Contacts of the helix formed by residues 310 - 323 (chain B) in PDB entry 1MDU
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 GLY 310 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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220B TYR* 5.7 0.2 - - - -
221B VAL* 3.6 19.5 - - - +
222B ALA 5.6 0.2 - - - -
223B LEU* 5.6 0.7 + - - +
308B TYR 3.4 0.4 + - - -
309B PRO* 1.3 71.4 - - - +
311B ILE* 1.3 62.9 + - - +
312B ALA 3.4 2.5 - - - -
313B ASP* 3.4 18.5 + - - +
314B ARG* 3.1 23.9 + - - +
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Residues in contact with ILE 311 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155B LEU* 5.7 1.1 - - + -
221B VAL* 3.5 25.5 - - + +
263B LEU* 4.9 9.2 - - + -
264B PHE* 3.5 29.4 - - + -
276B ILE* 4.5 8.1 - - + -
301B MET* 3.4 24.5 - - + -
305B THR 5.1 1.6 - - - +
306B THR* 3.2 34.3 - - + +
308B TYR* 3.2 22.8 + - + +
309B PRO 3.3 2.4 + - - -
310B GLY* 1.3 75.9 - - - +
312B ALA* 1.3 68.9 + - + +
314B ARG* 3.4 1.0 + - - +
315B MET* 3.0 29.7 + - + +
337B ARG* 4.4 4.3 - - - +
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Residues in contact with ALA 312 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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301B MET* 3.6 13.9 - - + -
310B GLY 3.4 0.8 - - - +
311B ILE* 1.3 80.0 - - + +
313B ASP* 1.3 70.1 + - - +
315B MET* 3.4 2.1 + - - +
316B GLN* 3.0 24.5 + - - +
331B ILE* 3.8 24.3 - - + +
333B ALA* 4.5 18.6 - - + -
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Residues in contact with ASP 313 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223B LEU* 3.7 19.3 - - + +
310B GLY* 3.4 19.0 + - - +
312B ALA* 1.3 79.5 - - - +
314B ARG* 1.3 58.7 + - - +
316B GLN* 3.4 7.3 + - - +
317B LYS* 3.0 28.4 + - - +
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Residues in contact with ARG 314 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221B VAL* 3.6 18.3 - - + +
222B ALA 3.0 17.9 + - - +
223B LEU* 3.3 31.9 + - + +
225B PHE* 4.8 8.4 - - - +
261B GLU* 2.9 42.0 + - - -
264B PHE* 3.5 36.5 - - + +
265B GLN* 4.9 2.2 - - - +
277B HIS* 6.0 0.2 + - - -
310B GLY 3.1 15.8 + - - +
311B ILE 3.7 2.7 - - - +
313B ASP* 1.3 77.2 - - - +
315B MET* 1.3 65.9 + - - +
317B LYS* 3.2 3.7 + - - +
318B GLU* 2.9 58.7 + - - +
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Residues in contact with MET 315 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155B LEU* 3.4 23.1 - - + -
264B PHE* 4.1 9.6 - - + -
276B ILE* 2.9 40.2 - - + +
277B HIS* 3.8 31.2 - - - -
280B THR* 4.4 6.5 - - + +
299B ASN* 5.4 3.1 - - + +
301B MET* 4.1 14.6 - - + -
311B ILE* 3.0 15.4 + - + +
312B ALA 3.8 3.4 - - - +
314B ARG* 1.3 76.4 - - - +
316B GLN* 1.3 63.7 + - - +
318B GLU* 3.3 1.6 + - - +
319B ILE* 3.0 37.4 + - + +
331B ILE* 4.0 19.1 - - + -
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Residues in contact with GLN 316 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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312B ALA 3.0 17.6 + - - +
313B ASP* 3.4 9.2 - - - +
315B MET* 1.3 77.1 - - - +
317B LYS* 1.3 58.9 + - - +
319B ILE* 4.1 1.4 - - - +
320B THR* 2.5 43.1 + - - -
329B ILE* 2.7 45.4 + - + +
330B LYS* 5.0 0.4 - - - -
331B ILE* 3.7 23.7 - - + +
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Residues in contact with LYS 317 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223B LEU* 3.1 42.7 + - + +
224B ASP* 3.4 27.1 + - - +
313B ASP 3.0 16.8 + - - +
314B ARG* 3.6 7.9 - - - +
316B GLN* 1.3 81.1 + - - +
318B GLU* 1.3 67.6 + - - +
320B THR* 3.4 7.8 + - - -
321B ALA* 3.0 26.7 + - + +
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Residues in contact with GLU 318 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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264B PHE* 4.4 2.7 - - + -
277B HIS* 3.6 44.8 + - + +
314B ARG* 2.9 58.9 + - + +
315B MET 4.0 1.3 - - - +
317B LYS* 1.3 86.6 + - + +
319B ILE* 1.3 65.3 + - - +
321B ALA* 3.4 10.6 + - - +
322B LEU* 3.3 27.4 + - - +
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Residues in contact with ILE 319 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277B HIS* 3.4 33.7 - - - +
280B THR* 4.0 20.9 - - + -
281B TYR* 4.4 10.5 - - + +
284B ILE* 5.1 2.7 - - + -
296B TYR* 3.8 33.4 - - + -
299B ASN* 5.0 2.7 - - - +
315B MET* 3.0 32.2 + - + +
318B GLU* 1.3 73.5 - - - +
320B THR* 1.3 58.2 + - - +
322B LEU* 2.9 5.6 + - + +
323B ALA* 2.7 33.1 + - - +
329B ILE* 3.9 19.1 - - + -
331B ILE* 4.9 6.1 - - + -
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Residues in contact with THR 320 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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316B GLN* 2.5 42.4 + - - -
317B LYS* 3.4 7.4 - - - -
318B GLU 3.2 0.2 - - - -
319B ILE* 1.3 78.2 - - - +
321B ALA* 1.3 63.7 + - - +
322B LEU 3.1 1.0 + - - -
323B ALA* 3.5 14.2 + - - +
324B PRO 5.3 1.0 - - - +
325B SER* 5.9 2.0 - - - -
329B ILE* 3.4 18.1 - - + +
404B CA 4.7 15.3 - - - -
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Residues in contact with ALA 321 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317B LYS* 3.0 14.6 + - + +
318B GLU* 3.7 15.7 - - - +
319B ILE 3.2 0.6 - - - -
320B THR* 1.3 75.9 - - - +
322B LEU* 1.3 64.2 + - + +
323B ALA 4.6 1.8 - - - +
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Residues in contact with LEU 322 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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277B HIS* 4.3 20.2 - - + +
278B GLU* 4.4 14.4 - - + -
281B TYR* 3.6 61.5 + - + -
318B GLU 3.3 14.5 + - - +
319B ILE* 2.9 8.7 + - - +
321B ALA* 1.3 82.6 - - + +
323B ALA* 1.3 64.7 + - - +
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Residues in contact with ALA 323 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281B TYR* 4.4 0.6 - - - -
296B TYR* 3.6 25.1 - - + -
319B ILE 2.7 19.3 + - - +
320B THR 3.5 9.5 + - - +
321B ALA 4.6 1.7 - - - +
322B LEU* 1.3 78.7 - - - +
324B PRO* 1.3 80.3 - - + +
325B SER* 3.6 1.7 + - - -
327B MET* 4.2 2.2 - - + -
329B ILE* 3.6 22.7 - - + -
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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