Contacts of the helix formed by residues 302 - 317 (chain B) in PDB entry 5HOO
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 SER 302 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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162B PHE* 3.4 17.1 - - - -
300B PHE* 4.2 0.3 - - - +
301B ASP* 1.3 78.4 + - - +
303B TYR* 1.3 65.6 + - - +
304B GLU* 3.4 13.9 - - - -
305B SER* 2.8 29.5 + - - -
306B VAL* 3.5 6.2 + - - +
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Residues in contact with TYR 303 (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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162B PHE* 4.1 19.1 - + - -
189B LYS* 5.7 7.2 - - + +
190B LYS 4.1 6.7 + - - -
191B THR* 3.5 33.2 - - + -
207B LEU* 3.7 6.7 - - + +
209B LYS* 3.6 43.6 - - + +
210B PRO* 3.2 22.5 - - - +
302B SER* 1.3 76.6 - - - +
304B GLU* 1.3 71.3 + - - +
305B SER 3.2 0.4 - - - -
306B VAL* 3.2 8.5 + - - +
307B LYS* 3.1 34.4 + - - +
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Residues in contact with GLU 304 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209B LYS* 6.2 0.3 - - - -
302B SER* 3.4 12.0 - - - -
303B TYR* 1.3 81.6 + - - +
305B SER* 1.3 60.4 + - - +
306B VAL 3.2 0.7 - - - -
307B LYS* 3.8 21.5 + - + +
308B LYS* 2.9 31.9 + - - +
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Residues in contact with SER 305 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300B PHE* 3.7 13.5 - - - -
301B ASP* 3.7 17.8 + - - +
302B SER* 2.8 35.6 + - - -
303B TYR 3.2 0.2 - - - -
304B GLU* 1.3 78.4 - - - +
306B VAL* 1.3 62.4 + - - +
308B LYS* 4.0 7.5 - - - +
309B TRP* 3.2 23.6 + - - +
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Residues in contact with VAL 306 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160B ILE* 4.4 22.4 - - + -
162B PHE* 4.4 15.9 - - + -
191B THR* 4.6 5.8 - - - +
207B LEU* 4.1 15.5 - - + -
300B PHE* 3.8 34.1 - - + -
302B SER 3.7 13.7 - - - +
303B TYR* 3.2 9.5 + - - +
305B SER* 1.3 76.6 - - - +
307B LYS* 1.3 66.8 + - - +
309B TRP* 3.1 5.7 + - + +
310B LEU* 2.9 39.9 + - + +
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Residues in contact with LYS 307 (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 TYR* 4.3 15.3 - - + +
207B LEU* 2.5 58.1 + - + +
209B LYS* 6.1 3.2 - - - +
303B TYR* 3.1 18.8 + - - +
304B GLU* 4.1 22.2 + - + +
306B VAL* 1.3 77.9 - - - +
308B LYS* 1.3 55.7 + - - +
310B LEU* 3.1 4.9 + - - +
311B ASP* 2.9 40.8 + - - +
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Residues in contact with LYS 308 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304B GLU 2.9 20.5 + - - +
305B SER* 4.0 7.6 - - - +
307B LYS* 1.3 76.3 - - - +
309B TRP* 1.3 62.9 + - - +
311B ASP* 3.5 9.3 + - - +
312B GLU* 3.2 44.3 + - - +
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Residues in contact with TRP 309 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160B ILE* 6.2 0.4 - - + -
291B MET* 4.2 17.0 - - + -
294B ALA* 3.5 43.0 + - + -
295B LEU* 4.1 17.3 - - + -
298B GLN* 3.6 32.5 + - + +
300B PHE* 3.8 16.6 - + + -
305B SER 3.2 16.6 + - - +
306B VAL* 3.1 6.1 + - + +
308B LYS* 1.3 76.3 - - - +
310B LEU* 1.3 77.2 + - + +
312B GLU* 3.9 11.1 - - - +
313B TRP* 3.0 62.6 + + + +
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Residues in contact with LEU 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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160B ILE* 4.5 4.5 - - + -
193B LEU* 3.8 36.1 - - + -
205B TYR* 4.0 14.4 - - + +
207B LEU* 4.0 6.1 - - + -
291B MET* 4.2 15.7 - - - -
306B VAL* 2.9 38.4 + - + +
307B LYS* 3.5 7.2 - - - +
309B TRP* 1.3 87.5 - - + +
311B ASP* 1.3 58.0 + - - +
313B TRP* 3.0 3.7 + - + +
314B PHE* 2.8 72.3 + - + -
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Residues in contact with ASP 311 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205B TYR* 2.5 32.7 + - - -
307B LYS* 2.9 25.7 + - - +
308B LYS* 3.8 8.5 + - - +
310B LEU* 1.3 76.7 - - - +
312B GLU* 1.3 65.0 + - + +
314B PHE* 4.2 4.4 - - - +
315B ALA* 3.4 21.3 + - - +
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Residues in contact with GLU 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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308B LYS* 3.2 48.0 + - - +
309B TRP* 3.9 9.5 - - - +
311B ASP* 1.3 80.2 - - + +
313B TRP* 1.3 58.0 + - - +
315B ALA* 3.8 3.6 - - - +
316B ALA* 2.9 31.3 + - - +
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Residues in contact with TRP 313 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287B LEU* 4.2 13.5 - - + -
290B SER* 3.4 32.1 - - - -
291B MET* 3.8 33.7 - - + -
294B ALA* 3.5 19.3 - - + +
309B TRP* 3.0 50.5 + + + +
310B LEU* 3.0 5.3 + - + +
312B GLU* 1.3 74.6 - - + +
314B PHE* 1.3 93.5 + + - +
316B ALA* 3.8 8.4 + - + +
317B LYS* 3.5 47.1 + - + +
321B PHE* 5.1 0.7 - + - -
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Residues in contact with PHE 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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193B LEU* 4.9 6.1 - - + -
195B VAL* 4.4 12.6 - - + -
202B VAL* 3.6 33.4 - - + -
205B TYR* 4.1 27.6 - + - -
287B LEU* 4.3 14.6 - - + -
291B MET* 5.1 3.4 - - + -
310B LEU* 2.8 56.1 + - + +
311B ASP* 4.2 5.2 - - - +
313B TRP* 1.3 98.0 - + - +
315B ALA* 1.3 64.9 + - - +
317B LYS* 3.1 17.9 + - - +
322B TYR* 3.0 26.0 + - - +
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Residues in contact with ALA 315 (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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311B ASP 3.4 15.1 + - - +
312B GLU* 3.9 3.1 - - - +
314B PHE* 1.3 79.0 - - - +
316B ALA* 1.3 62.8 + - - +
317B LYS 3.1 9.9 - - - +
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Residues in contact with ALA 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 GLU 2.9 19.9 + - - +
313B TRP* 3.8 13.5 - - + +
314B PHE 3.2 0.2 - - - -
315B ALA* 1.3 75.5 - - - +
317B LYS* 1.3 65.6 + - - +
318B ASP* 3.9 4.3 + - - +
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Residues in contact with LYS 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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290B SER* 4.4 1.6 + - - -
313B TRP* 3.5 50.0 - - + +
314B PHE* 3.1 13.6 + - - +
315B ALA* 3.1 14.4 - - - +
316B ALA* 1.3 81.8 - - - +
318B ASP* 1.3 72.7 + - - +
319B ASP* 5.2 0.5 - - - +
321B PHE* 3.9 41.6 - - + -
322B TYR* 4.2 11.4 - - + +
5C G 4.2 13.3 + - - -
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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