Contacts of the helix formed by residues 320 - 329 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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367A ILE* 5.9 0.9 - - + -
315D LEU* 2.7 26.7 + - + +
318D LYS* 4.7 5.2 - - + +
319D GLY* 1.3 80.0 - - - +
321D THR* 1.3 65.2 + - - +
322D GLU* 3.1 22.4 - - - +
323D LEU* 3.0 42.5 + - + +
324D THR 3.9 1.4 + - - -
353D HIS* 5.0 11.0 - - + -
357D LEU* 3.5 32.5 - - + -
364D TYR* 3.9 42.2 - - + +
371D MET* 6.1 1.3 - - - -
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Residues in contact with THR 321 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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315D LEU 4.8 0.4 - - - -
316D SER* 3.5 37.0 - - - +
319D GLY* 3.8 1.7 - - - -
320D LEU* 1.3 76.4 - - - +
322D GLU* 1.3 66.0 + - - +
324D THR* 2.8 32.4 + - - +
325D ASN* 4.2 5.9 + - - -
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Residues in contact with GLU 322 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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366A PRO 3.7 12.5 - - - +
367A ILE* 4.9 3.9 - - - +
369A LYS* 3.2 42.8 + - - +
319D GLY 5.5 0.5 - - - +
320D LEU* 4.0 22.0 - - - +
321D THR* 1.3 81.7 + - - +
323D LEU* 1.3 81.2 + - + +
325D ASN* 4.5 7.2 + - - +
326D VAL* 3.9 12.1 - - - +
353D HIS* 4.6 4.3 + - - -
364D TYR* 5.7 0.7 + - - -
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Residues in contact with LEU 323 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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315D LEU* 4.5 6.1 - - + -
320D LEU* 3.0 34.8 + - + +
321D THR 3.0 0.8 - - - -
322D GLU* 1.3 95.7 - - + +
324D THR* 1.3 65.5 + - - +
326D VAL* 2.9 10.8 + - + +
327D VAL* 2.9 32.9 + - + +
351D PRO* 3.8 33.0 - - + -
353D HIS* 4.1 27.8 - - + +
354D TYR* 4.3 23.1 - - + -
357D LEU* 6.2 0.2 - - + -
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Residues in contact with THR 324 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189D CYS* 5.1 1.9 - - - -
312D THR* 4.1 29.1 + - + +
315D LEU* 3.8 25.7 - - + +
320D LEU 3.9 0.6 + - - -
321D THR* 2.8 27.6 + - - +
323D LEU* 1.3 75.2 - - - +
325D ASN* 1.3 59.4 + - - +
327D VAL 4.6 0.2 - - - +
328D GLY* 2.7 33.8 + - - -
330D TRP* 3.6 21.5 - - + -
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Residues in contact with ASN 325 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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321D THR 4.2 6.7 + - - -
322D GLU* 5.0 4.7 + - - +
323D LEU 3.2 1.2 + - - -
324D THR* 1.3 81.6 - - - +
326D VAL* 1.3 61.8 + - + +
329D ASN* 2.8 23.9 + - - -
330D TRP* 3.0 48.5 + - + +
331D SER 5.2 1.5 - - - +
332D ASP* 5.5 12.2 + - + +
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Residues in contact with VAL 326 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228D ARG* 5.7 0.2 - - - -
322D GLU 3.9 14.8 - - - +
323D LEU* 2.9 14.6 + - + +
325D ASN* 1.3 75.7 - - + +
327D VAL* 1.3 67.6 + - - +
329D ASN* 3.2 12.5 + - - +
348D THR* 3.8 24.9 - - + +
349D ALA 3.6 28.0 - - - +
350D ILE* 3.7 8.5 - - + +
351D PRO* 4.6 10.3 - - + -
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Residues in contact with VAL 327 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188D ASN* 3.1 21.9 - - - +
189D CYS* 3.8 17.5 - - + -
228D ARG* 3.3 13.9 + - - +
315D LEU* 4.5 6.7 - - + -
323D LEU* 2.9 30.3 + - + +
324D THR 3.9 2.7 - - - +
326D VAL* 1.3 75.2 - - + +
328D GLY* 1.3 60.1 + - - +
350D ILE* 3.0 23.2 - - + +
351D PRO* 5.4 0.7 - - + -
354D TYR* 3.4 57.2 - - + +
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Residues in contact with GLY 328 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189D CYS* 3.5 18.8 - - - +
191D ARG* 5.4 0.5 + - - -
194D ASP* 5.1 1.7 - - - +
228D ARG* 3.9 7.1 + - - -
308D ARG* 3.2 16.3 + - - -
324D THR 2.7 14.6 + - - -
327D VAL* 1.3 72.6 - - - +
329D ASN* 1.3 71.1 + - - +
330D TRP* 3.5 25.1 - - - -
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Residues in contact with ASN 329 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191D ARG* 4.9 8.4 + - - +
222D THR* 5.1 2.6 + - - +
224D THR* 4.5 7.9 + - - +
226D VAL* 3.1 44.7 + - - +
227D SER 3.8 3.8 + - - -
228D ARG* 3.3 36.0 - - + +
308D ARG* 4.3 4.0 + - - -
325D ASN 2.8 14.3 + - - -
326D VAL* 3.2 9.7 + - - +
328D GLY* 1.3 81.2 - - - +
330D TRP* 1.3 65.1 + - - +
331D SER* 4.6 1.7 + - - -
15H T 4.1 4.9 + - - -
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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