Contacts of the helix formed by residues 320 - 335 (chain A) in PDB entry 1Z10
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 HIS 320 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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316A LEU* 3.0 27.7 + - + +
317A LEU 3.1 9.6 - - - +
318A MET 3.2 0.2 - - - -
319A LYS* 1.3 105.8 + - + +
321A PRO* 1.3 56.9 - - - +
322A GLU* 3.0 25.2 + - - +
323A VAL* 2.9 37.2 + - + +
324A GLU 3.3 1.7 + - - -
411A PHE* 3.5 48.7 + + + +
473A VAL* 5.7 1.8 - - - +
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Residues in contact with PRO 321 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317A LEU 3.5 6.5 - - - +
318A MET 3.7 11.9 - - - +
319A LYS 3.4 9.2 - - - +
320A HIS* 1.3 88.5 - - - +
322A GLU* 1.3 65.1 - - - +
324A GLU* 3.2 15.1 + - + +
325A ALA* 2.9 29.3 + - - +
468A PRO* 4.0 19.3 - - + -
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Residues in contact with GLU 322 (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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319A LYS 4.6 0.2 - - - +
320A HIS* 3.1 38.0 + - - +
321A PRO* 1.3 87.1 - - - +
323A VAL* 1.3 65.2 - - + +
325A ALA* 3.6 8.3 + - - +
326A LYS* 3.2 33.9 + - - +
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Residues in contact with VAL 323 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317A LEU* 3.9 17.7 - - + -
320A HIS* 2.9 30.7 + - + +
322A GLU* 1.3 82.6 - - + +
324A GLU* 1.3 67.0 + - - +
326A LYS* 3.2 4.1 + - - +
327A VAL* 3.0 21.2 + - + +
351A TYR* 3.6 23.3 - - - +
355A VAL* 3.8 22.0 - - + -
411A PHE* 4.4 6.7 - - + +
413A PRO* 4.0 20.9 - - + -
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Residues in contact with GLU 324 (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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317A LEU* 4.2 24.8 - - + +
318A MET* 5.8 1.0 - - - -
320A HIS 3.3 2.4 + - - -
321A PRO* 3.2 19.8 + - - +
323A VAL* 1.3 80.7 - - - +
325A ALA* 1.3 62.9 + - - +
327A VAL* 3.2 10.3 + - + +
328A HIS* 2.9 42.2 + - + +
457A MET* 4.9 9.5 - - - +
460A PHE 4.6 0.2 - - - +
461A ARG* 3.4 13.0 - - - +
462A LEU* 2.9 49.9 + - + +
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Residues in contact with ALA 325 (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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321A PRO 2.9 16.5 + - - +
322A GLU* 3.7 9.4 - - - +
323A VAL 3.2 0.2 - - - -
324A GLU* 1.3 77.5 - - - +
326A LYS* 1.3 62.5 + - + +
328A HIS* 3.2 11.6 + - - +
329A GLU* 3.0 22.2 + - - +
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Residues in contact with LYS 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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322A GLU* 3.2 18.5 + - - +
323A VAL* 3.2 4.1 + - - +
324A GLU 3.2 0.4 - - - -
325A ALA* 1.3 79.7 - - + +
327A VAL* 1.3 63.7 + - - +
329A GLU* 3.4 9.3 + - - +
330A GLU* 3.2 22.7 + - - +
351A TYR* 3.3 45.5 + - + +
414A GLN* 4.2 16.6 + - - -
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Residues in contact with VAL 327 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317A LEU* 4.8 4.7 - - + -
323A VAL* 3.0 20.9 + - + +
324A GLU* 3.2 12.3 + - + +
326A LYS* 1.3 76.0 - - - +
328A HIS* 1.3 60.1 + - + +
330A GLU* 3.2 6.4 + - - +
331A ILE* 2.9 44.6 + - + +
351A TYR* 4.0 17.5 - - + -
352A MET* 3.5 35.4 - - + +
