Contacts of the strand formed by residues 329 - 337 (chain A) in PDB entry 4X7C
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 LYS 329 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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328A GLY* 1.3 72.8 - - - +
330A ILE* 1.3 62.9 + - - +
350A THR* 4.0 9.6 - - + -
351A VAL 3.4 3.8 - - - -
352A TYR* 3.4 36.1 - - + -
388A VAL* 3.2 5.8 - - - +
389A ILE* 2.9 54.7 + - + +
391A ASP* 2.9 38.4 + - - +
392A GLY* 4.8 1.4 - - - -
393A SER* 5.1 1.0 + - - +
394A THR* 4.1 6.5 - - - +
399A GLU* 2.4 44.2 + - - +
400A PRO* 5.0 2.2 - - - +
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Residues in contact with ILE 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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242A PHE* 4.1 5.8 - - + -
284A CYS* 4.3 7.4 - - + +
324A PRO* 3.6 38.6 - - + -
326A PHE* 3.9 28.5 - - + -
328A GLY 4.8 0.4 - - - +
329A LYS* 1.3 76.0 - - - +
331A GLN* 1.3 62.3 + - - +
350A THR* 3.3 3.3 - - - -
351A VAL* 2.9 39.8 + - + +
353A THR* 4.0 12.3 - - + -
383A PHE* 3.6 24.7 - - + -
385A PRO* 3.9 17.3 - - + -
387A GLY 3.4 10.3 - - - +
388A VAL* 4.3 4.5 - - + -
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Residues in contact with GLN 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 LYS 3.9 1.4 + - - -
330A ILE* 1.3 73.2 - - - +
332A GLY* 1.3 62.7 + - - +
348A LYS* 3.4 41.7 + - + +
349A ALA 3.3 11.7 - - - +
350A THR* 3.2 19.4 + - + +
383A PHE* 3.9 2.5 - - - -
385A PRO* 3.8 1.0 - - - +
386A VAL* 2.8 23.7 + - - +
387A GLY 2.8 18.7 + - - +
389A ILE* 3.9 27.7 - - + +
441A CYS* 3.4 30.8 + - - +
442A SER* 5.5 2.2 - - - -
333B LEU* 4.1 6.7 - - + +
346B GLY 5.0 1.9 - - - +
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Residues in contact with GLY 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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331A GLN* 1.3 76.8 - - - +
333A LEU* 1.3 65.1 + - - +
348A LYS* 3.4 9.4 - - - +
349A ALA 2.8 30.6 + - - -
383A PHE* 3.6 8.8 - - - -
384A THR 3.1 15.5 - - - -
386A VAL* 3.9 11.0 - - - -
333B LEU* 4.7 2.5 - - - -
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Residues in contact with LEU 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 GLY* 1.3 77.8 - - - +
334A LEU* 1.3 59.9 + - - +
335A THR* 3.9 6.6 + - + +
346A GLY 5.9 0.7 - - - -
347A HIS* 3.5 4.9 - - - +
348A LYS* 3.5 29.8 - - - +
382A LYS 3.5 2.3 - - - +
383A PHE* 3.5 3.3 - - - -
384A THR* 2.9 32.4 + - - -
386A VAL* 4.8 0.8 - - - +
331B GLN* 4.6 8.5 - - + +
332B GLY* 4.1 19.5 - - - +
333B LEU* 3.9 21.3 - - + -
348B LYS* 3.9 18.6 - - + -
386B VAL* 3.8 41.1 - - + -
441B CYS* 4.7 6.7 - - + -
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Residues in contact with LEU 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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290A VAL* 5.1 2.9 - - + -
299A TYR* 5.0 8.3 - - + -
301A MET* 3.7 30.3 - - + -
332A GLY 4.2 0.2 - - - -
333A LEU* 1.3 72.5 - - - +
335A THR* 1.3 59.9 + - - +
346A GLY* 3.2 2.8 - - - -
347A HIS 2.8 36.7 + - - +
349A ALA* 3.8 18.6 - - + +
367A PHE* 4.1 24.9 - - + -
369A THR* 4.3 6.5 - - + -
375A PHE* 3.4 27.6 - - + -
381A THR* 4.0 12.6 - - + -
382A LYS 3.2 13.5 - - - +
383A PHE* 3.9 14.8 - - + -
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Residues in contact with THR 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 LEU* 4.3 7.6 - - + +
334A LEU* 1.3 80.1 - - - +
336A GLN* 1.3 63.0 + - - +
345A ARG 3.3 4.3 - - - -
346A GLY* 4.1 7.2 - - - -
375A PHE* 4.4 0.2 - - - -
380A ASN 4.1 0.2 - - - +
381A THR* 3.2 5.2 - - - +
382A LYS* 2.7 50.1 + - - +
384A THR* 5.1 0.7 + - - -
386B VAL* 4.0 19.7 - - + +
439B PRO* 3.7 18.6 - - + +
440B GLY 3.7 11.4 - - - -
441B CYS* 3.8 27.1 - - - -
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Residues in contact with GLN 336 (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 VAL* 3.7 8.9 - - - +
335A THR* 1.3 78.1 - - - +
337A THR* 1.3 65.3 + - - +
344A THR* 3.2 6.6 - - - -
345A ARG* 2.9 57.7 + - + +
375A PHE* 3.7 18.7 - - + -
376A GLU* 2.7 48.4 + - - +
379A GLN* 3.9 16.5 + - + -
380A ASN 3.3 14.1 - - - +
381A THR* 2.9 21.4 + - - +
440B GLY 4.0 1.9 + - - +
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Residues in contact with THR 337 (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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336A GLN* 1.3 80.7 - - - +
338A THR* 1.3 74.8 + - - +
339A LYS* 3.6 3.3 + - - +
342A GLY* 4.1 6.1 - - - -
343A SER 3.3 8.7 - - - +
344A THR* 3.5 18.8 - - + +
379A GLN* 3.5 19.6 - - - +
380A ASN* 3.2 18.1 + - - +
439B PRO* 5.5 1.0 - - - +
440B GLY 4.5 4.3 + - - -
447B MET* 3.8 25.1 - - + -
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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