Contacts of the helix formed by residues 312 - 324 (chain A) in PDB entry 4EEM
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 GLY 312 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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307A TYR* 3.9 5.8 - - - -
311A GLY* 1.3 69.9 - - - -
313A GLU* 1.3 64.9 + - - +
314A ASP* 3.0 4.2 + - - -
315A ASP* 3.0 4.0 + - - -
316A ASP* 2.9 19.8 + - - +
355A ARG* 4.4 3.1 - - - -
359A ILE* 3.5 14.1 - - - +
2D NAG 2.7 42.1 + - - -
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Residues in contact with GLU 313 (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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224A ARG* 2.8 30.4 + - + +
225A ALA* 3.8 32.8 - - + +
304A PRO* 4.3 1.0 - - + +
307A TYR* 3.6 35.8 - - + +
309A GLY 5.2 1.6 - - - +
311A GLY 3.2 13.1 + - - +
312A GLY* 1.3 71.3 + - - +
314A ASP* 1.3 63.0 + - - +
316A ASP* 3.4 5.3 + - - +
317A ILE* 3.0 32.8 + - + +
409A GOL 2.6 47.4 + - - -
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Residues in contact with ASP 314 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224A ARG* 4.5 4.9 - - - +
282A TYR* 4.4 0.9 + - - -
285A TYR* 3.7 4.0 - - - -
286A PHE* 4.0 13.2 + - + +
287A GLY* 3.5 32.8 + - - +
312A GLY 3.5 2.8 + - - -
313A GLU* 1.3 81.7 - - - +
315A ASP* 1.3 63.6 + - - +
317A ILE* 3.4 11.7 + - + +
318A PHE* 3.0 24.3 + - - +
409A GOL 3.4 11.4 - - - +
2D NAG 2.5 50.2 + - - -
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Residues in contact with ASP 315 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282A TYR* 2.7 30.6 + - - -
284A GLN 4.4 5.4 - - - +
285A TYR* 4.9 0.9 - - - -
286A PHE 5.2 0.3 + - - -
312A GLY* 3.0 7.3 + - - +
314A ASP* 1.3 79.2 + - - +
316A ASP* 1.3 60.7 + - - +
318A PHE* 3.2 8.1 + - - +
319A ASN* 2.9 36.7 + - - +
359A ILE* 4.1 17.3 - - + -
1D MMA 3.1 17.4 - - - +
2D NAG 2.7 35.3 + - - +
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Residues in contact with ASP 316 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304A PRO* 3.4 8.9 - - + +
307A TYR* 2.8 46.5 + - + +
312A GLY 2.9 6.2 + - - +
313A GLU 3.4 9.2 - - - +
315A ASP* 1.3 77.2 - - - +
317A ILE* 1.3 56.8 + - - +
319A ASN* 3.2 6.6 + - - +
320A ARG* 2.7 58.3 + - - +
358A ARG 4.4 0.5 - - - +
359A ILE* 4.1 2.1 - - - +
362A THR* 2.8 29.8 + - - +
365A THR* 4.6 4.5 + - - -
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Residues in contact with ILE 317 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224A ARG* 4.9 8.3 - - - +
225A ALA* 4.8 1.1 - - + -
228A LEU* 5.2 0.2 - - + -
286A PHE* 3.9 23.8 - - + -
292A LEU* 5.2 0.2 - - + -
300A ILE* 4.3 7.9 - - + -
303A PHE* 3.3 62.6 - - + -
304A PRO* 3.9 10.3 - - + -
313A GLU* 3.0 27.6 + - + +
314A ASP* 3.6 11.7 - - + +
315A ASP 3.2 0.4 - - - -
316A ASP* 1.3 73.9 - - - +
318A PHE* 1.3 64.6 + - - +
320A ARG* 3.1 8.2 + - - +
321A LEU* 3.1 24.2 + - + +
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Residues in contact with PHE 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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283A VAL 5.1 1.8 - - - -
