Contacts of the helix formed by residues 288 - 301 (chain B) in PDB entry 3PII
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 288 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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101B GLY* 3.4 22.0 + - - -
103B GLU* 3.4 27.7 + - - +
104B THR* 4.6 5.3 - - - +
155B LYS* 5.0 0.4 + - - -
287B GLY* 1.3 75.6 - - - +
289B ARG* 1.3 65.6 + - + +
290B LYS* 2.8 38.6 - - + +
291B ASP* 2.8 28.2 + - - +
292B LEU* 3.0 20.8 + - - +
99D LEU* 4.5 8.5 - - + +
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Residues in contact with ARG 289 (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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86B PRO* 6.0 0.9 - - + -
88B LEU* 5.6 3.5 - - + +
98B CYS 5.9 0.8 + - - -
103B GLU* 2.7 36.0 + - - +
129B ASP* 3.5 30.2 + - - +
130B TYR* 3.4 50.8 + - + +
131B VAL 5.4 0.7 - - - -
132B VAL* 4.1 24.5 - - + +
287B GLY 3.9 0.4 + - - -
288B THR* 1.3 73.5 - - + +
290B LYS* 1.3 56.6 + - - +
292B LEU* 3.3 4.9 + - - +
293B GLN* 3.1 32.0 + - - +
93D GLY 5.1 6.4 + - - -
94D HIS* 5.7 0.4 - - - -
99D LEU* 4.0 35.0 - - + +
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Residues in contact with LYS 290 (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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163A LYS* 4.7 6.3 - - - +
166A GLU* 5.7 2.0 - - - -
288B THR* 2.8 20.3 - - + +
289B ARG* 1.3 69.2 - - - +
291B ASP* 1.3 65.2 + - - +
292B LEU 3.1 1.6 - - - -
293B GLN* 3.0 18.7 + - - +
294B GLU* 2.6 68.4 + - - +
96D ASP* 4.7 27.3 + - - +
99D LEU* 3.8 37.6 - - + +
100D SER* 4.4 7.9 - - - +
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Residues in contact with ASP 291 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151B VAL* 3.6 6.7 - - + -
154B TYR* 3.7 6.1 - - + -
155B LYS* 2.6 43.1 + - + -
158B LYS* 2.9 25.5 + - - +
287B GLY* 3.5 8.4 - - - -
288B THR* 2.8 37.6 + - - +
290B LYS* 1.3 76.4 - - - +
292B LEU* 1.3 56.9 + - - +
294B GLU* 3.4 10.5 + - - +
295B ALA* 2.8 27.4 + - - +
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Residues in contact with LEU 292 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86B PRO* 4.0 13.7 - - + -
132B VAL* 3.8 15.5 - - + -
146B ILE* 3.6 25.8 - - + +
147B PHE* 3.5 38.1 - - + +
151B VAL* 3.1 25.5 - - + +
287B GLY 5.5 0.7 - - - +
288B THR 3.0 9.7 + - - +
289B ARG* 3.5 10.1 - - - +
291B ASP* 1.3 74.6 - - - +
293B GLN* 1.3 62.0 + - - +
295B ALA* 4.0 0.2 - - - -
296B LEU* 2.7 54.1 + - + +
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Residues in contact with GLN 293 (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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132B VAL* 4.1 18.0 - - + +
133B LYS 5.4 4.7 + - - +
135B PRO* 5.6 0.5 - - - +
289B ARG* 3.1 15.4 + - - +
290B LYS* 3.0 19.6 + - + +
292B LEU* 1.3 77.2 - - - +
294B GLU* 1.3 57.5 + - + +
296B LEU* 3.3 9.5 + - - +
297B GLN* 3.0 28.8 + - - +
94D HIS 4.6 3.0 + - - +
96D ASP* 3.7 22.6 + - - -
99D LEU* 3.4 25.6 - - - +
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Residues in contact with GLU 294 (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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163A LYS* 3.1 23.7 + - - -
154B TYR* 2.8 26.3 + - - +
158B LYS* 2.8 21.7 + - - -
290B LYS* 2.6 55.7 + - - +
291B ASP 3.4 5.2 - - - +
293B GLN* 1.3 72.3 - - - +
295B ALA* 1.3 67.0 + - - +
297B GLN* 3.4 13.1 + - - +
