Contacts of the helix formed by residues 314 - 328 (chain C) in PDB entry 1M7X
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 THR 314 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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209C GLU* 3.3 19.3 - - - +
265C TYR* 3.9 3.8 - - - -
308C PRO* 5.5 1.1 - - - -
310C ARG* 3.8 18.8 - - - +
313C GLY* 1.3 77.6 - - - +
315C ARG* 1.3 64.8 + - - +
316C ASP* 3.6 17.9 + - - +
317C ASP* 2.7 40.9 + - - +
318C PHE 3.5 4.2 + - - -
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Residues in contact with ARG 315 (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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184C ASN* 5.1 3.8 - - - +
208C PHE* 4.0 16.4 - - - +
209C GLU* 3.1 25.8 + - - +
221C CYS* 3.6 24.5 - - - +
222C GLY 3.4 27.1 + - - +
223C LEU 4.1 16.0 + - - +
224C PRO* 4.0 22.1 - - - +
308C PRO* 4.1 15.5 - - + -
314C THR* 1.3 75.5 - - - +
316C ASP* 1.3 86.8 + - - +
318C PHE* 3.2 2.6 + - - +
319C ARG* 3.0 22.8 + - - -
397C PHE* 3.2 36.6 - - + -
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Residues in contact with ASP 316 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209C GLU* 5.4 0.3 - - - +
224C PRO* 5.7 1.0 - - - +
266C ARG* 4.2 8.9 + - - +
314C THR* 3.1 13.6 + - - +
315C ARG* 1.3 110.2 + - - +
317C ASP* 1.3 59.7 + - - +
318C PHE 3.3 0.2 - - - -
319C ARG* 3.8 10.1 - - - +
320C TYR* 3.1 26.3 + - - +
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Residues in contact with ASP 317 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264C SER* 5.4 2.4 - - - -
265C TYR* 3.4 28.5 + - + +
266C ARG* 3.8 30.6 + - + +
312C PHE 4.2 2.6 - - - +
313C GLY* 3.7 13.7 - - - -
314C THR* 2.7 37.1 + - - +
316C ASP* 1.3 78.7 - - - +
318C PHE* 1.3 55.7 + - - +
320C TYR* 3.1 10.1 + - - +
321C PHE* 2.8 28.1 + - - -
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Residues in contact with PHE 318 (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 LEU* 5.0 0.4 - - + -
265C TYR* 3.5 40.9 - + + -
286C LEU* 4.2 19.1 - - + -
289C ILE* 3.7 31.2 - - + -
308C PRO* 4.2 12.3 - - + -
314C THR 3.5 1.8 + - - -
315C ARG 3.2 10.3 + - - +
317C ASP* 1.3 80.3 - - - +
319C ARG* 1.3 56.0 + - - +
320C TYR 3.1 0.2 - - - -
321C PHE* 3.0 8.0 + + - +
322C ILE* 2.9 55.7 + - + +
334C LEU* 5.1 2.0 - - + -
393C TRP* 3.7 26.7 - + - -
397C PHE* 3.3 31.9 - + + -
399C ILE* 4.9 8.5 - - + -
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Residues in contact with ARG 319 (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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224C PRO* 3.4 18.1 - - + +
225C GLU* 3.6 17.1 - - - +
226C LYS 4.1 8.7 + - - +
227C VAL* 3.0 27.3 - - - +
315C ARG* 3.0 16.5 + - - +
316C ASP* 3.8 11.7 - - - +
317C ASP 3.3 0.2 - - - -
318C PHE* 1.3 75.5 - - - +
320C TYR* 1.3 57.2 + - - +
322C ILE* 4.0 2.9 - - - +
323C ASP* 2.8 61.3 + - - +
396C ARG 2.9 23.3 + - - -
397C PHE* 3.6 32.1 - - + +
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Residues in contact with TYR 320 (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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266C ARG* 3.8 57.4 - - + +
269C ALA* 4.1 20.2 - - + -
270C ASP* 4.9 7.2 + - - -
316C ASP 3.1 17.8 + - - +
317C ASP* 3.3 6.7 - - - +
318C PHE 3.1 0.4 - - - -
319C ARG* 1.3 76.0 - - - +
321C PHE* 1.3 63.2 + - - +
323C ASP* 3.4 10.8 + - + +
324C ALA* 2.9 29.9 + - + +
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Residues in contact with PHE 321 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250C LEU* 4.2 7.6 - - + -
