Contacts of the helix formed by residues 309 - 327 (chain Y) in PDB entry 3UBT
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 PRO 309 (chain Y).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144Y ALA* 4.1 13.9 - - + -
149Y VAL* 3.9 25.4 - - + -
151Y GLN* 4.5 1.8 - - - +
153Y ARG* 3.7 26.5 - - - +
284Y GLN* 3.3 31.9 - - + +
307Y ALA 3.6 7.6 - - - +
308Y VAL* 1.3 90.5 - - + +
310Y VAL* 1.3 65.9 + - - +
312Y LEU* 3.2 10.7 + - + +
313Y ALA* 3.0 19.6 + - - +
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Residues in contact with VAL 310 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12Y GLY* 4.2 15.3 - - - +
15Y LEU* 3.9 39.7 - - + -
16Y GLY* 3.5 8.3 - - - +
19Y LYS* 4.4 18.6 - - - +
284Y GLN 3.0 8.2 + - - +
285Y GLY* 3.5 35.0 - - - +
286Y PHE* 4.1 10.5 - - + +
287Y PRO* 5.8 0.9 - - + -
308Y VAL 3.2 4.6 + - - +
309Y PRO* 1.3 70.5 - - - +
311Y ASN* 1.3 57.8 + - - +
313Y ALA* 3.3 4.7 + - - +
314Y TYR* 3.0 23.2 + - - +
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Residues in contact with ASN 311 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19Y LYS* 5.1 7.8 - - - +
147Y TYR 3.2 24.7 + - - +
148Y GLY* 4.0 21.7 - - - +
149Y VAL* 4.1 5.8 - - + +
175Y HIS* 4.5 3.0 + - - -
284Y GLN 4.8 0.6 + - - -
285Y GLY* 5.4 3.4 - - - -
309Y PRO* 3.3 1.2 - - - +
310Y VAL* 1.3 77.3 - - + +
312Y LEU* 1.3 64.7 + - - +
314Y TYR* 3.3 13.5 + - - +
315Y GLU* 3.1 41.7 + - - +
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Residues in contact with LEU 312 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142Y LEU* 4.0 28.3 - - + +
144Y ALA* 4.3 23.3 - - + +
147Y TYR* 4.2 30.1 - - + -
149Y VAL* 4.1 8.6 - - + +
153Y ARG* 5.4 3.4 - - - +
155Y ARG* 5.9 2.5 - - + -
157Y PHE* 3.6 26.7 - - + -
308Y VAL* 4.4 1.8 - - + -
309Y PRO* 3.2 28.8 + - + +
311Y ASN* 1.3 75.8 - - - +
313Y ALA* 1.3 66.4 + - - +
315Y GLU* 3.2 3.0 + - + +
316Y ILE* 3.1 37.1 + - + +
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Residues in contact with ALA 313 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12Y GLY 4.1 2.7 - - - +
13Y LEU* 3.9 38.1 - - + +
16Y GLY* 3.8 15.3 - - - -
17Y PHE* 4.0 4.0 - - + -
308Y VAL* 4.3 5.1 - - + +
309Y PRO 3.0 12.2 + - - +
310Y VAL 3.4 9.6 - - - +
312Y LEU* 1.3 75.3 - - - +
314Y TYR* 1.3 57.9 + - - +
316Y ILE* 3.3 8.7 + - - +
317Y ALA* 2.9 30.1 + - - +
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Residues in contact with TYR 314 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16Y GLY* 3.6 23.5 - - - +
19Y LYS* 3.6 49.0 + - + -
20Y ALA* 3.9 7.9 - - + -
310Y VAL 3.0 13.6 + - - +
311Y ASN* 3.5 20.4 - - - +
312Y LEU 3.2 0.4 - - - -
313Y ALA* 1.3 76.9 - - - +
315Y GLU* 1.3 79.4 + - - +
317Y ALA* 3.2 1.7 + - - +
318Y LYS* 3.0 69.2 + - + +
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Residues in contact with GLU 315 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147Y TYR* 4.1 27.5 - - + -
172Y PRO* 4.0 9.2 - - + +
173Y ILE 5.5 1.0 - - - +
175Y HIS* 3.2 36.4 + - + -
311Y ASN* 3.1 21.6 + - - +
312Y LEU* 3.2 7.6 + - + +
314Y TYR* 1.3 94.3 - - - +
316Y ILE* 1.3 60.5 + - + +
318Y LYS* 3.6 21.7 + - - +
319Y THR* 3.4 24.9 + - - +
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Residues in contact with ILE 316 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13Y LEU* 6.0 0.2 - - + -
107Y LEU* 4.3 21.8 - - + -
140Y ILE* 5.3 1.1 - - + -
142Y LEU* 4.1 12.6 - - + -
157Y PHE* 3.9 38.4 - - + -
159Y ILE* 3.9 26.5 - - + -
169Y TYR* 4.5 2.7 - - - +
172Y PRO* 4.1 7.2 - - + -
308Y VAL* 5.7 0.2 - - + -
312Y LEU* 3.1 33.7 + - + +
313Y ALA* 3.7 9.4 - - - +
315Y GLU* 1.3 74.6 - - - +
317Y ALA* 1.3 65.5 + - - +
319Y THR* 2.6 24.8 + - - -
320Y ILE* 3.2 11.0 + - + +
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Residues in contact with ALA 317 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17Y PHE* 3.5 44.2 - - + -
20Y ALA* 3.7 17.9 - - + -
22Y PHE* 3.6 11.8 - - + -
313Y ALA 2.9 18.3 + - - +
314Y TYR 3.2 5.8 + - - +
316Y ILE* 1.3 75.9 - - - +
318Y LYS* 1.3 62.1 - - - +
320Y ILE* 3.3 3.4 + - - +
