Contacts of the helix formed by residues 250 - 260 (chain C) in PDB entry 5MR4
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 ASN 250 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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249C PRO* 1.3 75.4 - - - +
251C CYS* 1.3 65.0 + - - +
252C LEU* 3.2 30.7 + - - +
253C ASP* 3.2 26.9 + - - +
254C LEU* 3.0 20.4 + - - +
323C CYS* 4.1 0.2 - - - -
324C SER 3.2 14.3 + - - -
325C CYS 3.7 0.4 - - - -
326C ARG 3.0 25.9 + - - +
327C GLY 4.1 9.2 - - - +
328C SER* 2.9 34.5 + - - +
335C CYS* 3.8 3.6 - - - -
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Residues in contact with CYS 251 (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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250C ASN* 1.3 73.6 - - - +
252C LEU* 1.3 58.8 + - - +
254C LEU* 3.4 3.8 + - - +
255C ARG* 2.9 27.4 + - - +
323C CYS* 2.2 48.2 - - - -
324C SER* 3.0 26.3 + - - -
335C CYS* 3.5 15.0 - - - +
338C PHE* 3.8 21.2 - - + -
339C LEU* 4.0 23.3 - - - -
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Residues in contact with LEU 252 (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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250C ASN* 3.2 10.0 + - - +
251C CYS* 1.3 73.9 - - - +
253C ASP* 1.3 64.1 + - - +
255C ARG* 3.5 39.2 + - - +
256C GLY* 3.0 23.0 + - - -
328C SER* 5.7 1.3 - - - +
331C MET* 3.8 30.3 - - + +
334C GLU* 4.0 17.3 - - - +
335C CYS* 3.7 40.8 - - + +
338C PHE* 4.2 10.5 - - + -
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Residues in contact with ASP 253 (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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249C PRO* 4.9 5.7 - - + +
250C ASN* 3.2 33.1 + - + +
252C LEU* 1.3 77.2 - - - +
254C LEU* 1.3 58.9 + - - +
256C GLY* 3.1 3.8 + - - -
257C VAL* 2.9 33.0 + - + +
327C GLY 5.5 1.0 - - - +
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Residues in contact with LEU 254 (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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249C PRO* 4.3 17.2 - - + +
250C ASN 3.0 12.7 + - - +
251C CYS* 3.5 9.4 - - - +
253C ASP* 1.3 70.9 - - - +
255C ARG* 1.3 56.4 + - - +
257C VAL* 3.1 11.1 + - + +
258C CYS* 2.8 33.8 + - - +
304C ASP* 3.5 37.5 - - + +
305C MET* 3.9 22.2 - - + -
321C PRO* 4.2 10.3 - - + -
322C TRP* 3.7 24.9 - - + +
323C CYS* 4.0 8.5 - - + -
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Residues in contact with ARG 255 (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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121C GLU* 5.2 2.8 + - - +
122C PHE* 3.5 28.6 + - - +
251C CYS 2.9 17.7 + - - +
252C LEU* 3.6 27.7 + - - +
254C LEU* 1.3 74.7 - - - +
256C GLY* 1.3 57.4 + - - +
258C CYS* 3.2 1.7 + - - +
259C ARG* 2.8 76.6 + - - +
268C LEU* 4.1 9.4 - - + -
272C HIS* 5.5 0.2 - - - -
305C MET* 3.7 10.0 - - - +
334C GLU* 3.0 29.9 + - - -
338C PHE* 3.6 31.6 - - + -
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Residues in contact with GLY 256 (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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252C LEU 3.0 15.0 + - - -
253C ASP* 3.1 6.0 + - - -
255C ARG* 1.3 76.7 - - - +
257C VAL* 1.3 60.4 + - - +
259C ARG* 3.2 14.4 + - - +
260C THR* 3.3 19.2 + - - +
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Residues in contact with VAL 257 (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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253C ASP* 2.9 19.5 + - + +
254C LEU* 3.6 13.2 - - + +
256C GLY* 1.3 74.8 - - - +
258C CYS* 1.3 64.2 + - - +
260C THR* 3.0 27.8 + - - +
261C ASP* 3.7 2.6 + - - +
304C ASP* 3.6 29.2 - - - +
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Residues in contact with CYS 258 (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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254C LEU 2.8 13.6 + - - +
255C ARG 3.5 2.2 - - - +
257C VAL* 1.3 74.0 - - - +
259C ARG* 1.3 63.1 + - - +
261C ASP 3.1 21.5 + - - +
264C CYS* 2.1 61.8 - - - +
265C ARG* 3.4 8.0 + - - -
268C LEU* 4.1 12.1 - - - -
304C ASP* 4.4 9.4 - - + +
305C MET* 3.5 33.7 - - + -
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Residues in contact with ARG 259 (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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121C GLU* 2.6 27.0 + - - +
122C PHE 3.4 16.0 + - - -
124C GLU* 3.3 44.6 + - - +
255C ARG* 2.8 66.1 + - + +
256C GLY* 3.2 6.2 + - - +
258C CYS* 1.3 73.4 - - - +
260C THR* 1.3 60.3 + - - +
261C ASP 3.3 0.7 + - - +
265C ARG* 3.3 41.0 + - + +
268C LEU* 4.2 22.3 - - + +
269C ALA* 6.3 1.0 - - - +
272C HIS* 4.6 3.6 + - - -
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Residues in contact with THR 260 (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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256C GLY 3.3 17.7 - - - +
257C VAL* 3.0 17.1 + - - +
258C CYS 3.2 1.0 - - - -
259C ARG* 1.3 76.3 - - - +
261C ASP* 1.3 58.9 + - - +
262C HIS* 4.1 7.8 + - - -
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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