Contacts of the helix formed by residues 299 - 312 (chain B) in PDB entry 4HRE
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 ASP 299 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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24B TYR* 3.0 11.7 - - + -
266B LYS* 4.5 1.9 - - - +
267B PRO* 4.2 25.4 - - + +
270B PHE* 3.8 11.1 - - - -
295B ARG* 2.7 56.2 + - - +
298B VAL* 1.3 75.8 - - + +
300B MET* 1.3 65.1 + - - +
302B LYS* 2.8 24.2 + - + +
303B ILE* 3.3 17.7 + - - +
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Residues in contact with MET 300 (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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24B TYR 2.9 3.8 + - - -
26B SER* 3.2 35.4 - - - +
274B LEU* 5.5 0.2 - - + -
291B ILE* 4.3 1.6 - - + +
292B MET* 3.6 46.7 - - + +
295B ARG* 3.2 22.4 + - + +
296B SER* 3.7 16.8 - - - +
298B VAL 3.7 0.2 - - - -
299B ASP* 1.3 76.1 + - - +
301B LEU* 1.3 61.7 + - - +
303B ILE* 3.4 15.8 + - + -
304B ARG* 3.1 22.8 + - - +
315B LEU* 4.2 22.4 - - - -
334B LEU 4.2 1.6 - - - +
335B CYS* 3.7 10.5 - - - +
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Residues in contact with LEU 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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23B ALA 3.4 24.5 - - - +
24B TYR* 2.8 29.2 + - + +
25B GLY 3.6 16.8 - - - +
26B SER* 4.0 8.1 - - - -
28B LYS* 5.6 2.7 - - - -
300B MET* 1.3 72.4 - - - +
302B LYS* 1.3 57.1 + - - +
304B ARG* 3.2 39.4 + - - +
305B SER* 2.9 28.9 + - - +
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Residues in contact with LYS 302 (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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24B TYR* 3.7 47.7 - - + -
267B PRO* 3.6 30.8 - - + +
299B ASP* 2.8 19.0 + - + +
301B LEU* 1.3 68.2 - - - +
303B ILE* 1.3 54.4 + - - +
305B SER* 2.8 13.7 + - - -
306B GLU* 2.7 43.3 + - + +
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Residues in contact with ILE 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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267B PRO* 3.8 25.5 - - + +
270B PHE* 3.7 16.2 - - + -
271B ALA* 3.7 19.2 - - - +
274B LEU* 3.6 26.9 - - + -
291B ILE* 4.9 2.7 - - + -
295B ARG* 3.6 20.0 - - + -
299B ASP* 3.3 30.7 + - - +
300B MET* 3.5 18.6 - - + +
302B LYS* 1.3 75.4 - - - +
304B ARG* 1.3 53.2 + - - +
306B GLU 3.5 0.5 + - - -
307B PHE* 2.6 36.9 + - + +
315B LEU* 4.7 7.0 - - + -
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Residues in contact with ARG 304 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B SER* 4.2 0.6 - - - +
300B MET* 3.1 20.8 + - - +
301B LEU* 3.2 33.4 - - - +
303B ILE* 1.3 73.8 - - - +
305B SER* 1.3 65.1 + - - +
307B PHE* 2.9 7.1 + - - +
308B LYS* 2.9 27.4 + - - +
315B LEU* 4.4 23.7 + - + -
335B CYS* 3.0 33.1 + - - -
336B GLY* 3.5 16.6 + - - -
337B GLY* 3.1 33.5 + - - -
338B ASP* 3.6 4.4 + - - +
339B ASP* 3.2 40.5 + - - +
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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
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301B LEU* 2.9 15.8 + - - +
302B LYS* 2.8 18.4 + - - -
304B ARG* 1.3 72.7 - - - +
306B GLU* 1.3 64.2 + - - -
308B LYS* 3.6 3.8 + - - +
309B ARG* 3.2 22.3 + - - +
339B ASP* 5.1 3.5 - - - -
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Residues in contact with GLU 306 (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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265B ASN* 3.0 24.5 + - - -
267B PRO* 3.9 8.1 - - + +
268B LEU* 3.8 38.0 - - + +
271B ALA* 4.1 3.4 - - + -
302B LYS* 2.7 27.9 + - + +
303B ILE 3.8 3.6 - - - +
305B SER* 1.3 74.1 - - - +
307B PHE* 1.3 64.8 + - - +
309B ARG* 2.3 41.6 + - - +
310B LYS* 3.2 26.2 + - - +
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Residues in contact with PHE 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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271B ALA* 3.4 35.9 - - - -
274B LEU* 4.2 9.9 - - + -
275B TYR* 3.6 28.9 - + + -
278B MET* 4.9 0.7 - - + -
303B ILE* 2.6 23.6 + - + +
304B ARG* 2.9 8.5 + - - +
306B GLU* 1.3 73.0 - - - +
308B LYS* 1.3 59.0 - - - +
311B TYR* 3.0 53.0 + + + +
313B LYS 3.3 15.7 - - - -
315B LEU* 3.4 29.6 - - + +
318B TYR* 3.6 42.0 - + + -
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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
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304B ARG 2.9 14.8 + - - +
305B SER* 4.2 3.6 - - - +
307B PHE* 1.3 77.7 - - - +
309B ARG* 1.3 59.4 + - - +
312B GLY* 2.7 41.7 + - - -
313B LYS* 3.3 26.6 + - - +
314B SER* 4.1 3.3 - - - +
339B ASP* 2.7 50.2 + - + +
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Residues in contact with ARG 309 (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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265B ASN* 5.3 0.8 - - - +
268B LEU* 4.5 12.7 - - - +
305B SER 3.2 17.9 + - - +
306B GLU* 2.3 38.8 + - - +
308B LYS* 1.3 78.9 - - - +
310B LYS* 1.3 72.4 + - - +
312B GLY* 4.2 2.6 + - - -
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Residues in contact with LYS 310 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268B LEU* 4.0 19.2 - - + +
272B ASP* 2.6 40.6 + - - +
306B GLU 3.2 12.6 + - - +
309B ARG* 1.3 88.7 - - - +
311B TYR* 1.3 91.9 + - + +
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Residues in contact with TYR 311 (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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271B ALA* 4.2 6.7 - - + -
272B ASP* 2.7 32.5 + - - +
275B TYR* 3.3 60.2 - + + +
276B ASP* 4.9 1.4 + - - -
307B PHE* 3.0 55.5 + + + +
310B LYS* 1.3 106.3 + - + +
312B GLY* 1.3 54.7 - - - +
313B LYS* 3.0 15.0 + - - +
318B TYR* 4.4 10.3 + - + +
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Residues in contact with GLY 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* 2.7 37.3 + - - +
309B ARG 4.2 1.9 + - - -
310B LYS 3.6 1.8 + - - -
311B TYR* 1.3 70.2 - - - +
313B LYS* 1.3 65.6 + - - +
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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