Contacts of the helix formed by residues 385 - 396 (chain B) in PDB entry 3M0V
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 VAL 385 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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29B LEU* 4.2 5.8 - - - -
348B ARG* 3.6 45.3 - - + +
351B ALA* 3.9 20.9 - - + -
352B GLN* 3.8 15.2 - - + +
355B LEU* 3.9 23.6 - - + -
383B THR* 3.2 13.2 + - + +
384B ASP* 1.3 71.9 + - - +
386B GLU* 1.3 65.2 + - - +
387B PRO* 3.1 4.3 - - - -
388B ILE* 2.8 26.6 + - + +
389B LEU* 3.1 12.0 + - + +
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Residues in contact with GLU 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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344B ASN* 5.8 0.5 - - - +
348B ARG* 2.9 37.8 + - - +
384B ASP* 3.1 19.0 + - - +
385B VAL* 1.3 77.9 - - - +
387B PRO* 1.3 63.0 - - + +
389B LEU* 3.1 7.8 + - - +
390B ALA* 2.8 32.9 + - + +
393B ARG* 3.1 27.0 + - - -
400B VAL 4.4 1.9 - - - +
401B ASP* 6.0 0.2 - - - -
382C ARG* 4.8 14.4 - - - +
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Residues in contact with PRO 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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22B LEU* 3.7 13.0 - - + +
25B ASP* 3.7 28.7 - - + +
26B TYR* 3.5 31.2 - - + +
29B LEU* 4.0 12.1 - - + -
384B ASP* 3.4 15.5 - - - +
385B VAL* 3.2 4.7 - - - -
386B GLU* 1.3 95.6 - - + +
388B ILE* 1.3 55.1 + - - +
390B ALA* 4.4 0.4 - - + -
391B GLU* 2.9 32.2 + - - +
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Residues in contact with ILE 388 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B TYR* 4.1 6.7 - - - -
29B LEU* 3.7 24.7 - - + -
33B LEU* 4.3 9.0 - - + -
40B ILE* 3.8 25.6 - - + -
43B VAL* 3.8 20.6 - - + -
44B THR* 3.5 29.4 - - - +
47B VAL* 4.0 20.4 - - + -
351B ALA* 5.1 1.6 - - + -
355B LEU* 5.2 1.6 - - + -
385B VAL* 2.8 23.8 + - + +
387B PRO* 1.3 73.4 - - - +
389B LEU* 1.3 63.9 + - + +
391B GLU* 3.5 1.0 + - - +
392B ALA* 2.9 28.9 + - - +
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Residues in contact with LEU 389 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B VAL* 3.9 17.0 - - + -
344B ASN* 3.7 11.9 - - + +
347B ARG* 3.7 30.1 + - + +
348B ARG* 3.4 51.4 - - + +
351B ALA* 4.2 10.5 - - + -
385B VAL 3.1 13.4 + - - +
386B GLU* 3.6 10.3 - - - +
388B ILE* 1.3 76.9 - - - +
390B ALA* 1.3 62.7 - - - +
392B ALA* 3.4 6.1 + - - +
393B ARG* 3.1 45.2 + - - +
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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
----------------------------------------------------------
22B LEU* 3.7 23.3 - - + -
386B GLU* 2.8 21.4 + - + +
387B PRO* 4.4 0.2 - - + -
389B LEU* 1.3 76.0 - - - +
391B GLU* 1.3 59.4 + - - +
393B ARG* 3.2 17.9 + - - +
394B ARG* 2.9 27.9 + - - +
400B VAL* 3.8 28.7 - - + +
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Residues in contact with GLU 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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22B LEU* 3.7 13.8 - - + +
26B TYR* 3.6 29.2 - - + +
44B THR* 4.4 2.5 - - + -
387B PRO 2.9 18.2 + - - +
388B ILE 3.9 2.0 - - - +
390B ALA* 1.3 74.3 - - - +
392B ALA* 1.3 60.1 + - - +
394B ARG* 2.8 41.8 + - - -
395B ARG* 2.5 81.1 + - - +
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Residues in contact with ALA 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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44B THR* 4.1 7.4 - - + +
47B VAL* 4.2 18.8 - - + -
48B GLU* 3.6 29.3 - - + +
347B ARG* 4.3 8.5 - - - +
388B ILE 2.9 18.8 + - - +
389B LEU 3.6 6.1 - - - +
391B GLU* 1.3 77.4 - - - +
393B ARG* 1.3 55.0 + - - +
395B ARG* 3.5 0.7 + - - +
396B THR* 2.7 38.3 + - - +
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Residues in contact with ARG 393 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91B LEU 3.6 8.7 - - - -
92B THR* 3.5 23.8 - - - +
344B ASN* 3.3 27.4 + - - +
347B ARG* 4.8 7.8 - - - +
386B GLU* 3.1 23.6 + - - -
389B LEU* 3.1 29.8 + - - +
390B ALA* 3.5 11.3 - - - +
391B GLU 3.2 0.2 - - - -
392B ALA* 1.3 74.9 - - - +
394B ARG* 1.3 62.5 + - - +
396B THR* 3.0 12.6 + - - -
397B GLY 3.2 0.2 + - - -
398B GLY* 2.7 31.4 + - - -
399B ALA 2.8 33.1 + - - +
400B VAL 2.8 21.4 + - - -
401B ASP* 4.8 0.2 - - - +
402B PRO* 3.3 26.0 - - - +
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Residues in contact with ARG 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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15B ASN* 4.3 13.3 - - + +
19B ALA* 5.5 10.8 - - - +
22B LEU* 4.1 12.7 - - - +
390B ALA 2.9 16.5 + - - +
391B GLU* 2.8 44.1 + - - +
393B ARG* 1.3 77.2 - - - +
395B ARG* 1.3 71.8 + - - +
396B THR 3.5 0.5 + - - -
397B GLY* 3.7 7.8 + - - -
398B GLY 4.0 10.7 + - - +
399B ALA 4.9 0.6 - - - -
400B VAL* 4.2 17.3 - - + -
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Residues in contact with ARG 395 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B TYR* 3.8 9.6 + - - -
41B GLU* 2.9 42.0 + - - -
44B THR* 4.0 14.3 - - - +
45B ALA 5.7 0.2 - - - +
48B GLU* 3.6 21.5 + - - +
391B GLU* 2.5 55.4 + - - +
392B ALA 3.9 4.3 - - - +
394B ARG* 1.3 86.4 - - - +
396B THR* 1.3 59.3 + - - +
397B GLY 3.5 1.0 + - - -
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Residues in contact with THR 396 (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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48B GLU* 3.5 38.6 - - + +
93B ARG* 3.2 45.0 + - - +
347B ARG* 5.4 1.6 + - - -
392B ALA 2.7 20.6 + - - +
393B ARG* 3.0 6.7 + - - -
395B ARG* 1.3 78.1 - - - +
397B GLY* 1.3 57.5 + - - +
398B GLY 3.4 0.2 - - - -
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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