Contacts of the helix formed by residues 284 - 295 (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 ARG 284 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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276B ASP 3.2 21.8 + - - -
277B SER* 2.6 45.3 + - - +
278B MET 4.3 0.4 - - - -
279B LYS* 3.9 1.6 - - - +
280B GLY* 3.7 24.0 - - - +
281B LYS 4.0 14.8 + - - +
282B GLY 4.1 0.6 + - - -
283B THR* 1.3 87.8 + - - +
285B ASP* 1.3 64.4 + - - +
286B LYS* 3.4 2.9 - - + +
287B VAL* 4.3 15.9 - - + -
288B LEU* 3.2 22.7 + - - +
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Residues in contact with ASP 285 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94B HIS* 3.3 47.1 + - + +
283B THR* 2.8 29.5 + - - +
284B ARG* 1.3 70.3 - - - +
286B LYS* 1.3 59.1 + - - +
288B LEU* 3.1 5.1 + - - +
289B ILE* 2.7 39.7 + - + +
322B ASP 5.5 0.3 - - - +
323B THR* 5.0 1.9 - - - +
327B TYR* 3.5 25.8 + - - +
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Residues in contact with LYS 286 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113B GLU* 5.2 5.6 - - - +
124B ASP* 2.6 38.1 + - - +
126B ASP* 6.5 0.2 - - - -
127B SER* 4.1 4.0 - - - +
284B ARG* 3.4 1.3 - - + -
285B ASP* 1.3 78.5 - - - +
287B VAL* 1.3 71.6 + - + +
289B ILE* 3.8 6.0 - - - +
290B ARG* 3.0 38.9 + - - +
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Residues in contact with VAL 287 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126B ASP* 6.0 4.7 - - + -
273B ARG* 4.0 29.6 - - - +
277B SER* 4.4 5.2 - - - -
284B ARG* 3.8 21.9 + - + +
285B ASP 3.4 0.2 - - - -
286B LYS* 1.3 84.1 - - + +
288B LEU* 1.3 64.9 + - - +
290B ARG* 3.8 27.9 - - - +
291B ILE* 3.2 42.3 + - + +
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Residues in contact with LEU 288 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274B LEU* 3.6 25.1 - - + -
277B SER* 4.1 8.2 + - - +
278B MET* 4.0 35.7 - - + -
283B THR* 5.0 9.0 - - - +
284B ARG 3.2 15.6 + - - +
285B ASP 3.1 5.2 + - - +
287B VAL* 1.3 79.2 - - - +
289B ILE* 1.3 62.6 + - - +
291B ILE* 4.0 1.4 - - - +
292B MET* 3.1 42.0 + - + +
315B LEU* 5.2 0.2 - - + -
319B ILE* 4.7 7.6 - - + -
323B THR* 4.1 13.7 - - + -
327B TYR* 4.4 4.3 - - - +
331B LEU* 3.7 27.4 - - + -
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Residues in contact with ILE 289 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94B HIS* 3.8 15.7 - - + +
97B THR* 3.9 23.6 - - + +
98B VAL* 3.6 30.1 - - + -
109B TYR* 4.1 9.0 - - - +
285B ASP* 2.7 25.4 + - + +
286B LYS* 3.8 4.0 - - - +
288B LEU* 1.3 69.5 - - - +
290B ARG* 1.3 66.2 + - - +
291B ILE 3.0 2.4 + - - -
292B MET* 3.1 4.6 + - - -
293B VAL* 2.8 46.0 + - + +
327B TYR* 3.3 36.8 - - + +
331B LEU* 4.5 4.9 - - + -
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Residues in contact with ARG 290 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109B TYR* 3.4 25.4 - - + +
113B GLU* 3.1 36.2 + - + +
126B ASP* 5.7 0.4 - - - +
127B SER* 3.1 34.7 + - - +
130B GLU* 2.6 43.1 + - - +
131B ILE* 4.5 13.0 - - + +
135B ARG* 5.8 1.8 - - - +
273B ARG* 3.1 14.6 - - - +
286B LYS* 3.0 37.0 + - - +
287B VAL* 3.8 18.2 - - - +
289B ILE* 1.3 75.4 - - - +
291B ILE* 1.3 57.0 + - - +
293B VAL 3.7 0.2 + - - -
294B SER* 3.0 34.3 + - - +
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Residues in contact with ILE 291 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130B GLU* 3.8 26.9 - - - +
270B PHE* 3.9 20.6 - - + +
273B ARG* 3.6 30.3 - - + -
274B LEU* 3.5 41.5 - - + -
287B VAL* 3.2 22.2 + - + +
289B ILE 3.1 0.4 - - - -
290B ARG* 1.3 73.1 - - - +
292B MET* 1.3 63.2 + - - +
293B VAL 3.1 1.3 - - - -
294B SER* 3.7 4.7 - - - -
295B ARG* 2.8 45.2 + - + +
300B MET* 5.1 0.4 - - + -
303B ILE* 4.9 0.9 - - + -
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Residues in contact with MET 292 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274B LEU* 4.5 7.0 - - - -
288B LEU* 3.1 32.9 + - + +
289B ILE 3.1 4.2 + - - +
291B ILE* 1.3 73.8 - - - +
293B VAL* 1.3 61.5 + - - +
296B SER* 3.2 23.9 + - - -
300B MET* 3.6 22.3 - - + +
315B LEU* 3.9 19.1 - - + -
319B ILE* 3.6 10.5 - - + -
331B LEU* 3.6 31.9 - - + +
334B LEU* 3.8 15.0 - - + +
335B CYS* 3.4 43.3 - - + +
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Residues in contact with VAL 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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98B VAL* 4.2 16.4 - - + +
101B GLY* 3.7 27.1 - - - +
102B LEU* 4.0 13.3 - - + +
109B TYR* 3.8 24.9 - - + +
289B ILE* 2.8 37.2 + - + +
292B MET* 1.3 79.0 - - + +
294B SER* 1.3 58.6 + - - +
296B SER* 2.8 21.0 + - - -
331B LEU* 6.2 0.2 - - + -
334B LEU* 4.3 15.9 - - + -
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Residues in contact with SER 294 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109B TYR* 4.7 7.2 - - - -
110B ASP* 4.5 6.7 - - - -
130B GLU* 5.0 2.6 + - - -
135B ARG* 3.6 26.9 + - - -
270B PHE* 5.2 0.5 - - - -
290B ARG* 3.0 22.6 + - - -
291B ILE* 3.2 7.3 + - - +
293B VAL* 1.3 79.0 - - - +
295B ARG* 1.3 77.8 + - - +
296B SER* 3.3 0.4 + - - -
297B GLU 4.6 1.4 + - - -
298B VAL* 3.7 17.3 - - - +
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Residues in contact with ARG 295 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134B SER 4.5 7.1 + - - -
135B ARG* 4.2 15.5 - - - +
139B GLU* 4.5 15.4 + - - -
266B LYS* 4.0 12.5 - - - +
270B PHE* 3.4 38.4 - - + -
291B ILE* 2.8 22.5 + - + +
294B SER* 1.3 86.5 + - - +
296B SER* 1.3 66.6 + - - +
297B GLU 3.2 2.9 - - - -
298B VAL* 3.0 38.0 + - - +
299B ASP* 2.7 46.4 + - - +
300B MET* 3.2 20.3 + - + +
303B ILE* 3.6 19.7 - - + -
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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