Contacts of the helix formed by residues 310 - 324 (chain D) in PDB entry 1UMD
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 310 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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366A GLU* 2.6 34.5 + - - +
216D GLU* 4.2 5.8 - - - -
305D LYS 3.8 22.7 - - - +
306D LEU* 4.9 8.1 - - + +
308D LEU 3.8 4.7 - - - +
309D PRO* 1.3 75.2 - - - +
311D VAL* 1.3 65.0 + - - +
312D THR* 3.6 4.5 + - - -
313D ARG* 3.0 21.4 + - - +
314D ILE* 3.0 25.9 + - - +
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Residues in contact with VAL 311 (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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216D GLU* 3.9 32.8 - - + +
219D GLN* 4.2 15.7 - - + -
220D ALA* 4.0 19.5 - - - +
223D GLU* 4.2 10.5 - - + +
310D THR* 1.3 74.4 - - - +
312D THR* 1.3 58.5 + - - +
314D ILE* 3.3 4.0 + - - +
315D LEU* 2.9 46.9 + - + +
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Residues in contact with THR 312 (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 GLU* 3.8 24.7 - - + +
310D THR* 3.6 8.4 + - - -
311D VAL* 1.3 81.1 - - - +
313D ARG* 1.3 57.6 + - - +
315D LEU* 3.3 9.0 + - - +
316D ASN* 2.9 54.0 + - - +
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Residues in contact with ARG 313 (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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362A LEU* 4.4 26.5 - - + +
363A LEU* 5.4 3.4 - - - +
366A GLU* 3.8 17.6 + - - +
292D VAL* 3.9 19.8 - - + +
293D THR 3.1 28.9 + - - +
295D PHE* 3.5 34.4 - - - -
306D LEU 4.2 5.5 + - - -
307D TYR 2.9 28.3 + - - -
309D PRO* 3.6 19.8 - - - +
310D THR* 3.0 25.1 + - - +
312D THR* 1.3 76.5 - - - +
314D ILE* 1.3 62.6 + - - +
316D ASN* 3.5 10.9 + - - +
317D ALA* 3.3 20.1 + - - +
320D ARG* 5.1 1.7 + - - -
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Residues in contact with ILE 314 (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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207D LEU* 4.6 15.0 - - + -
213D VAL* 5.0 0.4 - - + +
216D GLU* 3.7 32.3 - - + -
217D VAL* 3.8 26.7 - - + +
220D ALA* 3.7 18.2 - - + -
258D VAL* 4.8 2.6 - - + +
260D VAL* 4.0 31.4 - - + -
292D VAL* 4.2 14.8 - - + -
309D PRO* 4.4 5.2 - - + -
310D THR 3.0 10.4 + - - +
311D VAL* 3.6 6.5 - - - +
313D ARG* 1.3 77.5 - - - +
315D LEU* 1.3 58.2 + - - +
317D ALA* 3.2 5.5 + - - +
318D ALA* 2.9 25.2 + - + +
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Residues in contact with LEU 315 (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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220D ALA* 3.5 32.8 - - + +
223D GLU* 3.8 29.4 - - + -
224D LEU* 3.7 26.7 - - + +
311D VAL* 2.9 27.6 + - + +
312D THR* 3.7 7.9 - - - +
314D ILE* 1.3 76.0 - - - +
316D ASN* 1.3 60.9 + - - +
318D ALA* 3.1 4.3 + - - +
319D LYS* 2.9 30.1 + - - +
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Residues in contact with ASN 316 (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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362A LEU* 6.1 1.7 - - + +
365A GLU* 4.8 16.6 + - - +
366A GLU* 4.9 11.1 - - - +
312D THR* 2.9 41.0 + - - +
313D ARG* 3.7 9.9 - - + +
314D ILE 3.3 0.2 - - - -
315D LEU* 1.3 78.0 - - - +
317D ALA* 1.3 61.6 + - - +
319D LYS* 3.5 11.1 + - - +
320D ARG* 3.2 33.5 + - - +
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Residues in contact with ALA 317 (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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258D VAL* 3.9 7.7 - - + +