355A VAL* 4.0 21.3 - - + -
457A MET* 4.1 15.9 - - + -
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Residues in contact with HIS 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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324A GLU* 2.9 50.2 + - + +
325A ALA* 3.5 11.8 - - - +
327A VAL* 1.3 77.7 - - + +
329A GLU* 1.3 56.3 + - - +
331A ILE* 3.2 5.0 + - + -
332A ASP* 2.8 37.8 + - - +
457A MET* 3.0 38.9 + - + +
460A PHE 3.3 12.3 + - - -
461A ARG* 3.9 9.9 - - + -
494A ARG* 3.3 35.6 + - - +
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Residues in contact with GLU 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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325A ALA 3.0 13.2 + - - +
326A LYS* 3.7 11.2 - - - +
327A VAL 3.3 0.2 - - - -
328A HIS* 1.3 74.0 - - - +
330A GLU* 1.3 64.5 + - - +
332A ASP* 3.4 5.8 + - - +
333A ARG* 3.0 69.7 + - - +
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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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326A LYS 3.2 9.8 + - - +
327A VAL* 3.6 8.7 - - - +
329A GLU* 1.3 83.4 + - - +
331A ILE* 1.3 66.8 + - - +
333A ARG* 3.4 19.5 + - - +
334A VAL* 2.9 30.1 + - + +
348A LYS 4.3 0.4 - - - +
349A MET* 3.1 32.6 - - + +
350A PRO* 3.2 13.5 - - - +
351A TYR* 2.9 31.1 + - + +
352A MET* 2.8 29.5 + - - +
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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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327A VAL* 2.9 31.9 + - + +
328A HIS* 3.8 6.3 - - - +
330A GLU* 1.3 76.2 - - - +
332A ASP* 1.3 63.0 + - - +
335A ILE* 2.8 41.0 + - + +
336A GLY 2.9 7.5 + - - +
349A MET* 3.7 24.0 - - + -
352A MET* 4.0 4.9 - - + -
454A THR* 3.7 15.3 - - + +
457A MET* 3.6 33.2 - - + +
458A GLN* 3.7 33.2 - - + +
494A ARG* 5.3 0.4 - - - +
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Residues in contact with ASP 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 HIS 2.8 24.0 + - - +
329A GLU* 4.0 5.3 - - - +
331A ILE* 1.3 76.2 - - - +
333A ARG* 1.3 63.3 + - - +
336A GLY* 3.2 23.8 + - - +
337A LYS* 3.5 38.2 + - - +
458A GLN* 5.7 0.5 - - - +
494A ARG* 2.9 40.3 + - - -
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Residues in contact with ARG 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 GLU* 3.0 51.6 + - - +
330A GLU* 3.9 21.2 + - - +
332A ASP* 1.3 79.7 - - - +
334A VAL* 1.3 80.2 + - + +
335A ILE 5.0 0.3 - - - -
336A GLY 4.7 0.3 + - - -
348A LYS 4.8 3.4 + - - -
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Residues in contact with VAL 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 20.2 + - + +
333A ARG* 1.3 95.6 - - + +
335A ILE* 1.3 69.3 + - + +
339A ARG* 3.6 9.2 + - - -
345A ASP* 4.4 9.9 - - - +
348A LYS* 3.3 49.4 - - + +
349A MET* 3.9 19.1 - - + -
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Residues in contact with ILE 335 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331A ILE* 2.8 21.0 + - + +
333A ARG 5.0 0.2 - - - -
334A VAL* 1.3 77.6 - - + +
336A GLY* 1.3 58.5 + - - +
338A ASN 4.9 0.3 + - - -
339A ARG* 3.7 41.6 + - - +
341A PRO* 3.7 11.4 - - + -
345A ASP* 3.7 29.6 - - + +
349A MET* 3.7 23.1 - - + -
454A THR* 3.6 30.1 - - + -
458A GLN* 3.5 24.7 - - - +
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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