Contacts of the helix formed by residues 312 - 329 (chain F) in PDB entry 3SZ9
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 312 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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310F VAL 3.5 0.2 + - - -
311F GLN* 1.3 80.6 + - - +
313F ASP* 1.3 76.0 + - - +
314F ILE 3.2 1.2 + - - -
315F TYR* 3.3 13.8 + - - +
316F ASP* 4.7 1.9 + - - +
409F LYS* 3.8 30.8 - - + +
410F PHE 2.8 13.5 + - - +
411F LYS* 3.4 53.6 + - - +
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Residues in contact with ASP 313 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279F SER* 4.6 10.7 + - - -
311F GLN* 2.7 28.5 + - - +
312F GLU* 1.3 83.8 - - - +
314F ILE* 1.3 60.6 + - + +
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Residues in contact with ILE 314 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277F ILE* 3.8 22.2 - - + +
278F MET 3.6 23.1 - - - +
279F SER* 3.7 32.5 - - - +
281F ALA* 5.3 2.5 - - + +
283F MET* 3.8 23.8 - - + -
310F VAL* 3.7 12.1 - - + -
311F GLN 3.3 13.5 - - - +
313F ASP* 1.3 83.6 - - + +
315F TYR* 1.3 65.5 + - - +
316F ASP 3.5 2.2 - - - -
317F GLU* 3.3 8.4 + - - +
318F PHE* 2.9 25.2 + - + +
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Residues in contact with TYR 315 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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310F VAL* 3.7 20.6 - - + -
311F GLN 3.2 8.4 + - - +
312F GLU* 3.3 19.5 + - - +
314F ILE* 1.3 77.4 - - - +
316F ASP* 1.3 81.4 + - - +
318F PHE* 3.2 1.0 + - - +
319F VAL* 2.8 47.6 + - + +
368F LEU* 5.6 0.2 - - - +
387F GLY* 3.7 7.4 - - - -
388F ASP* 2.8 44.9 + - - -
407F ILE* 3.7 18.9 + - + -
408F LEU 4.0 6.7 - - - -
409F LYS* 3.7 46.7 - - + -
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Residues in contact with ASP 316 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312F GLU 4.7 1.5 + - - -
314F ILE 3.5 0.8 - - - -
315F TYR* 1.3 94.0 - - - +
317F GLU* 1.3 58.6 + - - +
319F VAL* 3.3 4.4 + - - +
320F GLU* 3.0 40.0 + - - +
409F LYS* 5.0 4.7 + - - -
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Residues in contact with GLU 317 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283F MET* 3.9 20.2 - - + +
314F ILE* 3.3 9.4 + - - +
315F TYR 3.2 0.6 - - - -
316F ASP* 1.3 75.8 - - - +
318F PHE* 1.3 67.6 + - - +
320F GLU* 3.2 14.4 + - - +
321F ARG* 2.8 63.6 + - + +
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Residues in contact with PHE 318 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277F ILE* 3.8 28.7 - - + -
283F MET* 3.9 19.4 - - + +
286F ALA* 4.0 6.5 - - + -
287F VAL* 3.8 28.2 - - + +
290F ALA* 3.5 27.6 - - + -
308F THR* 3.9 15.7 - - + -
310F VAL* 3.7 29.2 - - + -
314F ILE* 2.9 19.0 + - + +
315F TYR 3.6 3.1 - - - +
317F GLU* 1.3 78.9 - - - +
319F VAL* 1.3 60.0 + - - +
321F ARG* 3.3 1.6 + - - +
322F SER* 2.9 52.3 + - - -
405F MET* 4.6 0.9 - - + -
407F ILE* 4.3 10.8 - - + -
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Residues in contact with VAL 319 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315F TYR* 2.8 61.7 + - + +
316F ASP* 3.7 4.7 - - - +
318F PHE* 1.3 70.3 - - + +
320F GLU* 1.3 70.0 + - + +
322F SER* 3.2 5.9 + - - -
323F VAL* 2.9 27.3 + - + +
368F LEU* 3.5 31.6 - - + -
407F ILE* 3.9 21.8 - - + -
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Residues in contact with GLU 320 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316F ASP* 3.0 29.1 + - - +
317F GLU* 3.7 14.9 - - + +
319F VAL* 1.3 79.4 - - + +
321F ARG* 1.3 60.9 + - + +
323F VAL* 3.4 6.3 + - - +
324F ALA* 3.0 27.4 + - - +
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Residues in contact with ARG 321 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283F MET* 3.7 21.8 - - - +