298B PHE* 3.0 24.8 + - + -
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Residues in contact with ALA 295 (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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146B ILE* 4.0 5.8 - - + +
151B VAL* 3.9 30.1 - - + +
154B TYR* 4.0 10.1 - - + -
183B TYR* 2.6 38.9 + - + +
291B ASP 2.8 15.1 + - - +
292B LEU 3.1 7.8 + - - +
294B GLU* 1.3 79.0 - - - +
296B LEU* 1.3 62.8 + - - +
298B PHE* 3.4 8.3 + - - +
299B ALA* 3.7 1.9 + - - +
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Residues in contact with LEU 296 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132B VAL* 3.5 29.6 - - + -
133B LYS 3.8 11.0 - - - +
134B ILE* 4.9 1.3 - - - -
135B PRO* 4.1 17.2 - - + +
138B LEU* 3.8 28.0 - - + +
143B ALA* 4.3 4.5 - - + -
146B ILE* 3.8 22.0 - - + -
147B PHE* 3.9 21.5 - - + -
292B LEU* 2.7 28.1 + - + +
293B GLN* 3.5 7.0 - - - +
294B GLU 3.1 0.2 - - - -
295B ALA* 1.3 77.9 - - - +
297B GLN* 1.3 57.0 + - - +
299B ALA* 3.2 6.9 + - - +
300B ALA* 2.9 24.6 + - - +
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Residues in contact with GLN 297 (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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165A GLY 5.9 3.4 - - - +
135B PRO* 4.1 17.0 - - - +
137B ASN* 5.4 2.5 + - - +
293B GLN 3.0 16.6 + - - +
294B GLU* 3.8 8.5 - - - +
295B ALA 3.3 0.4 - - - -
296B LEU* 1.3 73.9 - - - +
298B PHE* 1.3 64.0 + - + +
300B ALA* 3.3 14.3 + - - +
301B GLU* 3.1 46.4 + - - +
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Residues in contact with PHE 298 (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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164A PRO* 3.7 29.8 - - + -
165A GLY* 3.8 15.7 - - - -
188A GLY 5.2 2.2 - - - -
154B TYR* 3.4 33.9 - + - -
183B TYR* 3.7 23.3 - + + -
186B ALA* 3.9 36.1 - - + -
187B MET* 4.5 2.7 - - + -
294B GLU* 3.0 24.1 + - + -
295B ALA 3.4 6.8 + - - +
296B LEU 3.3 0.6 - - - -
297B GLN* 1.3 77.5 - - - +
299B ALA* 1.3 59.8 + - - +
301B GLU* 3.3 11.4 + - - +
302B GLY 3.3 3.5 + - - -
303B LYS* 3.0 41.1 + - + +
304B VAL* 4.1 8.3 - - + -
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Residues in contact with ALA 299 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138B LEU* 3.8 28.8 - - + +
146B ILE* 4.1 23.3 - - + -
183B TYR* 4.8 0.4 + - - -
295B ALA 3.7 3.2 + - - +
296B LEU 3.2 10.2 + - - +
298B PHE* 1.3 75.7 - - - +
300B ALA* 1.3 67.3 + - - +
302B GLY* 2.8 15.4 + - - -
304B VAL* 3.5 25.9 - - + +
305B LYS* 6.1 0.3 - - - +
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Residues in contact with ALA 300 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135B PRO* 4.0 17.3 - - + -
137B ASN* 3.9 35.0 - - + +
138B LEU* 4.1 12.4 - - + +
296B LEU 2.9 13.3 + - - +
297B GLN* 3.5 18.4 - - - +
299B ALA* 1.3 76.9 - - - +
301B GLU* 1.3 56.9 + - - +
302B GLY* 3.2 4.5 + - - -
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Residues in contact with GLU 301 (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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165A GLY* 5.4 2.3 - - - +
167A TRP* 5.6 2.6 + - - -
190A ASN* 3.9 22.9 + - - -
297B GLN* 3.1 42.2 + - - +
298B PHE* 3.6 14.4 - - - +
299B ALA 3.1 0.6 - - - -
300B ALA* 1.3 74.2 - - - +
302B GLY* 1.3 60.1 + - - +
303B LYS* 3.2 38.7 + - - +
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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