 - - - +
421B TYR* 1.3 83.2 - - - +
422B LEU* 5.3 10.3 - - + -
442B ALA* 3.6 26.7 - - + +
443B ILE 4.2 2.2 - - - +
444B LEU* 4.5 10.8 - - + +
470B LEU* 6.3 2.9 - - + -
471B ILE* 5.6 11.7 - - + -
490B TYR* 3.8 28.7 - - + -
492B SER 3.4 13.3 + - - +
493B ILE* 4.1 19.7 - - + -
494B ILE* 2.9 28.5 + - - +
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Residues in contact with TYR 421 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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419B GLU* 3.1 23.9 + - + -
420B LEU* 1.3 75.5 - - - +
422B LEU* 1.3 73.6 + - - +
423B VAL* 5.1 1.3 - - + -
436B ARG* 6.6 0.4 - - + -
441B GLN* 3.1 23.7 + - + -
442B ALA 3.2 25.7 + - - +
443B ILE* 4.8 12.8 - - + -
444B LEU* 3.2 24.0 + - - +
494B ILE* 3.3 44.2 - - + -
496B MET* 3.5 39.3 - - + -
754B THR* 5.2 2.4 + - + -
755B MET* 4.0 25.2 - - + +
760B ARG* 3.2 15.4 + - - -
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Residues in contact with LEU 422 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
420B LEU* 5.3 9.2 - - + -
421B TYR* 1.3 84.5 - - - +
423B VAL* 1.3 57.6 + - - +
444B LEU* 3.5 39.0 - - + +
446B LEU* 4.4 20.4 - - + -
467B VAL* 5.2 10.5 - - + -
493B ILE* 6.1 4.7 - - + -
494B ILE 3.5 10.2 + - - +
495B ILE* 4.2 20.6 - - + +
496B MET 2.8 32.3 + - - +
510B LEU* 5.0 12.6 - - + -
514B PHE* 4.5 23.1 - - + -
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Residues in contact with VAL 423 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
421B TYR* 5.1 0.9 - - + -
422B LEU* 1.3 80.4 - - - +
424B GLU* 1.3 71.2 + - - +
428B ALA* 4.2 15.9 - - + +
429B GLY* 4.3 13.9 - - - +
432B ALA* 5.2 4.5 - - + -
443B ILE* 4.7 11.0 - - + -
444B LEU 3.8 2.2 + - - -
445B PRO* 4.7 8.7 - - + -
446B LEU* 3.1 34.4 + - - +
496B MET* 3.6 46.2 - - + +
742B LEU* 4.4 10.5 - - + -
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Residues in contact with GLU 424 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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423B VAL* 1.3 76.7 - - - +
425B GLY* 1.3 70.8 + - - +
426B ASP 5.1 2.5 - - - +
427B SER* 5.3 10.4 - - - +
428B ALA* 3.4 25.3 + - + +
446B LEU* 4.2 5.6 - - - +
448B GLY* 5.4 9.4 - - - +
498B ASP* 3.8 18.5 - - - +
742B LEU* 6.2 0.2 - - - +
122C TYR* 4.5 14.4 + - - -
14E G 3.1 25.3 - - - +
15H G 3.4 24.1 + - - +
16H T 5.4 2.0 + - - +
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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