Contacts of the helix formed by residues 326 - 342 (chain A) in PDB entry 4Z30
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 SER 326 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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156A ARG* 6.2 0.9 - - - -
160A GLU* 5.0 0.4 - - - -
324A PRO 3.5 4.0 + - - -
325A GLU* 1.3 74.1 - - - +
327A PHE* 1.3 59.0 + - - +
328A ALA* 4.0 10.5 - - - +
329A LYS* 3.0 27.3 + - - +
330A SER* 2.8 30.5 + - - -
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Residues in contact with PHE 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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156A ARG* 3.2 60.8 - - + +
159A GLY* 3.4 13.7 - - - -
160A GLU* 3.3 48.0 + - + -
163A VAL* 4.0 15.3 - - + -
325A GLU 3.6 0.8 + - - -
326A SER* 1.3 69.4 - - - +
328A ALA* 1.3 63.9 + - - +
330A SER* 3.1 9.7 + - - -
331A VAL* 3.1 25.8 + - + +
354A LEU* 3.9 24.0 - - + -
357A LEU* 3.9 8.1 - - + -
358A ALA* 3.6 25.1 - - + -
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Residues in contact with ALA 328 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156A ARG* 5.4 0.8 - - - +
326A SER* 3.2 9.6 - - - +
327A PHE* 1.3 79.4 - - - +
329A LYS* 1.3 62.7 + - - +
331A VAL* 3.0 18.7 + - - +
332A GLN* 3.2 11.7 + - - +
355A GLU* 5.2 7.7 - - - +
358A ALA* 4.4 12.1 - - + +
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Residues in contact with LYS 329 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325A GLU* 4.0 13.4 - - + +
326A SER* 3.0 25.0 + - - +
328A ALA* 1.3 75.1 - - - +
330A SER* 1.3 56.9 + - - +
332A GLN* 3.3 10.0 + - + +
333A GLU* 2.9 26.9 + - - +
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Residues in contact with SER 330 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160A GLU* 5.1 5.5 + - - +
163A VAL* 3.5 21.9 - - - +
164A THR* 5.4 4.8 + - - -
167A ILE* 3.5 11.7 - - - +
325A GLU* 3.4 28.6 + - - +
326A SER 2.8 16.7 + - - -
327A PHE* 3.1 10.7 + - - -
329A LYS* 1.3 76.9 - - - +
331A VAL* 1.3 58.8 + - - +
333A GLU* 3.2 6.7 + - - +
334A LEU 3.0 22.3 + - - -
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Residues in contact with VAL 331 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163A VAL* 4.0 19.1 - - + -
327A PHE* 3.1 33.6 + - + +
328A ALA* 3.0 10.8 + - - +
330A SER* 1.3 73.8 - - - +
332A GLN* 1.3 61.1 - - - +
334A LEU* 3.4 5.9 + - + +
335A THR* 2.8 33.5 + - - +
351A ARG* 3.9 23.1 - - + +
354A LEU* 4.1 18.2 - - + -
355A GLU* 3.4 28.3 - - - +
358A ALA* 5.5 0.4 - - + -
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Residues in contact with GLN 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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328A ALA 3.2 8.7 + - - +
329A LYS* 3.4 13.0 - - - +
331A VAL* 1.3 77.8 - - - +
333A GLU* 1.3 65.7 + - - +
335A THR* 3.3 13.0 + - - +
336A ILE* 3.2 42.5 + - + +
339A GLN* 6.0 1.0 - - - +
351A ARG* 3.6 20.3 + - - -
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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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167A ILE* 4.1 28.6 - - + +
294A ARG* 4.8 12.4 - - - +
325A GLU* 3.0 32.6 - - - +
329A LYS 2.9 14.3 + - - +
330A SER 3.2 9.8 + - - +
332A GLN* 1.3 74.3 - - - +
334A LEU* 1.3 62.2 + - - +
336A ILE* 3.0 21.8 + - + +
337A VAL* 3.2 18.7 + - + +
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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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163A VAL* 4.6 9.9 - - + -
166A LEU* 4.1 40.6 - - + -
167A ILE* 4.0 27.3 - - + +
170A HIS* 4.5 11.2 - - + +
330A SER 3.0 13.2 + - - +
331A VAL* 3.7 9.2 - - + +
332A GLN 3.3 0.2 - - - -
333A GLU* 1.3 72.9 - - - +
335A THR* 1.3 67.0 + - - +
337A VAL* 3.4 6.7 + - + +
338A LEU* 2.9 46.3 + - + +
347A LEU* 5.3 5.2 - - + +
354A LEU* 4.8 15.0 - - + -
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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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331A VAL* 2.8 22.6 + - - +
332A GLN* 3.3 21.5 - - - +
333A GLU 3.2 0.2 - - - -
334A LEU* 1.3 76.6 - - - +
336A ILE* 1.3 57.2 + - + +
338A LEU* 3.2 10.3 + - - +
339A GLN* 2.8 51.4 + - + +
348A ASN* 4.9 6.5 + - - +
351A ARG* 3.3 35.8 + - - +
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Residues in contact with ILE 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 GLN* 3.5 36.1 - - + +
333A GLU* 3.0 11.6 + - + +
335A THR* 1.3 75.0 - - + +
337A VAL* 1.3 68.7 + - + +
339A GLN* 3.0 22.0 + - - +
340A ARG* 2.8 64.2 + - + +
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Residues in contact with VAL 337 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167A ILE* 5.6 11.7 - - + +
170A HIS* 3.6 46.4 - - + +
333A GLU* 3.2 14.7 + - + +
334A LEU* 3.6 14.6 - - + +
336A ILE* 1.3 78.2 - - + +
338A LEU* 1.3 54.1 + - - +
340A ARG* 2.9 15.8 + - - +
341A THR* 2.8 38.9 + - + +
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Residues in contact with LEU 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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170A HIS* 4.5 13.7 - - + +
334A LEU* 2.9 40.3 + - + +
335A THR* 3.5 8.1 - - - +
337A VAL* 1.3 74.2 - - + +
339A GLN* 1.3 59.7 + - - +
341A THR* 3.3 10.2 + - - +
342A GLY* 2.8 27.4 + - - -
343A ASP* 3.2 36.4 + - + +
347A LEU* 3.8 35.2 - - + -
348A ASN* 3.9 22.4 - - + +
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Residues in contact with GLN 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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332A GLN* 6.0 1.2 - - - +
335A THR* 2.8 38.7 + - + +
336A ILE* 3.0 23.5 + - - +
338A LEU* 1.3 72.7 - - - +
340A ARG* 1.3 65.1 + - + +
342A GLY* 3.4 8.5 + - - -
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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 ILE* 2.8 47.7 + - + +
337A VAL* 3.4 11.7 - - - +
339A GLN* 1.3 76.2 - - + +
341A THR* 1.3 62.1 + - + +
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Residues in contact with THR 341 (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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170A HIS* 4.2 25.0 + - + -
337A VAL* 2.8 25.5 + - + +
338A LEU* 3.3 13.5 + - - +
340A ARG* 1.3 74.2 - - + +
342A GLY* 1.3 58.3 + - - +
343A ASP* 3.0 20.1 + - - -
344A PRO* 4.2 11.7 - - - +
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Residues in contact with GLY 342 (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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338A LEU 2.8 9.7 + - - -
339A GLN* 3.4 6.3 + - - -
340A ARG 3.4 3.0 + - - -
341A THR* 1.3 77.6 - - - +
343A ASP* 1.3 69.9 + - - +
344A PRO* 3.5 2.7 - - - +
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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