Contacts of the strand formed by residues 325 - 335 (chain A) in PDB entry 4X8P
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 325 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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324A LYS* 1.3 77.5 - - - +
326A ALA* 1.3 59.6 + - - -
327A TRP* 3.6 9.3 - - - -
396A ILE 3.8 0.9 - - - +
397A ASN* 3.5 7.8 - - - -
398A LEU* 2.8 36.2 + - - +
399A PRO* 5.1 0.9 - - - +
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Residues in contact with ALA 326 (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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325A GLY* 1.3 70.3 - - - -
327A TRP* 1.3 68.7 + - - +
395A TYR* 3.8 14.1 - - + +
396A ILE 3.2 6.1 - - - +
397A ASN* 3.6 13.4 + - - +
496A THR* 3.3 28.3 - - - +
497A TYR* 3.6 4.6 - - - -
498A ARG* 2.9 26.0 + - - +
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Residues in contact with TRP 327 (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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322A VAL* 3.5 29.4 - - + +
324A LYS 2.7 29.6 + - - -
325A GLY* 3.6 11.8 - - - -
326A ALA* 1.3 78.6 - - - +
328A TYR* 1.3 62.0 + - - +
346A TRP* 4.0 3.2 - - + -
394A PHE 3.6 0.7 - - - +
395A TYR* 3.4 7.6 - - - -
396A ILE* 2.9 42.5 + - + +
398A LEU* 5.7 0.4 - - + -
497A TYR* 4.3 2.7 - - - -
498A ARG* 3.4 60.6 - - + -
499A PRO 3.3 28.9 - - - -
500A MET* 3.9 19.3 - - - -
502A ASP* 3.7 7.9 - - + -
503A MET* 3.6 29.4 - - + -
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Residues in contact with TYR 328 (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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327A TRP* 1.3 75.0 - - - +
329A PHE* 1.4 81.6 + - - +
330A GLU* 4.0 17.9 + - + +
393A GLY* 3.1 22.5 - - - -
394A PHE 3.2 28.9 - - - -
395A TYR* 3.9 13.7 - + + -
450A TYR* 3.7 23.9 - + - +
453A GLY* 5.7 0.5 - - - -
488A PHE* 3.4 29.0 - + + -
490A TYR* 4.1 6.2 + - - +
492A PRO* 3.4 41.3 - - + +
497A TYR* 3.5 25.8 - + + -
498A ARG 3.1 6.2 + - - +
500A MET* 2.9 26.4 + - - +
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Residues in contact with PHE 329 (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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328A TYR* 1.4 77.6 - - - +
330A GLU* 1.3 65.5 + - - +
331A ILE* 3.4 26.5 - - + -
345A GLY 3.3 22.2 - - - -
346A TRP* 3.4 35.7 - + - -
393A GLY* 3.8 1.6 - - - -
394A PHE* 2.9 60.3 + + + -
470A PRO* 3.5 23.1 - - + -
471A ALA 4.3 0.4 - - - -
482A ILE* 3.6 22.9 - - + -
483A ASN 3.5 11.9 - - - +
484A PHE* 4.1 8.7 - - + -
488A PHE* 3.8 5.6 - - - -
500A MET* 4.0 9.2 - - + -
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Residues in contact with GLU 330 (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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328A TYR* 4.0 11.5 + - + -
329A PHE* 1.3 74.6 - - - +
331A ILE* 1.3 67.6 + - - +
332A THR* 5.5 1.1 - - - +
391A VAL* 3.7 19.2 - - + +
392A LEU 3.2 10.8 - - - +
393A GLY* 4.5 2.7 - - - -
482A ILE* 3.5 2.1 - - - +
483A ASN* 2.8 53.0 + - + +
488A PHE* 3.4 20.7 - - + +
489A LYS* 2.8 28.9 + - - +
490A TYR* 2.9 38.5 + - - +
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Residues in contact with ILE 331 (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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329A PHE* 3.4 24.2 - - + -
330A GLU* 1.3 78.0 - - - +
332A THR* 1.3 65.8 + - - +
333A VAL 4.8 0.4 - - - +
344A LEU* 3.8 28.0 - - + -
390A ASP 3.8 1.0 - - - +
391A VAL* 3.5 1.9 - - - -
392A LEU* 2.8 42.6 + - + +
394A PHE* 3.7 18.1 - - + -
471A ALA 4.5 2.0 - - - +
472A ILE* 3.7 25.1 - - + -
480A VAL* 3.8 28.3 - - + -
481A SER 3.2 7.9 - - - +
482A ILE* 3.9 18.2 - - + -
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Residues in contact with THR 332 (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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330A GLU* 4.4 1.8 - - - +
331A ILE* 1.3 74.3 - - - +
333A VAL* 1.4 65.8 - - - +
334A ASP* 3.3 23.6 + - - +
389A GLY* 5.1 4.9 - - - +
390A ASP 3.7 4.9 - - - +
391A VAL* 3.6 25.0 - - + +
480A VAL* 3.3 2.6 - - - -
481A SER* 2.7 44.9 + - - -
483A ASN* 6.0 0.9 - - - +
489A LYS* 3.5 26.8 + - - +
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Residues in contact with VAL 333 (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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332A THR* 1.4 70.4 - - - +
334A ASP* 1.3 59.9 + - - +
335A GLU 4.2 6.5 - - - +
336A MET* 3.7 29.8 - - + -
344A LEU* 4.9 2.7 - - + -
386A TYR* 4.1 14.1 - - + -
387A GLY 3.3 32.3 - - - +
388A GLN* 3.7 6.1 - - - +
389A GLY* 2.8 32.2 + - - -
390A ASP 3.1 7.0 + - - +
392A LEU* 3.7 26.9 - - + -
479A THR 3.9 4.9 - - - +
480A VAL* 4.2 12.3 - - + -
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Residues in contact with ASP 334 (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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306A THR* 4.2 1.4 - - - +
332A THR* 3.5 25.3 - - - +
333A VAL* 1.3 73.4 - - - +
335A GLU* 1.3 62.6 + - + +
388A GLN* 3.8 13.9 + - - +
389A GLY 5.0 0.2 + - - -
479A THR* 3.0 24.5 + - + +
480A VAL 3.5 4.2 - - - -
481A SER* 2.6 36.7 + - - -
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Residues in contact with GLU 335 (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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333A VAL* 3.4 3.1 - - - +
334A ASP* 1.3 80.8 - - + +
336A MET* 1.3 63.1 + - - +
337A PRO* 3.7 23.0 - - + +
388A GLN* 3.5 17.0 + - - +
477A SER 4.9 2.4 - - - +
478A CYS* 3.4 5.4 - - - +
479A THR* 2.8 49.0 + - - +
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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