321Y LYS* 3.0 18.7 + - - +
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Residues in contact with LYS 318 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20Y ALA* 4.2 7.8 - - + +
314Y TYR* 3.0 63.8 + - + +
315Y GLU* 3.7 23.4 + - - +
316Y ILE 3.2 0.2 - - - -
317Y ALA* 1.3 77.4 - - - +
319Y THR* 1.3 63.2 + - + +
321Y LYS* 3.3 5.7 + - - +
322Y SER* 3.0 25.5 + - - -
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Residues in contact with THR 319 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169Y TYR* 2.8 22.2 + - - -
170Y LEU 3.4 26.4 + - - +
171Y PRO 4.1 0.4 - - - +
172Y PRO* 3.7 24.2 - - + -
315Y GLU 3.4 15.0 - - - +
316Y ILE* 2.6 20.3 + - - -
318Y LYS* 1.3 77.2 - - + +
320Y ILE* 1.3 61.0 + - - +
322Y SER* 3.1 19.2 + - - -
323Y ALA* 3.2 13.9 + - - +
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Residues in contact with ILE 320 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17Y PHE* 4.0 19.5 - - + -
22Y PHE* 4.4 4.0 - - + -
105Y PHE* 3.8 49.1 - - + -
107Y LEU* 5.0 4.0 - - + -
159Y ILE* 4.2 19.7 - - + -
161Y PHE* 4.1 10.1 - - + -
169Y TYR* 4.2 15.5 - - + -
316Y ILE* 3.2 21.6 + - + +
317Y ALA* 3.6 6.3 - - - +
318Y LYS 3.2 0.2 - - - -
319Y THR* 1.3 82.8 + - - +
321Y LYS* 1.3 62.1 + - - +
323Y ALA* 3.3 3.1 + - - +
324Y LEU* 3.1 34.3 + - + +
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Residues in contact with LYS 321 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1Y MET* 5.1 20.4 - - + +
20Y ALA 3.3 26.0 - - - +
21Y GLY* 4.2 17.2 + - - -
22Y PHE* 3.7 23.2 - - + -
317Y ALA 3.0 17.0 + - - +
318Y LYS* 3.3 6.5 + - - +
320Y ILE* 1.3 77.6 - - - +
322Y SER* 1.3 61.4 + - - +
324Y LEU* 3.5 5.0 + - - +
325Y GLU* 3.1 60.2 + - + +
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Residues in contact with SER 322 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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318Y LYS 3.0 12.8 + - - -
319Y THR* 3.1 14.7 + - - -
321Y LYS* 1.3 74.6 - - - +
323Y ALA* 1.3 64.1 + - - +
325Y GLU* 3.4 9.1 + - - +
326Y ILE* 2.9 45.6 + - - +
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Residues in contact with ALA 323 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161Y PHE* 4.7 2.0 - - + -
167Y ILE* 3.8 22.9 - - + +
168Y ASN 3.9 15.7 - - - +
169Y TYR* 4.4 12.6 - - + -
170Y LEU 5.3 1.1 - - - +
319Y THR 3.2 15.1 + - - +
320Y ILE* 3.6 5.2 - - - +
321Y LYS 3.3 0.2 - - - -
322Y SER* 1.3 82.8 + - - +
324Y LEU* 1.3 57.6 + - - +
326Y ILE* 3.9 5.1 - - - +
327Y CYS* 3.1 34.7 + - - +
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Residues in contact with LEU 324 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1Y MET* 3.8 37.9 - - + +
22Y PHE* 5.1 1.1 - - + -
104Y ILE* 3.6 27.8 - - + -
105Y PHE* 4.0 24.7 - - + -
161Y PHE* 3.7 23.1 - - + -
167Y ILE* 4.1 15.0 - - + -
320Y ILE* 3.1 23.3 + - + +
321Y LYS* 3.9 6.5 - - - +
322Y SER 3.3 0.2 - - - -
323Y ALA* 1.3 76.8 - - - +
325Y GLU* 1.3 58.3 + - - +
328Y LYS* 3.0 40.5 + - + +
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Residues in contact with GLU 325 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1Y MET* 5.5 7.2 - - + -
321Y LYS* 3.1 53.6 + - + +
322Y SER* 3.9 7.0 - - - +
323Y ALA 3.3 0.2 - - - -
324Y LEU* 1.3 79.1 - - + +
326Y ILE* 1.3 63.7 + - + +
328Y LYS 3.9 14.1 + - - -
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Residues in contact with ILE 326 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322Y SER* 2.9 35.7 + - - +
323Y ALA* 3.9 4.9 - - - +
325Y GLU* 1.3 81.8 - - + +
327Y CYS* 1.3 69.1 + - - +
328Y LYS 3.3 2.1 + - - -
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Residues in contact with CYS 327 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165Y LEU 4.6 6.7 - - - +
166Y ASN 4.2 8.3 - - - +
167Y ILE* 3.6 18.2 - - + -
168Y ASN* 3.6 37.2 - - - -
323Y ALA* 3.1 20.2 + - - +
324Y LEU 3.8 0.2 - - - -
326Y ILE* 1.3 87.3 - - - +
328Y LYS* 1.3 67.3 + - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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