Contacts of the helix formed by residues 330 - 340 (chain A) in PDB entry 2ZJ4
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 GLU 330 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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326A LYS* 2.9 22.9 + - + +
327A GLU* 3.5 15.8 + - - +
328A ILE 3.2 0.8 - - - -
329A PHE* 1.3 76.0 - - - +
331A GLN* 1.3 56.2 + - - +
332A PRO* 3.4 3.1 - - - -
333A GLU* 3.0 27.8 + - + +
334A SER* 2.9 34.4 + - - +
337A ASN* 5.3 4.5 - - - +
465A ALA 4.0 6.1 - - - +
466A GLY* 5.4 1.0 - - - -
475A LYS* 2.9 37.9 + - + +
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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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327A GLU 3.6 9.6 - - - +
328A ILE* 2.8 30.4 + - - +
329A PHE 3.3 1.2 - - - -
330A GLU* 1.3 73.3 - - - +
332A PRO* 1.4 69.5 - - + +
334A SER* 3.2 6.3 - - - +
335A VAL* 3.1 28.4 + - - +
474A THR 3.6 3.6 - - - +
475A LYS* 3.9 15.0 - - + -
478A THR* 2.9 32.9 + - - +
516A ILE* 4.0 17.6 - - + +
650A ILE* 4.0 13.0 - - - +
653A GLN* 2.9 41.3 + - - +
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Residues in contact with PRO 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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329A PHE 3.5 11.4 - - - +
330A GLU 3.4 4.3 - - - -
331A GLN* 1.4 90.2 - - + +
333A GLU* 1.3 63.4 + - + +
335A VAL* 4.1 0.9 - - - +
336A VAL* 3.4 25.5 + - - +
513A PRO* 3.8 28.8 - - + +
516A ILE* 3.6 21.9 - - + -
517A LYS* 3.6 36.3 - - + -
520A LEU* 3.9 9.9 - - + -
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Residues in contact with GLU 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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329A PHE 5.3 2.3 - - - +
330A GLU* 3.0 26.4 + - + +
332A PRO* 1.3 79.1 - - + +
334A SER* 1.3 59.4 + - - +
335A VAL 3.3 0.4 - - - -
336A VAL* 3.3 7.4 + - - +
337A ASN* 2.8 39.2 + - - +
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Residues in contact with SER 334 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330A GLU* 2.9 16.7 + - - +
331A GLN* 3.2 24.4 + - - +
333A GLU* 1.3 70.1 - - - +
335A VAL* 1.3 61.1 + - - +
337A ASN* 3.3 9.5 + - - +
338A THR* 2.9 32.7 + - - -
464A ASN 4.5 0.7 - - - +
465A ALA* 4.1 18.8 - - - +
475A LYS* 3.6 27.7 + - - +
478A THR* 4.7 0.5 + - - -
479A SER* 3.6 11.5 + - - -
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Residues in contact with VAL 335 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331A GLN* 3.1 22.6 + - + +
332A PRO 4.1 2.5 - - - +
334A SER* 1.3 78.1 + - - +
336A VAL* 1.3 63.2 + - - +
338A THR* 3.2 8.2 + - - -
339A MET* 3.2 43.3 + - + +
478A THR* 4.6 21.3 - - - +
479A SER* 4.7 1.6 - - - +
482A VAL* 4.4 20.4 - - + -
512A LEU* 4.3 20.2 - - + -
513A PRO* 4.4 12.6 - - + -
516A ILE* 3.8 16.8 - - + -
646A ILE* 4.9 0.9 - - + -
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Residues in contact with VAL 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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332A PRO 3.4 15.3 + - - +
333A GLU* 3.3 11.0 + - - +
335A VAL* 1.3 76.3 - - - +
337A ASN* 1.3 63.4 + - - +
339A MET* 3.2 11.9 + - + +
340A ARG* 3.0 48.3 + - + +
513A PRO* 3.7 22.9 - - + -
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Residues in contact with ASN 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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330A GLU* 5.3 4.3 - - - +
333A GLU* 2.8 30.8 + - - +
334A SER* 3.3 6.9 + - - +
336A VAL* 1.3 74.2 - - - +
338A THR* 1.3 61.2 + - - +
340A ARG* 2.9 50.1 + - - +
342A ARG* 4.8 0.7 + - - -
464A ASN* 3.0 46.2 + - - +
465A ALA* 5.3 3.0 - - - +
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Residues in contact with THR 338 (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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334A SER 2.9 15.4 + - - -
335A VAL* 3.2 8.7 + - - -
337A ASN* 1.3 74.0 - - - +
339A MET* 1.3 56.8 + - - +
342A ARG* 3.0 31.0 + - - +
463A ILE 2.7 21.8 + - - +
464A ASN 4.4 1.0 + - - -
479A SER* 2.6 36.2 + - - +
482A VAL* 3.9 11.9 - - + -
483A SER* 3.4 25.8 - - - +
486A MET* 3.4 12.9 - - + +
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Residues in contact with MET 339 (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 VAL* 3.2 32.7 + - + +
336A VAL* 3.2 9.2 + - + +
338A THR* 1.3 75.0 - - - +
340A ARG* 1.3 62.3 + - - +
341A GLY 3.6 0.3 + - - -
342A ARG* 3.1 2.6 + - - -
343A VAL* 3.1 37.3 + - + +
345A PHE* 4.1 19.5 - - + -
482A VAL* 3.8 18.4 - - + -
486A MET* 4.1 13.7 - - - -
509A LEU* 3.4 59.0 - - + +
510A LYS* 5.2 0.2 - - - -
513A PRO* 4.8 4.9 - - + -
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Residues in contact with ARG 340 (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 VAL* 3.0 35.3 + - + +
337A ASN* 2.9 43.0 - - - +
338A THR 3.4 2.0 - - - -
339A MET* 1.3 76.7 - - - +
341A GLY* 1.3 65.7 + - - +
342A ARG* 3.3 13.2 + - - +
464A ASN* 5.3 5.4 - - - +
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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