Contacts of the helix formed by residues 312 - 324 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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307B TYR* 3.8 7.2 - - - -
311B GLY* 1.3 68.5 - - - -
313B GLU* 1.3 63.1 + - - +
314B ASP* 3.0 4.3 - - - -
315B ASP* 3.2 18.0 + - - -
316B ASP* 2.9 19.6 + - - +
355B ARG* 4.5 1.1 - - - -
359B ILE* 3.2 15.9 - - - +
2E NAG 2.8 29.1 + - - -
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Residues in contact with GLU 313 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224B ARG* 2.9 28.0 + - + +
225B ALA* 3.5 33.7 - - + +
304B PRO* 4.4 0.8 - - + +
307B TYR* 3.7 33.9 - - + +
309B GLY 5.1 2.1 - - - +
311B GLY 3.3 9.9 + - - +
312B GLY* 1.3 72.4 - - - +
314B ASP* 1.3 62.6 + - - +
316B ASP* 3.3 5.4 + - - +
317B ILE* 3.1 31.7 + - + +
412B GOL 2.4 51.7 + - - -
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Residues in contact with ASP 314 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224B ARG* 4.5 4.9 - - - +
282B TYR* 4.4 0.9 + - - -
285B TYR* 3.7 4.7 - - - -
286B PHE* 4.0 10.6 - - - +
287B GLY* 3.5 31.9 + - - +
312B GLY 3.5 0.5 - - - -
313B GLU* 1.3 87.1 + - - +
315B ASP* 1.3 64.2 + - - +
317B ILE* 3.2 12.0 + - + +
318B PHE* 3.0 26.9 + - - +
412B GOL 3.4 12.5 + - - +
2E NAG 2.6 48.1 + - - -
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Residues in contact with ASP 315 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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282B TYR* 2.6 32.1 + - - -
284B GLN* 4.5 4.9 - - - +
285B TYR* 5.0 0.9 - - - -
286B PHE 5.1 0.5 + - - -
312B GLY* 3.2 8.4 + - - +
314B ASP* 1.3 77.1 + - - +
316B ASP* 1.3 61.0 + - - +
318B PHE* 3.4 8.7 + - + +
319B ASN* 2.9 38.5 + - - +
359B ILE* 4.0 16.8 - - + -
1E MMA 3.7 11.6 - - - +
2E NAG 2.7 39.8 + - - +
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Residues in contact with ASP 316 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304B PRO* 3.3 10.4 - - + +
307B TYR* 2.7 46.5 + - + +
312B GLY 2.9 6.2 + - - +
313B GLU 3.4 10.1 - - - +
314B ASP 3.2 0.2 - - - -
315B ASP* 1.3 76.9 - - - +
317B ILE* 1.3 57.8 + - - +
319B ASN* 3.1 5.0 + - - +
320B ARG* 2.8 56.5 + - - +
358B ARG 4.1 0.7 - - - +
359B ILE* 4.1 1.7 - - - +
362B THR* 2.8 30.3 + - - +
365B THR* 4.7 4.0 + - - -
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Residues in contact with ILE 317 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224B ARG* 5.0 7.9 - - - +
225B ALA* 4.8 7.2 - - + -
228B LEU* 5.2 1.6 - - + -
286B PHE* 3.9 24.2 - - + -
292B LEU* 5.0 0.2 - - + -
300B ILE* 4.4 3.8 - - + -
303B PHE* 3.4 60.6 - - + -
304B PRO* 3.9 10.1 - - + -
313B GLU* 3.1 25.5 + - + +
314B ASP* 3.5 11.4 - - - +
315B ASP 3.1 0.2 - - - -
316B ASP* 1.3 74.9 - - - +
318B PHE* 1.3 65.5 + - - +
320B ARG* 3.1 9.1 + - - +
321B LEU* 3.0 26.3 + - + +
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Residues in contact with PHE 318 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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283B VAL 5.1 1.1 - - - -
284B GLN* 3.2 74.3 - - + +
286B PHE* 4.0 10.2 - - + -
314B ASP 3.0 12.9 + - - +
315B ASP* 3.5 9.9 - - - +
317B ILE* 1.3 76.8 - - - +
319B ASN* 1.3 78.1 + - - +
321B LEU* 3.1 12.3 + - - +
322B VAL* 3.0 45.7 + - + +
328B ILE* 3.7 34.1 - - + -
330B ARG* 5.9 0.2 - - - -
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Residues in contact with ASN 319 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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284B GLN* 5.4 1.0 - - - +
315B ASP* 2.9 26.9 + - - +
316B ASP 3.1 7.1 + - - +
318B PHE* 1.3 91.5 - - - +
320B ARG* 1.3 63.2 + - - +
322B VAL* 3.3 4.5 + - - +
323B PHE* 2.9 52.8 + - + -
359B ILE* 2.8 36.0 + - - +
362B THR* 3.2 12.4 + - + -
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Residues in contact with ARG 320 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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300B ILE* 3.2 33.2 + - + +
301B ASN 3.5 5.5 + - - -
302B GLY 3.0 28.8 + - - -
303B PHE* 4.0 0.6 - - - +
304B PRO* 3.4 32.8 - - - +
316B ASP* 2.8 33.5 + - - +
317B ILE* 3.1 9.6 + - - +
319B ASN* 1.3 77.4 - - - +
321B LEU* 1.3 62.8 + - - +
323B PHE* 3.4 1.0 + - - -
324B ARG* 3.2 20.1 + - - +
362B THR* 3.5 11.8 - - + +
365B THR* 4.6 2.8 + - - -
366B MET* 3.6 45.2 + - + +
369B ASP* 2.6 33.5 + - - +
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Residues in contact with LEU 321 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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266B PRO* 3.8 24.0 - - + -
286B PHE* 3.6 38.6 - - + -
292B LEU* 4.2 11.0 - - + -
296B GLN* 4.6 2.7 - - + +
300B ILE* 3.8 22.0 - - + -
317B ILE* 3.0 20.7 + - + +
318B PHE* 3.5 6.1 - - - +
320B ARG* 1.3 76.6 - - - +
322B VAL* 1.3 63.4 + - + +
324B ARG* 3.1 9.2 + - - +
325B GLY 3.3 0.3 + - - -
326B MET* 3.1 51.5 + - + +
328B ILE* 4.1 12.8 - - + -
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Residues in contact with VAL 322 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318B PHE* 3.0 48.1 + - + +
319B ASN* 3.8 6.3 - - - +
321B LEU* 1.3 77.5 - - + +
323B PHE* 1.3 72.8 + - + +
325B GLY* 3.0 18.9 + - - -
326B MET 3.8 16.1 - - - +
327B SER* 5.4 3.1 - - - -
328B ILE* 5.7 1.3 - - + -
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Residues in contact with PHE 323 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319B ASN* 2.9 47.0 + - + +
320B ARG 3.9 4.0 - - - +
322B VAL* 1.3 88.0 - - + +
324B ARG* 1.3 63.9 + - - +
325B GLY 3.3 1.6 + - - -
362B THR* 4.3 1.6 - - - -
363B LYS* 3.8 51.8 - - + -
366B MET* 4.2 13.7 - - - -
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Residues in contact with ARG 324 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299B THR* 3.3 43.6 + - + +
300B ILE* 3.9 5.8 - - + -
320B ARG 3.2 14.5 + - - +
321B LEU 3.1 6.0 + - - +
323B PHE* 1.3 83.4 - - - +
325B GLY* 1.3 60.8 + - - +
326B MET* 3.3 23.6 + - + +
366B MET* 4.0 15.4 - - + +
367B LEU* 3.5 31.7 - - - +
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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