Contacts of the strand formed by residues 468 - 479 (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 GLY 468 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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297A TRP* 3.3 4.5 - - - -
298A HIS* 2.8 37.6 + - - +
327A TYR* 5.7 2.9 + - - -
466A LYS 3.7 1.0 + - - -
467A PHE* 1.3 75.2 - - - +
469A ILE* 1.3 67.6 + - - -
8C ILE* 4.7 10.5 - - - +
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Residues in contact with ILE 469 (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* 3.6 38.4 - - + +
297A TRP* 3.4 37.5 - - + -
468A GLY* 1.3 72.9 - - - +
470A GLY* 1.3 65.1 + - - +
8C ILE* 4.0 2.4 - - - +
9C PHE* 3.1 39.8 + - + +
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Residues in contact with GLY 470 (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* 3.2 20.3 + - - -
296A TYR 2.6 24.1 + - - -
298A HIS* 3.4 7.9 - - - -
468A GLY 3.5 1.4 + - - -
469A ILE* 1.3 79.9 - - - +
471A ASP* 1.3 60.8 + - - -
472A GLY 3.4 2.5 - - - -
6C SER* 3.3 7.9 - - - -
7C LYS 3.1 11.9 - - - -
9C PHE* 4.1 6.6 - - - +
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Residues in contact with ASP 471 (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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184A ASP* 4.1 16.9 + - - +
185A ASP* 4.6 0.5 - - - +
295A ARG* 3.7 9.1 + - - +
470A GLY* 1.3 70.8 - - - -
472A GLY* 1.3 59.3 + - - +
473A ASN 4.3 0.2 + - - -
5C LEU 4.6 1.9 - - - +
6C SER* 3.4 4.0 + - - -
7C LYS* 2.8 72.3 + - - +
9C PHE* 4.2 26.4 - - + +
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Residues in contact with GLY 472 (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* 3.6 3.7 - - - -
296A TYR* 3.2 26.8 + - - +
470A GLY 3.4 0.8 - - - -
471A ASP* 1.3 81.6 - - - +
473A ASN* 1.3 67.5 + - - +
4C VAL* 3.9 13.9 - - - -
6C SER* 3.0 19.7 + - - -
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Residues in contact with ASN 473 (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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284A GLY* 3.9 10.1 - - - +
293A THR* 4.2 12.1 - - + +
294A CYS 3.4 10.7 - - - +
295A ARG* 2.9 52.3 + - - +
471A ASP 4.3 0.6 + - - -
472A GLY* 1.3 73.0 - - - -
474A LEU* 1.3 59.9 + - - +
475A GLN* 3.7 18.9 + - - +
4C VAL* 3.4 19.7 - - - +
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Residues in contact with LEU 474 (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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282A THR* 3.7 31.4 - - + +
283A ALA 3.8 5.2 - - - +
292A ALA 4.1 0.2 - - - +
293A THR* 3.7 0.5 - - - -
294A CYS* 2.9 38.1 + - + +
296A TYR* 4.3 12.9 - - + +
453A LEU* 4.1 21.3 - - + -
473A ASN* 1.3 71.9 - - - +
475A GLN* 1.3 62.9 + - - +
476A TYR* 4.0 16.6 - - + +
495A LEU* 5.8 2.7 - - + +
503A GOL 3.4 34.1 - - - +
3C LYS* 3.7 14.8 - - + -
4C VAL* 3.6 17.5 - - + -
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Residues in contact with GLN 475 (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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282A THR* 3.1 8.5 - - - -
283A ALA 2.9 40.8 + - - +
284A GLY 3.1 26.3 + - - -
285A VAL 3.4 9.7 + - - -
286A VAL* 4.0 17.5 - - + +
290A PRO* 4.0 12.8 - - + -
292A ALA 3.4 2.9 - - - -
293A THR* 3.4 35.8 + - - +
473A ASN* 3.7 16.3 + - - +
474A LEU* 1.3 73.0 - - - +
476A TYR* 1.3 62.3 + - - +
477A TYR* 3.3 29.8 - - + +
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Residues in contact with TYR 476 (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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280A VAL* 5.0 2.2 - - + -
281A TYR 3.6 5.8 - - - -
282A THR* 3.6 20.8 - - + +
290A PRO* 3.3 7.4 - - - +
291A ILE* 2.8 47.6 + - + -
292A ALA* 2.9 13.7 + - + +
294A CYS* 3.7 29.6 - - + -
362A LEU* 4.0 17.5 - - + -
453A LEU* 3.8 9.2 - - - +
455A LEU* 3.5 10.2 - - - +
474A LEU* 4.0 20.4 - - + +
475A GLN* 1.3 77.9 - - - +
477A TYR* 1.3 57.9 + - - +
491A VAL* 4.0 11.4 - - + -
493A LEU* 2.7 44.7 + - + -
494A VAL* 4.1 5.2 - - - -
495A LEU* 4.5 4.5 + - + -
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Residues in contact with TYR 477 (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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280A VAL* 3.3 8.6 - - - +
281A TYR* 2.8 76.4 + + + +
283A ALA* 3.8 18.4 - - + -
285A VAL 2.8 10.0 + - - -
286A VAL* 3.4 2.6 - - - -
287A LEU* 2.7 52.2 + - + -
288A PRO 3.9 5.8 - - - -
290A PRO* 3.5 30.2 - - + +
291A ILE* 4.5 2.2 - - - -
475A GLN* 3.3 35.9 - - + +
476A TYR* 1.3 73.7 - - - +
478A LEU* 1.3 65.2 + - - +
504A GOL 3.4 9.0 - - - +
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Residues in contact with LEU 478 (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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235A ILE* 3.6 39.3 - - + -
242A MET* 4.3 13.5 - - + -
279A ALA 3.3 8.7 - - - +
280A VAL* 3.5 30.5 - - + -
281A TYR* 4.9 1.8 + - - -
291A ILE* 4.0 17.5 - - + +
362A LEU* 4.3 11.4 - - + -
477A TYR* 1.3 76.4 - - - +
479A TYR* 1.3 60.3 + - - +
480A ASN 4.0 1.6 + - - -
481A TRP* 3.9 30.2 - - + +
483A CYS* 4.1 4.3 - - - -
504A GOL 3.0 30.8 + - - -
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Residues in contact with TYR 479 (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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264A ILE* 6.2 1.1 - - + -
268A THR* 3.9 20.4 + - + +
272A ASN* 5.7 0.4 - - - -
277A PHE 4.4 1.3 - - - -
278A GLN* 3.2 6.4 - - - +
279A ALA* 2.8 41.1 + - + +
281A TYR* 4.3 10.9 - + + -
477A TYR 4.2 0.4 - - - -
478A LEU* 1.3 70.5 - - - +
480A ASN* 1.3 84.9 + - + +
481A TRP* 3.3 2.2 + - - +
1000C MYR 3.8 60.8 - - + -
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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