Contacts of the helix formed by residues 296 - 311 (chain B) in PDB entry 1W5A
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 296 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231B LEU* 3.9 4.0 - - - -
294B ASP 3.3 15.5 - - - +
295B LEU* 1.3 80.8 - - - +
297B LEU* 1.3 65.0 + - - +
298B GLU* 3.5 13.3 + - - +
299B GLU* 3.1 41.7 + - + +
300B ALA* 3.3 9.2 + - - +
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Residues in contact with LEU 297 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209A LYS* 6.3 0.9 - - - -
231B LEU* 3.5 47.7 - - + +
232B ILE* 4.0 19.3 - - + -
296B THR* 1.3 70.8 - - - +
298B GLU* 1.3 74.1 + - + +
300B ALA* 3.3 7.6 + - + +
301B ARG* 3.0 34.9 + - - +
319B TRP* 4.5 15.9 - - + -
321B ALA* 5.1 0.7 - - + -
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Residues in contact with GLU 298 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205A LYS* 4.6 12.2 - - + +
206A LEU* 4.7 10.7 - - - +
209A LYS* 3.2 15.0 + - - +
296B THR* 3.1 12.1 - - - +
297B LEU* 1.3 80.2 - - + +
299B GLU* 1.3 63.3 + - + +
301B ARG* 2.4 46.2 + - - +
302B GLU* 3.1 20.8 + - - +
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Residues in contact with GLU 299 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261B ARG* 2.7 56.3 + - - +
262B ALA* 3.7 20.6 + - + +
289B VAL* 5.5 1.1 - - + -
294B ASP 3.8 1.4 - - - +
295B LEU* 3.5 12.9 - - + +
296B THR* 3.1 36.2 + - - +
298B GLU* 1.3 77.0 - - + +
300B ALA* 1.3 64.0 + - - +
302B GLU* 3.0 17.5 + - - +
303B VAL* 3.1 18.2 + - - +
331B VAL* 4.1 0.9 - - - +
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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
----------------------------------------------------------
289B VAL* 4.2 16.9 - - + +
295B LEU* 5.0 1.2 - - + +
296B THR 3.3 5.5 + - - +
297B LEU* 3.3 14.8 + - - +
298B GLU 3.2 0.2 - - - -
299B GLU* 1.3 79.3 - - - +
301B ARG* 1.3 57.6 + - - +
303B VAL* 3.2 5.9 + - - +
304B VAL* 3.0 31.3 + - - +
319B TRP* 3.6 24.2 - - + -
321B ALA* 4.0 21.8 - - + -
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Residues in contact with ARG 301 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205A LYS* 3.1 34.3 + - + +
206A LEU* 4.6 4.0 - - - +
208A PHE* 5.7 13.2 - - - +
209A LYS* 2.6 35.8 - - - +
297B LEU* 3.0 24.1 + - - +
298B GLU* 2.4 42.8 + - - +
300B ALA* 1.3 74.4 - - - +
302B GLU* 1.3 61.8 + - - +
304B VAL* 3.8 7.2 - - + +
305B ALA* 2.8 31.2 + - - +
319B TRP* 4.2 24.7 - - + -
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Residues in contact with GLU 302 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205A LYS* 3.9 36.0 + - + +
260B LYS* 6.0 0.5 - - - +
262B ALA* 4.2 7.4 - - + +
263B LYS* 2.8 62.7 + - + +
266B VAL* 6.0 0.4 - - + -
298B GLU 3.1 11.3 + - - +
299B GLU* 3.0 13.0 + - - +
301B ARG* 1.3 77.1 - - - +
303B VAL* 1.3 57.5 + - + +
305B ALA* 3.7 2.1 - - - +
306B THR* 2.8 34.1 + - - +
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Residues in contact with VAL 303 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262B ALA* 3.8 30.1 - - + +
266B VAL* 3.8 24.9 - - + +
287B ILE* 3.9 24.5 - - + -
289B VAL* 4.0 19.3 - - + -
299B GLU 3.1 15.0 + - - +
300B ALA 3.2 7.9 - - - +
301B ARG 3.1 0.2 - - - -
302B GLU* 1.3 76.0 - - - +
304B VAL* 1.3 66.9 + - - +
306B THR* 3.2 5.0 + - - -
307B VAL* 3.1 23.5 + - + +
333B VAL* 4.1 16.6 - - + -