290D ILE* 3.5 24.1 - - + +
292D VAL* 3.4 33.4 - - + -
313D ARG 3.3 4.4 + - - +
314D ILE 3.2 6.6 + - - +
315D LEU 3.2 0.4 - - - -
316D ASN* 1.3 78.0 - - - +
318D ALA* 1.3 64.0 + - - +
320D ARG* 3.3 20.4 + - - +
321D ALA* 3.0 19.4 + - - +
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Residues in contact with ALA 318 (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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205D LEU* 3.6 27.6 - - + -
207D LEU* 5.2 3.8 - - + -
220D ALA* 6.5 0.2 - - + -
224D LEU* 4.2 20.0 - - + -
258D VAL* 4.0 7.4 - - + +
314D ILE* 2.9 14.5 + - + +
315D LEU* 3.1 12.5 + - - +
317D ALA* 1.3 78.2 - - - +
319D LYS* 1.3 56.8 - - - +
321D ALA* 3.2 3.3 + - - +
322D LEU* 2.8 35.5 + - + +
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Residues in contact with LYS 319 (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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224D LEU* 5.7 0.6 - - - +
315D LEU 2.9 16.5 + - - +
316D ASN* 3.7 10.5 - - - +
318D ALA* 1.3 76.2 - - - +
320D ARG* 1.3 56.2 + - - +
322D LEU* 4.3 8.3 - - - -
323D ASP* 2.7 64.0 + - - +
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Residues in contact with ARG 320 (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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362A LEU* 4.1 26.7 - - - +
365A GLU* 4.9 1.8 + - - -
279B GLU* 5.0 3.8 + - - +
290D ILE* 3.7 30.6 - - + +
313D ARG 5.1 1.4 + - - -
316D ASN* 3.2 16.2 + - - +
317D ALA* 3.3 34.4 - - - +
319D LYS* 1.3 81.3 - - - +
321D ALA* 1.3 61.1 + - - +
323D ASP* 4.0 2.9 - - - +
324D TYR* 3.2 26.9 + - + +
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Residues in contact with ALA 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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205D LEU* 5.0 4.9 - - + -
256D ARG* 2.8 43.2 + - + -
257D VAL 4.9 3.6 - - - +
258D VAL* 4.2 13.9 - - + -
287D ALA* 3.3 17.8 - - + +
288D PRO* 4.9 1.1 - - - +
290D ILE* 4.0 14.8 - - + -
317D ALA 3.0 13.0 + - - +
318D ALA 3.6 7.0 - - - +
320D ARG* 1.3 76.4 - - - +
322D LEU* 1.3 59.3 + - - +
324D TYR* 3.5 2.6 + - - -
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Residues in contact with LEU 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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204D ASP* 3.9 25.4 - - + +
205D LEU* 4.4 11.7 - - + -
224D LEU* 4.2 15.5 - - + -
229D VAL* 3.9 38.8 - - + -
256D ARG* 3.2 24.5 + - - +
318D ALA* 2.8 26.8 + - + +
319D LYS* 3.7 7.9 - - - +
321D ALA* 1.3 78.5 - - - +
323D ASP* 1.3 65.0 + - - +
324D TYR* 3.2 1.0 - - - +
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Residues in contact with ASP 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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319D LYS* 2.7 56.0 + - - +
320D ARG* 4.0 3.8 - - - +
322D LEU* 1.3 77.8 - - - +
324D TYR* 1.3 63.2 + - - +
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Residues in contact with TYR 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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282B LEU* 3.9 12.2 - - + +
283B ASP* 3.5 37.6 + - - +
256D ARG* 3.3 16.5 + - - -
286D LEU 3.4 22.4 - - - +
287D ALA* 3.7 8.3 - - + -
288D PRO* 3.4 32.3 - - + -
320D ARG* 3.2 19.8 + - + +
321D ALA 3.6 9.9 - - - +
322D LEU 3.2 2.5 - - - +
323D ASP* 1.3 82.4 - - - +
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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