Contacts of the helix formed by residues 331 - 344 (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 MET 331 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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252C LEU* 3.8 19.1 - - + -
328C SER* 3.3 21.2 + - - +
329C GLY 3.3 1.0 - - - -
330C ASN* 1.3 96.8 - - + +
332C GLU* 1.3 57.3 + - - +
333C GLU* 3.2 2.9 - - - +
334C GLU* 3.3 22.0 + - + +
335C CYS* 2.9 28.8 + - - +
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Residues in contact with GLU 332 (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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325C CYS* 4.6 9.6 - - + +
328C SER* 3.5 23.4 - - - -
329C GLY 3.8 11.9 + - - +
330C ASN 3.4 3.8 + - - -
331C MET* 1.3 76.4 - - - +
333C GLU* 1.3 56.1 + - - +
335C CYS* 3.4 0.9 + - - +
336C GLU* 2.9 56.5 + - + +
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Residues in contact with GLU 333 (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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330C ASN 4.9 2.8 + - - +
331C MET* 3.2 0.8 - - - -
332C GLU* 1.3 79.4 - - - +
334C GLU* 1.3 56.8 + - - +
336C GLU* 3.8 8.3 - - - +
337C LYS* 3.0 28.5 + - - +
340C ARG* 5.2 1.2 + - - -
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Residues in contact with GLU 334 (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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122C PHE* 3.6 22.0 - - + +
252C LEU* 4.0 14.7 - - + +
255C ARG* 3.0 36.5 + - - -
331C MET* 3.3 25.0 + - + +
333C GLU* 1.3 77.9 - - - +
335C CYS* 1.3 64.3 + - - +
337C LYS* 3.6 8.8 - - + +
338C PHE* 3.0 24.4 + - - +
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Residues in contact with CYS 335 (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* 3.8 10.5 - - - -
251C CYS* 3.5 23.3 - - - -
252C LEU* 3.7 18.5 - - + +
325C CYS* 2.8 40.8 - - - -
328C SER* 3.4 22.4 - - - +
331C MET 2.9 17.0 + - - +
332C GLU 3.7 2.9 - - - +
334C GLU* 1.3 76.0 - - - +
336C GLU* 1.3 57.1 + - - +
338C PHE* 3.1 6.4 + - - +
339C LEU* 2.9 24.6 + - - +
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Residues in contact with GLU 336 (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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325C CYS* 3.7 22.1 - - + +
332C GLU* 2.9 50.3 + - - +
333C GLU* 3.8 6.5 - - - +
335C CYS* 1.3 76.4 - - - +
337C LYS* 1.3 56.9 + - - +
339C LEU* 3.4 3.2 + - + +
340C ARG* 3.0 51.1 + - + +
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Residues in contact with LYS 337 (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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122C PHE* 3.7 25.6 - - + -
123C TYR* 3.1 32.2 + - - -
333C GLU 3.0 17.3 + - - +
334C GLU* 3.6 8.5 - - + +
336C GLU* 1.3 73.8 - - - +
338C PHE* 1.3 66.8 + - - +
340C ARG* 3.4 32.1 + - - +
341C ASP* 3.6 17.0 + - - +
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Residues in contact with PHE 338 (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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122C PHE* 3.6 14.0 - + + -
251C CYS* 3.8 36.8 - - + -
252C LEU* 4.2 9.4 - - + -
255C ARG* 3.6 34.3 - - + -
268C LEU* 4.4 3.6 - - + -
272C HIS* 4.1 26.2 - + - -
305C MET* 3.7 35.0 - - + -
321C PRO* 4.8 5.8 - - + -
323C CYS* 4.9 0.4 - - - -
334C GLU 3.0 14.1 + - - +
335C CYS 3.3 8.3 - - - +
337C LYS* 1.3 77.6 - - - +
339C LEU* 1.3 64.5 + - - +
340C ARG 3.3 0.3 + - - -
341C ASP* 3.3 19.3 + - - +
342C PHE* 3.7 22.8 - + - -
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Residues in contact with LEU 339 (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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251C CYS* 4.0 26.7 - - - -
320C SER* 3.6 23.8 - - - +
321C PRO* 3.9 15.7 - - + -
323C CYS* 4.3 7.2 - - - +
324C SER* 4.9 4.7 - - - -
325C CYS* 4.3 15.3 - - + +
335C CYS 2.9 15.4 + - - +
336C GLU* 3.4 4.7 + - + +
337C LYS 3.3 0.2 - - - -
338C PHE* 1.3 79.6 - - + +
340C ARG* 1.3 58.4 + - + +
342C PHE* 2.9 22.2 + - - +
343C THR* 3.0 28.7 + - + +
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Residues in contact with ARG 340 (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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333C GLU 5.2 1.0 + - - -
336C GLU* 3.0 45.4 + - + +
337C LYS* 3.8 29.1 - - - +
338C PHE 3.2 0.6 - - - -
339C LEU* 1.3 72.4 - - - +
341C ASP* 1.3 59.7 + - - +
342C PHE 3.0 5.4 - - - -
343C THR* 3.5 8.5 - - - +
344C GLU* 2.9 71.2 + - + +
345C ASN* 3.4 1.0 + - - +
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Residues in contact with ASP 341 (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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122C PHE* 3.9 5.0 - - - -
123C TYR* 2.8 39.9 + - - -
271C PHE* 3.4 23.1 - - + -
272C HIS* 4.1 8.5 + - + +
276C ARG* 5.7 4.9 - - - +
277C ALA* 5.6 4.0 + - - +
337C LYS* 3.6 14.0 + - - +
338C PHE* 3.3 10.9 + - - +
339C LEU 3.2 0.4 - - - -
340C ARG* 1.3 75.5 - - - +
342C PHE* 1.3 60.1 + - + +
345C ASN* 2.9 34.9 + - - +
348C LEU* 4.2 0.9 - - - +
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Residues in contact with PHE 342 (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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268C LEU* 4.3 3.8 - - + -
271C PHE* 3.6 34.8 - + - -
272C HIS* 5.2 0.7 - - - -
297C TYR* 4.9 5.8 - + - -
300C MET* 3.9 30.3 - - + -
305C MET* 4.3 3.4 - - + -
307C PRO* 4.4 18.6 - - + -
319C VAL* 3.4 16.0 - - + +
320C SER* 4.1 1.6 - - - -
321C PRO* 3.7 39.3 - - + -
338C PHE* 3.7 35.7 - + - -
339C LEU* 2.9 9.6 + - - +
341C ASP* 1.3 81.4 - - + +
343C THR* 1.3 55.6 + - + +
344C GLU 3.5 0.7 - - - -
345C ASN 4.6 0.2 - - - -
348C LEU* 3.7 11.4 - - - +
501C FMT 2.7 30.5 + - - -
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Residues in contact with THR 343 (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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317C ILE 5.1 0.5 - - - +
318C VAL* 4.1 20.7 - - + +
319C VAL 3.5 17.0 - - - +
320C SER* 3.8 16.2 - - - -
339C LEU* 3.0 33.2 + - + +
340C ARG* 3.5 8.7 - - - +
342C PHE* 1.3 79.5 - - - +
344C GLU* 1.3 76.3 + - - +
501C FMT 2.8 20.3 + - - -
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Residues in contact with GLU 344 (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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340C ARG* 2.9 47.8 + - + +
343C THR* 1.3 87.2 + - - +
345C ASN* 1.3 58.6 + - - +
346C PRO* 3.4 10.7 - - - +
501C FMT 5.1 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