265C TYR* 3.5 26.2 - + + +
268C LEU* 3.4 35.0 - - + -
269C ALA* 3.7 15.3 - - - -
272C LEU* 3.3 26.5 - - + -
273C VAL* 4.2 7.6 - - + +
284C LEU* 3.9 17.9 - - + -
286C LEU* 3.9 25.4 - - + -
317C ASP 2.8 13.0 + - - +
318C PHE* 3.0 18.6 + + - +
320C TYR* 1.3 79.3 - - - +
322C ILE* 1.3 71.7 + - + +
324C ALA* 3.1 5.4 + - - +
325C ALA* 2.9 26.9 + - + +
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Residues in contact with ILE 322 (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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318C PHE* 2.9 41.1 + - + +
319C ARG* 4.1 4.7 - - - +
321C PHE* 1.3 87.4 - - + +
323C ASP* 1.3 61.0 + - - +
325C ALA* 2.9 4.8 + - - +
326C HIS* 2.8 57.9 + - + +
332C VAL* 3.7 33.7 - - + -
397C PHE 3.4 26.5 - - - +
398C GLY 4.0 4.9 - - - +
399C ILE* 4.6 5.2 - - + +
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Residues in contact with ASP 323 (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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227C VAL* 4.9 4.3 - - - +
319C ARG* 2.8 53.4 + - - +
320C TYR* 3.6 12.7 - - + +
321C PHE 3.3 0.2 - - - -
322C ILE* 1.3 78.3 - - - +
324C ALA* 1.3 58.0 + - - +
326C HIS* 3.8 9.3 + - - +
327C ALA* 2.8 28.9 + - - +
397C PHE 5.1 0.2 - - - +
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Residues in contact with ALA 324 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269C ALA* 3.6 32.5 - - + +
273C VAL* 3.5 5.7 - - + +
320C TYR* 2.9 18.3 + - + +
321C PHE 3.3 8.7 - - - +
323C ASP* 1.3 76.5 - - - +
325C ALA* 1.3 63.0 - - - +
327C ALA* 3.5 8.0 - - - +
328C ALA* 3.0 24.3 + - - +
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Residues in contact with ALA 325 (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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273C VAL* 3.9 18.3 - - + +
284C LEU* 4.7 7.4 - - + -
321C PHE* 2.9 13.8 + - + +
322C ILE* 3.3 9.2 - - + +
324C ALA* 1.3 74.5 - - - +
326C HIS* 1.3 66.7 + - - +
328C ALA* 3.0 9.2 + - - +
330C LEU* 3.0 33.3 + - + +
332C VAL* 3.5 28.5 - - + -
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Residues in contact with HIS 326 (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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227C VAL* 4.8 7.2 - - + +
233C ARG* 3.5 47.9 + - - +
322C ILE* 2.8 34.8 + - + +
323C ASP* 3.8 9.5 + - - +
325C ALA* 1.3 77.4 - - - +
327C ALA* 1.3 53.3 + - - +
329C GLY* 2.7 25.8 + - - -
330C LEU 3.6 12.1 - - - -
332C VAL* 4.4 4.5 - - + +
397C PHE 4.9 0.2 - - - -
398C GLY* 3.0 26.7 + - - -
400C ASP* 2.7 28.0 + - - -
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Residues in contact with ALA 327 (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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323C ASP 2.8 20.9 + - - +
324C ALA* 3.5 11.0 - - - +
325C ALA 3.2 0.2 - - - -
326C HIS* 1.3 77.8 - - - +
328C ALA* 1.3 55.9 + - - +
329C GLY 3.2 2.3 + - - -
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Residues in contact with ALA 328 (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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273C VAL* 3.3 33.9 - - + -
274C PRO* 5.5 1.1 - - + -
277C LYS* 3.4 40.6 - - + +
324C ALA 3.0 6.5 + - - +
325C ALA 3.0 3.3 + - - +
327C ALA* 1.3 75.0 - - - +
329C GLY* 1.3 64.8 + - - +
330C LEU* 3.5 2.8 - - + +
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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