284A GLN* 3.5 72.7 - - + +
285A TYR 5.6 0.2 - - - -
286A PHE* 4.1 9.7 - - + -
314A ASP 3.0 13.6 + - - +
315A ASP* 3.4 10.1 - - - +
317A ILE* 1.3 74.4 - - - +
319A ASN* 1.3 77.3 + - - +
321A LEU* 3.1 13.1 + - - +
322A VAL* 3.1 46.0 + - + +
328A ILE* 3.6 35.9 - - + -
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Residues in contact with ASN 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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284A GLN* 5.5 0.5 - - - +
315A ASP* 2.9 23.7 + - - +
316A ASP 3.2 7.6 + - - +
318A PHE* 1.3 84.0 - - - +
320A ARG* 1.3 63.6 + - - +
322A VAL* 3.2 5.7 + - - +
323A PHE* 2.9 43.6 + - + -
359A ILE* 2.9 38.0 + - - +
362A THR* 3.2 19.7 + - + -
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Residues in contact with ARG 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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300A ILE* 3.2 33.4 + - + +
301A ASN 3.4 6.3 + - - -
302A GLY 3.0 29.4 + - - -
303A PHE* 3.9 0.8 - - - +
304A PRO* 3.5 29.9 - - - +
316A ASP* 2.7 35.5 + - - +
317A ILE* 3.1 11.9 + - - +
319A ASN* 1.3 74.7 - - - +
321A LEU* 1.3 64.7 + - - +
323A PHE 3.3 1.7 + - - -
324A ARG* 3.1 20.8 + - - +
362A THR* 3.6 9.9 - - + -
365A THR* 4.6 2.6 + - - -
366A MET* 3.5 46.9 + - + +
369A ASP* 2.7 34.1 + - - +
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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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266A PRO* 3.7 32.1 - - + -
286A PHE* 3.7 32.5 - - + -
292A LEU* 3.9 13.5 - - + -
296A GLN* 4.7 1.3 - - + +
300A ILE* 3.7 31.4 - - + -
317A ILE* 3.1 16.2 + - + +
318A PHE* 3.1 6.0 + - - +
320A ARG* 1.3 74.6 - - - +
322A VAL* 1.3 64.0 + - + +
324A ARG* 3.1 8.7 + - - +
325A GLY 3.3 0.3 + - - -
326A MET* 3.1 40.7 + - + +
328A ILE* 4.0 14.6 - - + -
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Residues in contact with VAL 322 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318A PHE* 3.1 46.5 + - + +
319A ASN* 3.7 8.3 - - - +
321A LEU* 1.3 76.5 - - + +
323A PHE* 1.3 70.0 + - + +
325A GLY* 3.1 17.5 + - - -
326A MET 3.8 17.3 + - - +
327A SER* 5.3 3.6 - - - -
328A ILE* 5.6 1.1 - - + -
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Residues in contact with PHE 323 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319A ASN* 2.9 46.8 + - + +
320A ARG 3.3 3.5 + - - +
322A VAL* 1.3 86.9 - - + +
324A ARG* 1.3 81.2 + - - +
325A GLY 3.4 1.0 + - - -
362A THR* 4.2 2.2 - - + -
363A LYS* 3.6 63.8 - - + -
366A MET* 4.3 8.1 - - - -
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Residues in contact with ARG 324 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299A THR* 3.7 37.5 + - + +
300A ILE* 4.0 1.6 - - + -
320A ARG 3.1 14.6 + - - +
321A LEU 3.1 3.8 + - - -
323A PHE* 1.3 98.0 + - - +
325A GLY* 1.3 58.9 + - - -
326A MET* 3.5 27.6 + - + +
363A LYS* 5.2 5.7 + - - +
366A MET* 3.6 34.0 + - + +
367A LEU* 3.6 28.9 - - - +
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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