Contacts of the helix formed by residues 310 - 324 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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216B GLU* 4.3 4.9 - - - -
305B LYS 3.7 23.6 - - - +
306B LEU* 5.2 5.6 - - + +
308B LEU 3.7 5.2 - - - +
309B PRO* 1.3 73.2 - - - +
311B VAL* 1.3 64.6 + - - +
312B THR* 3.6 5.8 + - - -
313B ARG* 3.0 22.3 + - - +
314B ILE* 3.1 25.4 + - - +
366C GLU* 2.8 28.5 + - - +
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Residues in contact with VAL 311 (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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216B GLU* 3.8 32.3 - - + +
219B GLN* 3.3 33.9 - - - +
220B ALA* 4.0 16.6 - - - +
223B GLU* 3.5 23.1 - - - +
310B THR* 1.3 73.9 - - - +
312B THR* 1.3 58.0 + - - +
314B ILE* 3.3 4.5 + - - +
315B LEU* 2.9 42.9 + - + +
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Residues in contact with THR 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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310B THR* 3.1 9.9 + - - -
311B VAL* 1.3 80.4 - - - +
313B ARG* 1.3 59.2 + - - +
315B LEU* 3.1 10.8 + - - +
316B ASN* 2.8 47.8 + - - +
366C GLU* 3.9 21.3 - - + +
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Residues in contact with ARG 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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292B VAL* 3.9 22.5 - - + +
293B THR 3.0 30.1 + - - +
295B PHE* 3.7 28.4 - - - -
306B LEU 4.6 4.0 + - - -
307B TYR 3.0 27.7 + - - -
308B LEU 4.1 0.2 - - - -
309B PRO* 3.4 22.2 - - - +
310B THR* 3.0 24.4 + - - +
312B THR* 1.3 76.0 - - - +
314B ILE* 1.3 61.6 + - - +
316B ASN* 3.4 11.1 + - + +
317B ALA* 3.2 20.8 + - - +
320B ARG* 4.8 1.2 + - - -
362C LEU* 4.4 28.1 - - + +
363C LEU* 5.2 1.3 - - - +
366C GLU* 3.4 20.6 + - - +
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Residues in contact with ILE 314 (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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207B LEU* 4.5 15.9 - - + -
213B VAL* 5.1 0.4 - - + +
216B GLU* 3.8 26.7 - - + -
217B VAL* 3.8 26.9 - - + +
220B ALA* 3.8 18.4 - - + -
258B VAL* 4.9 1.9 - - + +
260B VAL* 4.0 31.2 - - + -
292B VAL* 4.2 15.3 - - + -
309B PRO* 4.6 4.9 - - + -
310B THR 3.1 14.4 + - - +
311B VAL 3.6 5.6 - - - +
313B ARG* 1.3 76.1 - - - +
315B LEU* 1.3 57.8 + - - +
317B ALA* 3.2 4.2 + - - +
318B ALA* 2.9 26.6 + - + +
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Residues in contact with LEU 315 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220B ALA* 3.7 30.3 - - + +
223B GLU* 3.3 29.4 - - + +
224B LEU* 3.9 24.9 - - + +
311B VAL* 2.9 35.6 + - + +
312B THR* 3.6 8.5 - - - +
314B ILE* 1.3 74.5 - - - +
316B ASN* 1.3 61.8 + - - +
318B ALA* 3.3 5.2 + - + +
319B LYS* 2.9 28.9 + - - +
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Residues in contact with ASN 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 THR* 2.8 39.8 + - - +
313B ARG* 3.7 9.5 - - - +
314B ILE 3.3 0.2 - - - -
315B LEU* 1.3 77.6 - - - +
317B ALA* 1.3 62.1 + - - +
319B LYS* 3.4 12.0 + - - +
320B ARG* 3.1 46.4 + - - +
362C LEU* 6.3 0.2 - - - +
365C GLU* 4.7 14.1 + - - +
366C GLU* 5.0 4.8 + - - +
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Residues in contact with ALA 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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258B VAL* 3.8 8.9 - - + +
