Contacts of the helix formed by residues 401 - 410 (chain C) 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 ASP 401 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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379B ARG* 4.0 19.0 + - - -
14C GLU 5.6 0.4 + - - -
15C ASN* 4.9 0.4 - - - +
18C ARG* 3.6 29.3 + - - +
393C ARG* 4.7 0.2 - - - +
399C ALA* 4.1 1.3 - - - +
400C VAL* 1.3 78.4 - - + +
402C PRO* 1.3 65.5 - - - +
403C VAL* 3.5 6.9 + - - +
404C ALA* 3.0 27.6 + - + +
405C THR* 3.0 24.5 + - - -
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Residues in contact with PRO 402 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91C LEU* 3.6 21.2 - - + +
92C THR* 4.3 2.0 - - + -
340C ILE* 3.2 25.4 - - + -
341C ASN* 5.7 0.9 - - - +
344C ASN* 3.9 10.5 - - - +
393C ARG* 3.2 43.5 - - - +
399C ALA* 3.6 14.3 - - + +
400C VAL 3.4 1.8 - - - +
401C ASP* 1.3 86.2 - - - +
403C VAL* 1.3 58.5 + - - +
405C THR* 3.2 1.6 + - - -
406C TYR* 2.8 30.2 + - - +
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Residues in contact with VAL 403 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371B LEU* 4.0 16.6 - - + -
372B MET* 4.6 10.1 - - - -
337C GLU* 4.0 24.9 - - + +
340C ILE* 4.2 6.3 - - + -
341C ASN* 3.3 38.4 - - - +
401C ASP* 3.5 6.5 + - - +
402C PRO* 1.3 75.8 - - - +
404C ALA* 1.3 64.8 + - - +
406C TYR* 3.2 6.7 + - - +
407C ARG* 2.9 47.7 + - - +
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Residues in contact with ALA 404 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14C GLU* 5.1 0.8 - - - +
18C ARG* 3.2 32.1 - - - +
401C ASP* 3.0 30.9 + - + +
403C VAL* 1.3 78.7 - - - +
405C THR* 1.3 58.0 + - - +
407C ARG* 3.4 6.1 + - - +
408C ALA* 2.9 28.6 + - - +
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Residues in contact with THR 405 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6C ILE* 4.5 2.7 - - + -
10C VAL* 4.2 7.2 - - + +
11C VAL* 4.1 26.9 - - + -
14C GLU* 3.4 27.6 - - + +
15C ASN* 4.8 0.5 + - - -
18C ARG* 5.3 0.3 + - - -
91C LEU* 3.9 21.3 - - + -
399C ALA* 3.2 17.8 - - + +
401C ASP* 3.0 14.0 + - - +
402C PRO 3.6 7.4 - - - -
404C ALA* 1.3 73.7 - - - +
406C TYR* 1.3 65.8 + - - +
408C ALA* 3.2 1.6 + - - +
409C SER* 3.0 23.4 + - - -
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Residues in contact with TYR 406 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6C ILE* 4.9 0.4 - - + -
87C VAL* 3.9 18.6 - - + -
91C LEU* 3.8 12.3 - - + +
334C ASP* 2.7 29.2 + - - -
336C ILE* 3.5 27.7 - - + +
337C GLU* 3.3 42.4 - - + -
340C ILE* 4.4 5.4 - - + -
402C PRO 2.8 17.9 + - - +
403C VAL* 3.2 6.3 + - - +
405C THR* 1.3 76.0 - - - +
407C ARG* 1.3 64.1 + - + +
409C SER* 2.6 23.8 + - - -
410C GLY 3.6 3.6 + - - -
411C TYR* 3.7 30.8 + + + -
412C ARG* 3.4 25.7 + - + +
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Residues in contact with ARG 407 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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364B TYR* 5.1 2.2 - - - -
369B ASP* 2.8 41.6 + - - -
371B LEU* 4.2 4.8 - - - +
372B MET* 3.4 20.4 - - - +
337C GLU* 2.6 44.6 + - - +
403C VAL* 2.9 26.3 + - - +
404C ALA* 3.8 5.8 - - - +
406C TYR* 1.3 77.2 - - + +
408C ALA* 1.3 63.0 + - - +
410C GLY* 3.2 13.2 + - - -
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Residues in contact with ALA 408 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10C VAL* 4.3 9.3 - - + +
14C GLU* 3.9 31.4 - - + +
17C ARG* 5.7 0.9 - - - +
404C ALA 2.9 18.1 + - - +
405C THR 3.2 4.9 + - - +
407C ARG* 1.3 77.1 - - - +
409C SER* 1.3 59.9 + - - +
410C GLY 3.5 0.3 + - - -
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Residues in contact with SER 409 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6C ILE* 3.6 31.6 - - - +
7C ALA 5.5 0.7 - - - -
10C VAL* 4.0 16.1 - - - +
405C THR 3.0 12.9 + - - -
406C TYR 2.6 20.4 + - - -
408C ALA* 1.3 77.9 - - - +
410C GLY* 1.3 60.2 + - - +
411C TYR* 3.2 18.0 + - - +
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Residues in contact with GLY 410 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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406C TYR 3.6 1.5 + - - -
407C ARG 3.2 14.9 + - - -
408C ALA 3.3 1.5 - - - -
409C SER* 1.3 78.2 + - - +
411C TYR* 1.3 64.3 + - - +
412C ARG 3.4 2.7 - - - -
413C ALA* 3.4 12.8 + - - +
414C ARG* 3.1 20.5 + - - +
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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