Contacts of the helix formed by residues 384 - 395 (chain B) in PDB entry 4M83
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 384 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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380B MET 4.0 4.8 + - - -
381B ALA 5.0 2.2 - - - -
382B GLN* 3.2 5.5 - - - +
383B GLU* 1.3 78.2 - - - +
385B GLY* 1.3 66.4 + - - +
386B THR* 3.6 0.9 + - - +
387B ARG* 3.7 15.9 + - - +
388B ARG* 3.4 24.7 + - - -
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Residues in contact with GLY 385 (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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211B VAL* 3.0 26.0 + - - +
213B ALA 3.9 14.8 - - - -
214B CYS* 5.1 1.6 - - - -
383B GLU 3.5 1.2 + - - -
384B GLY* 1.3 76.5 - - - +
386B THR* 1.3 65.5 + - - -
389B ALA* 3.0 24.5 + - - +
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Residues in contact with THR 386 (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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25B GLU* 3.8 14.3 + - + +
26B VAL* 4.2 7.4 + - - +
29B GLU* 4.0 11.5 - - - +
213B ALA 4.4 4.8 + - - +
214B CYS* 3.5 36.5 - - - +
215B GLN 5.0 5.2 - - - +
384B GLY 3.6 0.2 + - - -
385B GLY* 1.3 71.1 - - - +
387B ARG* 1.3 65.0 + - + +
389B ALA* 3.4 2.4 + - - +
390B ALA* 3.0 28.2 + - - +
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Residues in contact with ARG 387 (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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29B GLU* 5.1 4.0 - - + +
33B ARG* 3.3 19.6 + - - +
384B GLY* 3.7 12.3 + - - +
386B THR* 1.3 87.1 - - + +
388B ARG* 1.3 63.9 + - + +
390B ALA* 3.5 0.8 + - - -
391B ASP* 2.9 33.4 + - - +
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Residues in contact with ARG 388 (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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209B THR* 3.7 27.9 - - - +
210B PHE 4.0 4.4 + - - -
211B VAL* 4.5 1.5 - - + +
382B GLN 3.9 9.8 + - - -
383B GLU* 2.6 37.8 + - - +
384B GLY* 3.4 24.4 + - - +
385B GLY 3.3 2.2 + - - -
387B ARG* 1.3 82.2 - - + +
389B ALA* 1.3 56.5 + - - +
391B ASP* 3.1 8.6 + - + +
392B LEU* 2.7 60.7 + - + +
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Residues in contact with ALA 389 (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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26B VAL* 4.0 22.4 - - + -
130B LEU* 6.0 1.1 - - + -
189B LEU* 3.6 18.1 - - + +
211B VAL* 4.0 23.2 - - + +
385B GLY 3.0 17.7 + - - +
386B THR 3.6 4.7 - - - +
388B ARG* 1.3 76.0 - - - +
390B ALA* 1.3 62.7 + - - +
392B LEU 3.2 0.9 + - - -
393B ILE* 3.0 30.2 + - - +
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Residues in contact with ALA 390 (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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26B VAL* 4.5 4.1 - - + +
29B GLU* 4.1 11.9 - - + -
30B LEU* 3.9 25.5 - - + +
33B ARG* 3.4 28.0 - - - +
386B THR 3.0 16.9 + - - +
387B ARG 3.8 0.4 - - - +
389B ALA* 1.3 76.1 - - - +
391B ASP* 1.3 59.9 + - - +
393B ILE* 3.4 6.4 + - - +
394B GLU* 3.1 27.4 + - - +
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Residues in contact with ASP 391 (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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33B ARG* 3.0 25.1 + - - +
387B ARG* 2.9 18.2 + - - +
388B ARG* 3.3 15.2 - - + +
390B ALA* 1.3 77.7 - - - +
392B LEU* 1.3 59.1 + - + +
394B GLU* 3.2 11.0 + - - +
395B ALA* 2.9 26.2 + - - +
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Residues in contact with LEU 392 (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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187B ARG* 4.1 16.4 + - - +
189B LEU* 3.9 18.2 - - + -
209B THR* 3.7 28.3 - - + +
211B VAL* 3.9 12.3 - - + -
388B ARG* 2.7 52.9 + - + +
389B ALA 3.8 3.6 - - - +
391B ASP* 1.3 72.0 - - + +
393B ILE* 1.3 64.1 + - - +
395B ALA* 3.4 23.5 + - + +
396B GLU* 3.4 15.3 - - - +
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Residues in contact with ILE 393 (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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9B ILE* 4.5 11.4 - - + -
26B VAL* 3.9 22.0 - - + -
30B LEU* 4.1 16.8 - - + -
106B LEU* 4.0 24.3 - - + +
108B LEU* 3.7 36.1 - - + -
128B VAL* 4.5 6.3 - - + -
130B LEU* 4.5 2.0 - - + -
189B LEU* 3.8 18.2 - - + -
389B ALA 3.0 21.3 + - - +
390B ALA* 3.7 4.7 - - - +
391B ASP 3.2 0.2 - - - -
392B LEU* 1.3 75.6 - - - +
394B GLU* 1.3 60.5 + - - +
396B GLU* 2.8 28.2 + - - +
397B LEU* 3.5 6.2 + - + +
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Residues in contact with GLU 394 (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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30B LEU* 4.6 3.9 - - + +
33B ARG* 3.1 41.2 + - - +
35B HIS* 2.6 42.0 + - + +
390B ALA 3.1 13.0 + - - +
391B ASP* 3.2 12.0 + - - +
393B ILE* 1.3 76.6 - - + +
395B ALA* 1.3 63.1 + - - +
396B GLU 3.0 0.9 + - - -
397B LEU* 3.0 30.3 + - + +
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Residues in contact with ALA 395 (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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391B ASP 2.9 14.0 + - - +
392B LEU* 3.4 21.8 - - + +
393B ILE 3.1 0.2 - - - -
394B GLU* 1.3 75.3 - - - +
396B GLU* 1.3 63.7 - - + +
397B LEU 3.5 5.1 + - - +
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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