284F ASP* 2.8 30.1 + - - +
287F VAL* 3.9 24.6 - - + +
317F GLU* 2.8 47.6 + - + +
320F GLU* 1.3 76.8 - - + +
322F SER* 1.3 61.6 + - - +
324F ALA* 3.4 7.2 + - - +
325F ARG* 2.9 29.1 + - - +
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Residues in contact with SER 322 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287F VAL* 4.1 13.5 + - - +
291F HIS* 5.0 3.0 + - - -
318F PHE* 2.9 45.6 + - - -
319F VAL 3.7 3.1 - - - -
321F ARG* 1.3 75.6 - - - +
323F VAL* 1.3 60.3 + - - +
325F ARG* 3.1 4.3 + - - +
326F ALA* 2.9 30.2 + - - +
385F VAL* 4.6 3.2 - - - +
405F MET* 4.3 14.7 - - - +
407F ILE* 4.1 18.6 - - - -
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Residues in contact with VAL 323 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319F VAL* 2.9 23.0 + - + +
320F GLU* 3.7 5.6 - - - +
322F SER* 1.3 73.4 - - - +
324F ALA* 1.3 65.8 + - - +
326F ALA* 3.2 7.9 + - - +
327F LYS* 3.1 37.5 + - + +
368F LEU* 3.6 53.2 - - + +
369F CYS* 4.2 8.7 - - + -
385F VAL* 4.2 11.7 - - + -
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Residues in contact with ALA 324 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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320F GLU 3.0 16.8 + - - +
321F ARG* 3.8 7.9 - - - +
322F SER 3.3 0.4 - - - -
323F VAL* 1.3 77.6 - - - +
325F ARG* 1.3 63.8 + - - +
327F LYS* 3.5 8.8 + - - +
328F SER* 3.2 21.8 + - - -
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Residues in contact with ARG 325 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287F VAL* 4.8 7.6 - - + -
288F GLU* 3.0 39.1 + - - +
291F HIS* 3.4 50.4 + - + +
321F ARG 2.9 18.8 + - - +
322F SER* 3.1 7.4 + - - +
324F ALA* 1.3 79.1 - - - +
326F ALA* 1.3 60.2 + - - +
328F SER* 2.8 32.8 + - - -
329F ARG* 3.2 14.6 + - - +
340F GLU* 3.0 30.3 + - - -
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Residues in contact with ALA 326 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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291F HIS* 4.0 10.5 - - - -
295F PHE* 4.5 7.9 - - + -
322F SER 2.9 16.3 + - - +
323F VAL 3.6 4.3 - - - +
325F ARG* 1.3 76.9 - - - +
327F LYS* 1.3 61.9 + - - +
329F ARG* 3.2 18.5 + - - +
369F CYS* 3.8 10.1 - - - -
383F PRO* 3.7 24.3 - - + +
385F VAL* 3.6 26.2 - - + -
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Residues in contact with LYS 327 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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323F VAL* 3.1 32.1 + - + +
324F ALA* 4.0 7.4 - - - +
325F ARG 3.4 0.2 - - - -
326F ALA* 1.3 74.8 - - - +
328F SER* 1.3 58.6 + - - +
329F ARG 3.7 3.8 + - - +
368F LEU 4.6 3.7 + - - -
369F CYS* 3.9 28.0 - - + +
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Residues in contact with SER 328 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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324F ALA 3.2 12.3 + - - -
325F ARG* 2.8 37.2 + - - -
326F ALA 3.2 0.2 - - - -
327F LYS* 1.3 75.9 - - - +
329F ARG* 1.3 66.1 + - - +
330F VAL* 3.1 15.4 + - - +
340F GLU* 3.9 2.6 - - - +
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Residues in contact with ARG 329 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291F HIS* 2.9 38.0 + - + -
292F PHE* 5.8 1.4 - - - +
295F PHE* 3.3 38.9 + - - +
296F PHE* 4.4 4.9 - - - +
297F ASN 5.0 2.0 - - - +
298F GLN 5.1 1.0 - - - +
325F ARG* 3.2 13.4 + - - +
326F ALA 3.2 17.4 + - - +
327F LYS 4.3 3.5 - - - +
328F SER* 1.3 78.4 + - - +
330F VAL* 1.3 62.5 + - - +
331F VAL* 3.5 10.0 + - - +
340F GLU* 3.4 48.4 + - + +
341F GLN* 3.3 34.2 + - + +
383F PRO* 3.9 12.7 - - + +
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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