Contacts of the helix formed by residues 317 - 328 (chain A) in PDB entry 4ZSL
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 ASP 317 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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156A LEU* 3.6 37.9 - - + +
160A ARG* 5.1 3.0 + - - -
256A LEU* 5.8 0.8 - - - +
315A GLY 3.9 0.4 + - - -
316A ALA* 1.3 72.8 - - - +
318A ARG* 1.3 59.8 + - - +
319A GLN* 3.3 9.6 + - - +
320A ALA* 2.8 36.0 + - + +
321A LEU* 3.0 28.1 + - - +
346A PHE* 3.5 13.5 - - - -
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Residues in contact with ARG 318 (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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316A ALA 3.3 5.0 + - - +
317A ASP* 1.3 70.4 + - - +
319A GLN* 1.3 69.3 + - + +
321A LEU* 3.4 6.8 + - - +
322A SER* 2.9 29.7 + - - -
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Residues in contact with GLN 319 (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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160A ARG* 5.9 0.4 - - - +
317A ASP* 3.3 11.3 + - - +
318A ARG* 1.3 80.7 - - + +
320A ALA* 1.4 64.7 + - - +
322A SER* 3.4 7.3 + - - -
323A LEU 3.2 17.2 + - - -
344A HIS* 3.3 26.3 + - - -
345A PRO* 3.7 28.5 - - + +
346A PHE* 3.8 23.8 - - + +
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Residues in contact with ALA 320 (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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252A PHE* 3.3 27.2 - - + -
256A LEU* 4.4 16.4 - - + -
317A ASP* 2.8 32.1 + - + +
318A ARG 3.3 0.2 - - - -
319A GLN* 1.4 72.8 - - - +
321A LEU* 1.3 57.1 + - + +
323A LEU 3.3 2.3 + - - -
324A LEU* 2.9 25.3 + - - +
346A PHE* 3.6 23.7 - - + -
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Residues in contact with LEU 321 (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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256A LEU* 4.3 7.6 - - + -
309A TRP* 3.6 37.4 - - + +
310A GLU* 3.8 23.1 - - + +
313A TYR* 3.9 29.4 - - + +
316A ALA* 3.9 33.4 - - + +
317A ASP 3.0 17.2 + - - +
318A ARG* 3.9 6.3 - - - +
320A ALA* 1.3 72.6 - - - +
322A SER* 1.3 59.4 + - - +
324A LEU* 3.5 15.1 - - + +
325A GLY* 3.0 26.5 + - - -
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Residues in contact with SER 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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318A ARG* 2.9 18.8 + - - -
319A GLN* 3.5 13.9 + - - -
320A ALA 3.3 0.2 - - - -
321A LEU* 1.3 77.5 - - - +
323A LEU* 1.4 60.8 + - - +
325A GLY* 3.4 8.0 + - - -
326A ARG* 3.4 18.2 + - - +
344A HIS* 3.1 18.1 + - - -
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Residues in contact with LEU 323 (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 LEU* 3.8 28.7 - - + -
252A PHE* 3.9 3.1 - - + -
319A GLN 3.2 10.5 + - - +
320A ALA 3.7 6.3 - - - +
322A SER* 1.4 73.8 - - - +
324A LEU* 1.4 66.9 + - - +
326A ARG* 3.1 18.5 + - + +
327A MET* 3.4 29.5 + - + +
336A ILE* 4.0 14.1 - - + -
341A ALA* 4.0 25.6 - - + +
344A HIS* 3.5 35.4 + - + -
346A PHE* 4.1 11.9 - - + -
347A LEU* 4.3 6.1 - - + -
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Residues in contact with LEU 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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249A GLY* 3.3 29.4 - - - +
252A PHE* 3.6 22.5 - - + -
253A GLY* 4.0 7.2 - - - +
256A LEU* 4.6 5.6 - - + -
309A TRP* 3.6 21.5 - - + -
313A TYR* 3.6 34.1 - - + -
320A ALA 2.9 17.0 + - - +
321A LEU* 3.5 15.7 - - + +
323A LEU* 1.4 74.4 - - - +
325A GLY* 1.3 62.3 + - - +
327A MET* 3.1 16.0 + - - +
328A LEU* 3.2 26.7 + - + +
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Residues in contact with GLY 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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309A TRP* 3.7 24.5 + - - -
321A LEU 3.0 14.2 + - - -
322A SER 3.4 4.9 + - - -
323A LEU 3.3 0.4 - - - -
324A LEU* 1.3 75.6 - - - +
326A ARG* 1.4 58.6 + - - +
327A MET 3.3 0.6 + - - -
328A LEU 4.0 5.6 - - - +
329A ARG* 3.3 27.8 + - - +
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Residues in contact with ARG 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 SER* 3.4 17.9 - - - +
323A LEU* 3.1 14.2 + - + +
325A GLY* 1.4 74.8 - - - +
327A MET* 1.3 55.2 + - - +
329A ARG* 3.7 22.4 - - - +
334A ALA 3.9 18.0 + - - +
335A ARG* 3.2 9.6 + - - -
336A ILE* 2.8 78.6 + - + +
340A ALA* 6.0 0.2 - - - +
344A HIS* 4.9 6.7 - - + +
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Residues in contact with MET 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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163A LEU* 4.5 1.3 - - + -
167A LEU* 4.1 16.6 - - + -
245A LEU* 3.7 22.6 - - + +
246A TRP* 4.2 1.7 - - - -
248A VAL* 3.7 32.3 - - + -
249A GLY* 3.8 17.7 - - - -
252A PHE* 4.0 17.3 - - + -
323A LEU* 3.6 41.7 - - + +
324A LEU* 3.1 6.8 + - - +
326A ARG* 1.3 79.2 - - - +
328A LEU* 1.3 60.6 + - - +
329A ARG 3.2 1.4 + - - -
335A ARG* 3.1 33.2 + - - -
336A ILE* 3.7 13.7 - - + -
341A ALA* 4.2 6.5 - - + -
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Residues in contact with LEU 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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246A TRP* 3.3 59.9 - - + +
249A GLY* 3.7 15.0 - - - -
250A CYS* 3.9 4.7 - - - +
261A LEU* 3.5 31.9 - - + -
262A PHE* 4.6 2.2 - - + -
278A LEU* 3.8 14.1 - - + +
309A TRP* 3.5 31.4 + - + -
324A LEU* 3.2 24.0 + - + +
325A GLY 4.0 5.4 + - - +
326A ARG 3.8 0.2 - - - -
327A MET* 1.3 72.0 - - - +
329A ARG* 1.3 65.9 + - - +
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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