Contacts of the helix formed by residues 320 - 329 (chain A) in PDB entry 1M6X
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 LEU 320 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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315A LEU* 2.9 23.0 + - + +
318A LYS* 4.3 7.9 - - + -
319A GLY* 1.3 80.5 - - - +
321A THR* 1.3 66.4 + - - +
322A GLU* 3.0 22.7 - - - +
323A LEU* 3.0 42.5 + - + +
324A THR 3.8 1.9 + - - -
353A HIS* 4.9 7.9 - - + -
357A LEU* 3.7 29.6 - - + -
364A TYR* 3.6 49.1 - - + +
371A MET* 5.6 2.5 - - - -
334D ARG* 5.5 0.9 - - - +
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Residues in contact with THR 321 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315A LEU 3.8 0.6 + - - -
316A SER* 3.7 33.9 - - - +
319A GLY* 3.8 1.7 - - - -
320A LEU* 1.3 76.6 - - - +
322A GLU* 1.3 66.0 + - - +
324A THR* 2.9 29.4 + - - +
332D ASP* 3.3 27.9 + - + +
334D ARG* 3.2 30.7 + - - +
335D ALA* 4.1 12.3 - - + -
348D THR* 6.4 1.8 - - + -
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Residues in contact with GLU 322 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320A LEU* 4.0 18.9 - - - +
321A THR* 1.3 80.9 + - - +
323A LEU* 1.3 75.0 + - + +
325A ASN* 4.5 4.0 + - - +
326A VAL* 3.9 12.0 - - - +
353A HIS* 4.3 16.6 + - - -
364A TYR* 5.6 1.4 + - - -
369A LYS* 5.7 2.4 + - - +
334D ARG* 3.3 48.9 + - - +
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Residues in contact with LEU 323 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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315A LEU* 4.3 7.2 - - + -
320A LEU* 3.0 31.2 + - + +
321A THR 3.0 0.8 - - - -
322A GLU* 1.3 94.1 - - + +
324A THR* 1.3 64.9 + - - +
325A ASN 3.4 0.2 - - - -
326A VAL* 3.1 7.2 + - + +
327A VAL* 2.9 34.1 + - + +
351A PRO* 3.5 34.8 - - + -
353A HIS* 3.8 31.4 - - + +
354A TYR* 4.3 22.7 - - + -
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Residues in contact with THR 324 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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312A THR* 4.5 13.8 + - + +
315A LEU* 3.7 28.0 - - + +
316A SER* 4.9 0.5 + - - -
320A LEU 3.8 0.8 + - - -
321A THR* 2.9 29.3 + - - +
323A LEU* 1.3 76.5 - - - +
325A ASN* 1.3 58.6 + - - +
328A GLY 2.7 29.1 + - - -
330A TRP* 3.4 26.9 - - + -
335D ALA* 4.7 10.4 - - + +
339D ALA* 3.9 17.0 - - + -
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Residues in contact with ASN 325 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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321A THR 4.2 0.8 + - - -
322A GLU 4.5 3.2 + - - +
323A LEU 3.4 0.8 - - - -
324A THR* 1.3 77.9 - - - +
326A VAL* 1.3 61.8 + - + +
329A ASN* 2.9 23.6 + - - -
330A TRP* 3.0 30.5 + - - +
331A SER 4.3 2.6 - - - +
332A ASP* 3.3 31.2 + - + +
333D LYS 4.9 1.0 + - - -
334D ARG 2.9 30.7 + - - -
335D ALA* 3.4 1.8 - - - +
336D SER* 2.9 44.8 + - - +
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Residues in contact with VAL 326 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228A ARG* 5.6 0.5 + - - -
322A GLU 3.9 14.6 - - - +
323A LEU* 3.1 12.3 + - + +
325A ASN* 1.3 74.9 - - + +
327A VAL* 1.3 67.5 + - - +
329A ASN* 3.2 13.6 + - - +
332A ASP* 6.0 0.4 - - - +
348A THR* 3.7 31.0 - - + -
349A ALA* 4.0 20.9 - - - +
350A ILE* 4.3 5.4 - - - +
351A PRO* 4.3 16.8 - - + -
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Residues in contact with VAL 327 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188A ASN 3.3 15.2 - - - +
189A CYS* 3.8 16.8 - - + -
228A ARG* 3.4 14.2 + - - -
315A LEU* 4.2 9.9 - - + -
323A LEU* 2.9 31.1 + - + +
324A THR 4.0 1.1 - - - +
326A VAL* 1.3 77.5 - - + +
328A GLY* 1.3 61.0 + - - +
329A ASN 3.5 0.2 + - - -
350A ILE* 3.6 28.5 - - + -
351A PRO* 5.2 0.9 - - + -
354A TYR* 3.5 53.2 - - + +
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Residues in contact with GLY 328 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189A CYS* 3.7 19.6 - - - +
228A ARG* 4.3 2.8 + - - -
308A ARG* 2.5 29.1 + - - -
324A THR 2.7 13.9 + - - -
327A VAL* 1.3 74.2 - - - +
329A ASN* 1.3 64.1 + - - +
330A TRP* 3.4 22.9 - - - -
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Residues in contact with ASN 329 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191A ARG* 4.8 10.3 + - - +
194A ASP* 6.1 0.4 - - - +
222A THR* 5.1 2.2 + - - +
224A THR* 4.5 7.7 + - - +
226A VAL* 3.1 45.1 + - - +
227A SER 3.9 3.0 + - - -
228A ARG* 3.3 37.5 - - + +
308A ARG* 4.1 3.6 + - - -
325A ASN 2.9 12.0 + - - -
326A VAL 3.2 10.3 + - - +
328A GLY* 1.3 83.0 - - - +
330A TRP* 1.3 64.3 + - - +
15I T 4.2 4.7 + - - -
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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