Contacts of the strand formed by residues 344 - 352 (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 THR 344 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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336A GLN 3.2 5.2 - - - -
337A THR* 3.5 21.1 - - + +
342A GLY 3.7 11.4 - - - +
343A SER* 1.3 81.1 - - - +
345A ARG* 1.3 70.1 + - - +
440B GLY* 3.5 26.7 - - - -
442B SER* 3.1 29.1 + - - -
443B GLY 2.9 20.1 + - - -
445B PRO* 3.4 7.3 - - + +
447B MET* 3.8 10.5 - - - -
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Residues in contact with ARG 345 (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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335A THR* 3.3 1.7 - - - -
336A GLN* 2.9 66.2 + - + +
338A THR* 3.1 23.8 + - - +
343A SER* 2.9 36.4 + - - -
344A THR* 1.3 79.0 + - - +
346A GLY* 1.3 59.4 + - - +
347A HIS* 4.5 1.1 - - + +
374A ASP* 3.3 50.7 + - - +
375A PHE* 4.0 17.2 - - + +
376A GLU* 3.4 15.1 + - - -
440B GLY 3.6 2.1 - - - +
441B CYS 3.3 11.2 - - - -
442B SER* 4.5 0.4 - - - +
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Residues in contact with GLY 346 (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* 5.3 1.8 - - - -
334A LEU 3.2 10.5 - - - -
335A THR* 4.1 11.4 - - - -
345A ARG* 1.3 77.0 - - - +
347A HIS* 1.3 73.1 + - - -
375A PHE* 4.7 0.2 - - - -
331B GLN* 5.3 0.4 - - - -
348B LYS* 3.1 23.2 + - - -
441B CYS* 2.8 18.6 + - - +
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Residues in contact with HIS 347 (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* 3.7 6.4 - - - +
334A LEU* 2.8 37.1 + - - +
345A ARG* 4.5 1.1 - - + +
346A GLY* 1.3 86.5 + - - -
348A LYS* 1.3 68.2 + - - +
369A THR* 4.8 3.1 - - + -
370A ASP 5.8 0.2 - - - +
371A THR* 3.8 29.0 + - + +
374A ASP* 2.8 34.9 + - + +
375A PHE* 3.5 33.7 - + + -
348B LYS* 4.2 9.3 + - - +
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Residues in contact with LYS 348 (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* 3.4 36.6 + - + +
332A GLY 3.4 10.3 - - - +
333A LEU* 3.5 10.6 - - + +
347A HIS* 1.3 74.4 - - - +
349A ALA* 1.3 64.1 + - - +
369A THR* 3.5 22.3 - - - -
370A ASP* 4.2 6.2 + - + +
333B LEU* 4.1 19.1 - - + -
346B GLY 3.4 23.0 + - - +
347B HIS* 4.4 9.7 - - - +
348B LYS* 4.8 13.2 - - + +
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Residues in contact with ALA 349 (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* 3.3 4.3 - - - +
332A GLY 2.8 35.1 + - - +
334A LEU* 3.8 30.7 - - + -
347A HIS 4.0 0.2 - - - +
348A LYS* 1.3 78.5 - - - +
350A THR* 1.3 63.4 + - - +
367A PHE* 4.5 4.9 - - + -
368A SER 3.2 11.7 - - - +
369A THR* 4.0 8.7 - - + -
383A PHE* 3.5 14.3 - - + -
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Residues in contact with THR 350 (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* 4.0 12.1 - - + -
330A ILE 3.3 13.9 - - - +
331A GLN* 3.2 26.2 + - - +
349A ALA* 1.3 73.8 + - - +
351A VAL* 1.3 64.1 + - - +
352A TYR* 3.6 29.1 - - + -
366A GLN 4.2 0.2 - - - +
367A PHE* 3.4 6.4 - - - -
368A SER* 2.9 39.5 + - - -
389A ILE* 3.8 23.0 - - + +
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Residues in contact with VAL 351 (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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286A PHE* 4.2 13.2 - - + -
328A GLY 3.6 2.3 - - - +
329A LYS* 3.4 1.6 - - - -
330A ILE* 2.9 58.9 + - + +
350A THR* 1.3 74.1 - - - +
352A TYR* 1.3 65.4 + - - +
353A THR* 3.7 3.1 + - + +
358A PHE* 3.9 32.8 - - + -
365A VAL* 4.8 4.3 - - + -
366A GLN 3.7 15.3 - - - +
367A PHE* 3.8 18.1 - - + -
383A PHE* 4.1 15.9 - - + -
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Residues in contact with TYR 352 (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 GLY 3.7 4.9 - - - -
329A LYS* 3.4 43.3 - - + +
350A THR* 3.6 27.6 - - + +
351A VAL* 1.3 75.7 - - - +
353A THR* 1.3 62.2 + - - +
354A GLY 3.1 4.5 - - - +
355A SER* 2.7 44.1 + - - +
358A PHE* 3.7 5.7 - - - +
366A GLN 4.6 3.4 + - - +
368A SER* 3.8 23.9 + - - -
389A ILE* 4.6 2.1 - - - +
391A ASP* 4.0 14.6 + - - -
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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