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Residues in contact with VAL 304 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287B ILE* 4.1 15.4 - - + +
289B VAL* 5.6 0.4 - - + -
300B ALA 3.0 15.9 + - - +
301B ARG* 3.8 10.1 - - + +
303B VAL* 1.3 74.5 - - - +
305B ALA* 1.3 57.6 + - - +
307B VAL* 3.3 2.3 + - - +
308B SER* 2.8 34.3 + - - -
317B ILE* 4.1 27.1 - - + +
319B TRP* 3.5 49.8 - - + +
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Residues in contact with ALA 305 (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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204A LEU* 3.7 19.9 - - + +
205A LYS* 3.7 27.8 - - + +
301B ARG 2.8 18.8 + - - +
302B GLU* 3.7 4.9 - - - +
304B VAL* 1.3 78.0 - - - +
306B THR* 1.3 62.1 + - - +
308B SER* 3.3 7.6 + - - -
309B SER* 3.3 23.0 + - - -
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Residues in contact with THR 306 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263B LYS* 4.2 19.5 + - + -
266B VAL* 4.2 19.9 - - + +
267B SER* 5.6 2.7 - - - +
270B LEU* 3.8 18.8 - - + -
302B GLU* 2.8 21.0 + - - +
303B VAL 3.2 8.0 + - - -
305B ALA* 1.3 77.0 - - - +
307B VAL* 1.3 57.9 + - - +
309B SER* 3.1 19.9 + - - -
310B ARG* 3.5 19.2 + - - +
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Residues in contact with VAL 307 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266B VAL* 3.6 26.9 - - + -
270B LEU* 4.2 14.4 - - + -
285B ALA* 4.8 4.3 - - + -
287B ILE* 3.8 31.4 - - + -
303B VAL* 3.1 7.8 + - + +
304B VAL 3.8 1.6 - - - +
306B THR* 1.3 74.4 - - - +
308B SER* 1.3 67.4 + - - +
310B ARG* 2.9 19.4 + - - +
311B LEU* 3.4 29.6 + - + +
317B ILE* 5.1 0.4 - - + -
335B LEU* 4.0 19.7 - - + -
337B ILE* 4.8 6.3 - - + -
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Residues in contact with SER 308 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164A MET* 5.3 13.2 + - - +
204A LEU* 6.5 0.4 - - - -
304B VAL* 2.8 21.1 + - - -
305B ALA* 3.5 9.6 - - - -
307B VAL* 1.3 76.8 - - - +
309B SER* 1.3 61.8 + - - +
311B LEU* 3.3 20.2 + - - +
312B ASP 5.2 1.2 - - - +
313B PRO* 5.5 2.1 - - - +
317B ILE* 3.7 27.6 - - - +
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Residues in contact with SER 309 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204A LEU* 5.7 9.2 - - - -
305B ALA 3.3 8.4 + - - -
306B THR* 3.1 17.0 + - - -
308B SER* 1.3 79.9 - - - +
310B ARG* 1.3 65.8 + - - +
311B LEU 3.3 5.7 + - - +
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Residues in contact with ARG 310 (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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267B SER* 5.9 2.6 + - - +
270B LEU* 3.7 42.0 + - + +
271B ASN* 5.2 6.7 + - - -
279B ILE* 3.9 23.9 - - + +
280B ASP* 3.6 24.4 + - - +
306B THR* 3.5 23.6 + - - +
307B VAL* 2.9 9.6 + - - +
309B SER* 1.3 86.1 + - - +
311B LEU* 1.3 61.8 + - + +
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Residues in contact with LEU 311 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279B ILE* 3.6 37.5 - - + +
280B ASP 4.2 1.8 - - - -
282B ALA* 3.9 11.2 - - + +
284B GLY 4.4 4.7 - - - +
285B ALA* 3.8 28.0 - - + -
307B VAL* 3.5 24.9 - - + +
308B SER 3.3 13.6 + - - +
309B SER 3.9 5.2 - - - +
310B ARG* 1.3 85.8 - - - +
312B ASP* 1.3 70.7 + - - +
313B PRO* 3.4 5.2 - - - +
315B ALA* 4.1 12.8 - - + -
317B ILE* 4.3 17.3 - - + -
337B ILE* 4.5 9.2 - - + -
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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