Contacts of the strand formed by residues 292 - 300 (chain A) in PDB entry 6PAU
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 ALA 292 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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290A PRO* 3.3 5.1 - - - +
291A ILE* 1.3 87.9 - - + +
293A THR* 1.3 65.2 + - - +
294A CYS* 4.2 2.2 - - - -
474A LEU 4.1 0.2 - - - +
475A GLN* 3.4 3.1 - - - -
476A TYR* 2.9 30.7 + - + +
486A THR* 3.8 15.5 - - + +
487A ASP 4.5 3.6 - - - +
491A VAL* 3.3 34.3 - - + -
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Residues in contact with THR 293 (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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290A PRO* 4.4 7.4 - - - +
292A ALA* 1.3 75.5 - - - +
294A CYS* 1.3 65.7 + - - +
454A ASP* 5.0 1.4 - - - +
473A ASN* 4.2 21.8 - - + +
474A LEU 3.7 2.9 - - - -
475A GLN* 3.4 32.4 + - - +
486A THR 5.0 1.0 + - - -
488A SER* 3.6 16.9 + - - +
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Residues in contact with CYS 294 (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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293A THR* 1.3 78.9 - - - +
295A ARG* 1.3 60.8 + - - +
453A LEU* 4.0 21.8 - - + -
454A ASP* 3.3 10.3 - - - +
455A LEU* 4.1 16.4 - - - -
473A ASN* 3.4 7.6 - - - +
474A LEU 2.9 36.5 + - - +
476A TYR* 3.7 28.7 - - + -
488A SER* 3.7 21.1 - - - -
491A VAL* 4.4 6.5 - - - -
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Residues in contact with ARG 295 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294A CYS* 1.3 74.6 - - - +
296A TYR* 1.3 71.8 + - - +
297A TRP* 3.5 17.9 - - - +
453A LEU* 3.4 4.5 - - - -
454A ASP* 2.9 45.8 + - - +
469A ILE* 3.6 19.8 - - + +
470A GLY 3.2 28.4 + - - -
471A ASP* 3.7 19.8 + - - +
472A GLY 3.6 6.9 - - - +
473A ASN* 2.9 38.3 + - - +
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Residues in contact with TYR 296 (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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295A ARG* 1.3 78.7 - - - +
297A TRP* 1.3 53.2 + - - +
298A HIS* 4.0 4.9 - + - +
401A TYR* 4.9 0.5 + - - -
420A TYR* 4.1 23.1 - + - -
451A ASN* 4.6 7.4 - - + -
452A ALA* 3.7 15.0 - - - -
453A LEU* 3.4 39.7 - - + +
470A GLY* 2.6 32.6 + - - -
472A GLY 3.2 14.0 + - - +
474A LEU* 4.3 11.9 - - + -
503A GOL 2.5 46.7 - - - -
4C VAL* 3.9 14.8 - - + -
6C SER* 3.4 34.1 - - - +
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Residues in contact with TRP 297 (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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295A ARG* 3.5 25.4 - - + +
296A TYR* 1.3 79.2 - - - +
298A HIS* 1.3 67.8 + - - +
451A ASN* 3.4 3.6 - - - +
452A ALA 2.8 36.5 + - - +
454A ASP* 4.1 8.1 + - + +
459A LYS* 6.4 1.1 - - + -
462A LEU* 3.5 32.8 - - + +
463A GLU* 4.0 32.1 - - + -
467A PHE* 3.7 39.4 - - + -
468A GLY 3.3 9.0 - - - -
469A ILE* 3.4 43.7 - - + -
470A GLY 4.0 0.4 - - - +
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Residues in contact with HIS 298 (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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296A TYR* 4.0 12.1 - + + +
297A TRP* 1.3 75.3 + - - +
299A ARG* 1.3 58.7 + - - +
300A SER* 3.9 2.7 + - - -
311A PHE* 3.8 6.7 - + - -
449A VAL* 4.0 6.3 - - + -
450A PHE 3.7 4.3 - - - -
451A ASN* 2.9 29.9 + - - +
466A LYS 4.3 0.7 - - - +
467A PHE* 3.8 3.4 - - - -
468A GLY* 2.8 35.1 + - - -
470A GLY* 3.4 22.2 - - - -
6C SER* 2.8 52.5 + - - -
7C LYS 3.4 16.1 + - - -
8C ILE* 3.6 26.3 - - + +
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Residues in contact with ARG 299 (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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298A HIS* 1.3 70.9 - - - +
300A SER* 1.3 84.3 + - - +
301A LEU* 3.4 5.0 + - - +
326A LEU 4.8 0.2 + - - -
327A TYR* 2.9 40.4 + - - +
328A ARG 4.6 2.0 + - - -
329A LEU* 3.4 34.4 - - - +
439A LEU* 3.7 21.3 - - + +
449A VAL* 3.3 3.6 - - - +
450A PHE 2.8 41.4 + - - +
465A LEU* 2.8 29.4 + - - +
466A LYS* 3.8 26.9 - - - +
467A PHE* 3.6 29.6 - - + +
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Residues in contact with SER 300 (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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298A HIS 3.9 3.5 + - - -
299A ARG* 1.3 98.7 + - - +
301A LEU* 1.3 59.4 + - - +
303A PRO* 4.2 12.5 - - - +
306A LEU* 3.5 28.7 - - - +
312A SER* 4.5 4.5 + - - -
327A TYR* 4.0 36.3 + - - +
448A ASP 4.3 0.2 - - - -
449A VAL* 4.3 0.2 - - - +
466A LYS 5.0 2.2 + - - -
8C ILE* 3.9 12.5 - - - +
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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