290B ILE* 3.6 21.0 - - + +
292B VAL* 3.3 33.4 - - + -
313B ARG 3.2 4.8 + - - +
314B ILE 3.5 7.0 - - - +
315B LEU 3.2 0.4 - - - -
316B ASN* 1.3 77.3 - - - +
318B ALA* 1.3 65.1 + - - +
320B ARG* 3.2 21.0 + - - +
321B ALA* 3.0 20.4 + - - +
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Residues in contact with ALA 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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205B LEU* 3.6 27.8 - - + -
207B LEU* 5.3 3.1 - - + -
224B LEU* 4.2 21.1 - - + -
258B VAL* 4.0 6.9 - - + +
314B ILE* 2.9 14.7 + - + +
315B LEU* 3.3 12.5 + - + +
317B ALA* 1.3 75.6 - - - +
319B LYS* 1.3 57.7 + - - +
321B ALA* 3.3 2.4 + - - +
322B LEU* 2.8 37.0 + - + +
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Residues in contact with LYS 319 (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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224B LEU* 5.9 0.4 - - - +
315B LEU 2.9 17.2 + - - +
316B ASN* 3.5 12.3 - - - +
317B ALA 3.2 0.2 - - - -
318B ALA* 1.3 74.5 - - - +
320B ARG* 1.3 61.1 + - + +
322B LEU* 4.4 7.2 - - - -
323B ASP* 2.8 63.0 + - - +
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Residues in contact with ARG 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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288B PRO* 5.7 0.2 - - - +
290B ILE* 3.5 20.8 - - + +
313B ARG 4.8 1.2 + - - -
316B ASN* 3.1 30.4 + - - +
317B ALA* 3.2 42.1 + - - +
319B LYS* 1.3 76.3 - - + +
321B ALA* 1.3 62.2 + - - +
323B ASP* 3.9 3.1 - - - +
324B TYR* 3.1 26.9 + - - +
362C LEU* 3.2 33.2 - - - +
365C GLU* 4.0 10.7 + - - -
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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
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205B LEU* 4.0 22.2 - - + -
256B ARG* 3.0 33.9 + - + -
257B VAL 4.9 3.6 - - - +
258B VAL* 4.1 6.7 - - + -
287B ALA* 3.3 18.8 - - + +
288B PRO* 5.0 0.9 - - - +
290B ILE* 3.7 14.1 - - + +
317B ALA 3.0 11.3 + - - +
318B ALA 3.6 7.6 - - - +
320B ARG* 1.3 80.3 - - - +
322B LEU* 1.3 57.0 + - - +
324B TYR 3.6 1.6 + - - -
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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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204B ASP* 3.7 28.0 - - + +
205B LEU* 4.3 15.5 - - + -
224B LEU* 4.5 10.1 - - + -
229B VAL* 3.8 37.5 - - + -
256B ARG* 3.4 23.8 + - + +
318B ALA 2.8 26.4 + - - +
319B LYS* 3.8 5.8 - - - +
321B ALA* 1.3 78.0 - - - +
323B ASP* 1.3 63.9 + - - +
324B TYR* 4.3 0.5 - - - +
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Residues in contact with ASP 323 (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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319B LYS* 2.8 59.0 + - - +
320B ARG* 3.9 3.6 - - - +
322B LEU* 1.3 77.9 - - - +
324B TYR* 1.3 66.2 + - - +
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Residues in contact with TYR 324 (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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256B ARG* 3.5 15.4 + - - -
286B LEU 3.4 22.6 - - - +
287B ALA* 3.7 18.4 - - + -
288B PRO* 3.3 32.5 - - + -
320B ARG 3.1 17.5 + - - +
322B LEU 3.3 1.9 - - - +
323B ASP* 1.3 83.4 - - - +
282D LEU* 4.0 12.1 - - + +
283D ASP* 3.5 38.3 + - - +
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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