Contacts of the helix formed by residues 320 - 333 (chain D) in PDB entry 1UU1
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 LYS 320 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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295B ARG* 5.7 6.9 - - - +
30D PRO* 3.9 28.5 - - + +
31D PHE* 4.5 18.8 - - + -
32D PRO* 5.8 4.7 - - - +
257D PHE* 4.8 2.9 - - - -
319D GLY* 1.3 73.0 - - - -
321D ARG* 1.3 68.4 + - - +
322D GLU* 3.0 8.1 - - + +
323D GLU* 2.7 41.6 + - + +
324D ASN* 2.9 11.6 + - - -
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Residues in contact with ARG 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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257D PHE* 3.7 18.4 - - + -
261D GLU* 3.0 24.2 - - - +
264D ARG* 4.1 12.8 + - - +
320D LYS* 1.3 71.8 - - - +
322D GLU* 1.3 69.6 + - - +
324D ASN* 3.3 4.0 + - - +
325D ASP* 2.7 55.5 + - - +
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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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320D LYS* 3.0 7.5 - - + +
321D ARG* 1.3 92.0 - - - +
323D GLU* 1.3 66.0 + - + +
325D ASP* 3.4 5.1 + - - +
326D MET* 3.2 20.3 + - - +
329D ARG* 5.0 1.9 + - - -
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Residues in contact with GLU 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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21D LYS 4.9 1.7 - - - +
22D THR* 3.7 37.8 + - - +
23D TYR 4.7 2.9 + - - +
24D LEU* 4.1 16.4 - - + +
30D PRO* 5.2 0.9 - - - +
319D GLY* 3.5 7.2 - - - -
320D LYS* 2.7 51.9 + - + +
322D GLU* 1.3 74.6 - - + +
324D ASN* 1.3 64.6 + - - +
326D MET* 3.0 19.1 + - - +
327D ILE* 3.1 17.8 + - - +
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Residues in contact with ASN 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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24D LEU* 5.5 1.7 - - - +
257D PHE* 4.5 0.4 - - - -
261D GLU* 3.0 27.9 + - + +
264D ARG* 4.0 12.1 - - - +
265D MET* 3.1 35.0 - - + +
317D THR 4.7 0.7 - - - +
318D ILE* 3.9 1.1 - - - +
319D GLY 2.8 40.1 + - - +
320D LYS 2.9 21.0 + - - -
321D ARG 3.6 3.6 - - - +
323D GLU* 1.3 75.9 - - - +
325D ASP* 1.3 63.5 + - - +
327D ILE* 2.9 19.4 + - - +
328D LEU* 3.2 14.8 + - - +
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Residues in contact with ASP 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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264D ARG* 2.3 34.4 + - - +
321D ARG* 2.7 52.8 + - - +
322D GLU* 3.6 6.1 - - - +
324D ASN* 1.3 75.8 - - - +
326D MET* 1.3 57.7 + - - +
328D LEU* 3.6 7.6 + - - +
329D ARG* 2.9 49.2 + - - +
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Residues in contact with MET 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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22D THR* 4.8 8.3 - - - -
24D LEU* 6.1 0.4 - - - -
300D LEU* 4.6 2.5 - - + -
303D LYS* 5.2 3.1 - - + -
305D VAL* 3.5 35.7 - - + -
322D GLU 3.2 10.1 + - - +
323D GLU* 3.2 15.5 - - - +
324D ASN 3.0 0.8 - - - -
325D ASP* 1.3 77.2 - - - +
327D ILE* 1.3 70.9 + - + +
329D ARG* 3.5 26.6 - - - +
330D GLU* 2.9 53.9 + - + +
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Residues in contact with ILE 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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24D LEU* 3.9 16.4 - - + -
265D MET* 4.7 8.1 - - - -
269D LEU* 5.1 2.7 - - + -
284D VAL* 6.1 0.7 - - + -
300D LEU* 5.0 7.2 - - + -
305D VAL* 4.5 9.9 - - + -
307D VAL* 4.6 4.3 - - + -
316D ILE* 3.8 40.6 - - + -
323D GLU 3.1 14.7 + - - +
324D ASN* 2.9 13.1 + - - +
326D MET* 1.3 89.2 - - + +
328D LEU* 1.3 72.2 + - + +
330D GLU* 3.2 1.9 + - - +
331D LEU* 2.8 49.4 + - + +
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Residues in contact with LEU 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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264D ARG* 4.5 20.0 - - + +
265D MET* 3.7 34.3 - - + +
268D ALA* 3.5 28.0 - - + -
269D LEU* 3.3 33.9 - - + -
272D MET* 3.3 15.7 - - + +
324D ASN 3.2 6.2 + - - +
325D ASP* 4.0 8.1 - - - +
327D ILE* 1.3 83.6 - - + +
329D ARG* 1.3 58.0 + - + +
331D LEU* 3.4 2.1 + - - -
332D GLU* 2.9 28.6 + - - +
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Residues in contact with ARG 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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272D MET* 5.3 0.2 - - - -
322D GLU 5.0 1.6 + - - -
325D ASP* 2.9 30.5 + - + +
326D MET* 3.5 35.4 + - - +
328D LEU* 1.3 77.5 - - + +
330D GLU* 1.3 67.4 + - - +
332D GLU* 3.2 10.4 - - - +
333D VAL* 3.1 22.5 + - - +
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Residues in contact with GLU 330 (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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296D LEU* 5.3 0.2 - - - +
299D HIS* 3.1 18.6 + - - +
300D LEU* 3.7 22.7 - - + -
303D LYS* 2.9 46.3 + - + +
326D MET* 2.9 44.1 + - + +
327D ILE 3.2 3.6 + - - +
329D ARG* 1.3 81.3 + - - +
331D LEU* 1.3 62.2 - - + +
333D VAL* 2.9 27.7 - - - +
334D PHE* 3.3 8.0 + - - +
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Residues in contact with LEU 331 (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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269D LEU* 3.4 31.6 - - + -
272D MET* 4.7 0.4 - - - -
274D TYR* 2.7 54.1 + - + +
286D VAL* 4.7 8.7 - - + -
288D MET* 5.6 2.2 - - + -
296D LEU* 3.7 35.2 - - + -
300D LEU* 5.4 3.4 - - + -
314D VAL* 6.2 1.3 - - + -
316D ILE* 4.1 17.3 - - + -
327D ILE* 2.8 31.4 + - + +
328D LEU 3.9 3.1 - - - +
330D GLU* 1.3 74.7 - - + +
332D GLU* 1.3 65.5 + - - +
334D PHE* 3.1 7.3 + - - -
335D LYS 3.3 3.3 + - - -
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Residues in contact with GLU 332 (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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272D MET* 3.6 34.5 - - + +
328D LEU 2.9 18.9 + - - +
329D ARG* 3.2 11.7 - - - +
330D GLU 3.1 0.2 - - - -
331D LEU* 1.3 75.5 - - - +
333D VAL* 1.3 59.0 + - + +
334D PHE 3.0 8.4 + - - -
335D LYS 3.6 6.4 + - - -
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Residues in contact with VAL 333 (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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299D HIS* 3.6 24.2 - - + +
329D ARG 3.1 6.8 + - - +
330D GLU* 2.9 29.8 - - - +
332D GLU* 1.3 80.3 - - + +
334D PHE* 1.3 58.7 + - - +
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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