Contacts of the helix formed by residues 284 - 295 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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276C ASP 3.4 18.9 + - - -
277C SER* 2.7 45.0 + - - +
278C MET 3.9 1.4 - - - -
279C LYS* 3.6 1.6 - - - +
280C GLY* 3.4 28.5 - - - +
281C LYS 3.5 22.2 + - - -
282C GLY 4.1 1.6 + - - -
283C THR* 1.3 79.4 + - - +
285C ASP* 1.3 62.5 + - - +
286C LYS* 3.5 2.7 - - + -
287C VAL* 3.9 14.8 + - + -
288C LEU* 3.4 20.6 + - - +
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Residues in contact with ASP 285 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94C HIS* 3.1 40.2 + - + +
283C THR* 3.1 28.5 + - - +
284C ARG* 1.3 71.6 - - - +
286C LYS* 1.3 61.1 + - - +
288C LEU* 3.2 3.8 + - - +
289C ILE* 2.8 39.7 + - + +
322C ASP 5.3 0.3 - - - +
323C THR* 4.6 3.6 - - - +
327C TYR* 2.9 34.7 + - - +
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Residues in contact with LYS 286 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113C GLU* 6.0 1.1 - - - +
124C ASP* 2.3 44.3 + - - +
126C ASP* 6.5 0.2 - - - -
127C SER* 3.7 7.9 - - - -
284C ARG* 3.5 1.3 - - + -
285C ASP* 1.3 77.9 - - - +
287C VAL* 1.3 66.9 + - + +
289C ILE* 4.1 6.0 - - - +
290C ARG* 3.2 36.6 + - - +
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Residues in contact with VAL 287 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126C ASP* 6.0 4.7 - - + +
127C SER* 5.7 0.4 - - - +
130C GLU* 4.3 1.6 - - - +
273C ARG* 4.2 26.7 - - - +
277C SER* 4.3 6.1 - - - -
284C ARG* 3.9 18.9 + - + +
285C ASP 3.3 0.2 - - - -
286C LYS* 1.3 81.6 - - + +
288C LEU* 1.3 67.2 + - - +
290C ARG* 3.9 27.9 - - - +
291C ILE* 3.2 42.2 + - + +
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Residues in contact with LEU 288 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274C LEU* 3.7 24.7 - - + -
277C SER* 4.0 8.2 - - - +
278C MET* 3.9 34.5 - - + -
283C THR* 4.8 9.6 - - - +
284C ARG 3.4 15.6 + - - +
285C ASP 3.2 4.8 + - - +
287C VAL* 1.3 78.4 - - - +
289C ILE* 1.3 63.2 + - - +
291C ILE* 4.1 1.2 - - - +
292C MET* 3.1 40.1 + - + +
319C ILE* 4.8 6.1 - - + -
323C THR* 4.0 16.2 - - + -
327C TYR* 4.1 6.5 - - - +
331C LEU* 3.8 27.6 - - + -
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Residues in contact with ILE 289 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94C HIS* 4.0 4.7 - - + +
97C THR* 3.3 30.1 - - - +
98C VAL* 3.6 37.2 - - + +
109C TYR* 4.4 6.5 - - - +
285C ASP* 2.8 31.2 + - + +
286C LYS* 4.1 5.4 - - - +
288C LEU* 1.3 70.9 - - - +
290C ARG* 1.3 55.5 + - - +
292C MET* 3.2 5.7 + - - +
293C VAL* 2.8 42.4 + - + +
327C TYR* 3.4 32.5 - - + +
331C LEU* 4.7 4.5 - - + -
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Residues in contact with ARG 290 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109C TYR* 3.4 30.1 + - + +
110C ASP* 6.1 0.4 - - - +
113C GLU* 3.8 30.0 + - + -
126C ASP* 5.7 0.2 - - - +
127C SER* 3.3 34.9 + - - +
130C GLU* 2.3 43.5 + - - +
131C ILE* 4.9 7.6 - - - +
135C ARG* 5.8 1.8 - - - +
273C ARG* 3.2 14.5 - - - +
286C LYS* 3.2 36.2 + - - +
287C VAL* 3.9 18.7 - - - +
288C LEU 3.4 0.4 - - - -
289C ILE* 1.3 78.9 - - - +
291C ILE* 1.3 53.4 + - - +
293C VAL* 3.7 1.7 - - - +
294C SER* 2.8 39.5 + - - +
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Residues in contact with ILE 291 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130C GLU* 4.0 16.6 - - - +
270C PHE* 3.8 24.7 - - + +
273C ARG* 3.6 31.0 - - + -
274C LEU* 3.6 40.8 - - + +
287C VAL* 3.2 26.6 + - + +
290C ARG* 1.3 79.3 - - - +
292C MET* 1.3 59.4 + - - +
294C SER* 3.7 6.1 - - - -
295C ARG* 2.8 47.0 + - + +
300C MET* 5.7 0.7 - - - -
303C ILE* 4.8 1.3 - - + -
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Residues in contact with MET 292 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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274C LEU* 4.4 11.4 - - + -
288C LEU* 3.1 32.2 + - + +
289C ILE 3.7 2.9 - - - +
291C ILE* 1.3 76.3 - - - +
293C VAL* 1.3 59.5 + - + +
296C SER* 3.1 27.4 + - - +
300C MET* 4.1 14.1 - - - +
315C LEU* 3.9 20.6 - - + -
319C ILE* 3.6 15.5 - - + -
331C LEU* 3.5 43.1 - - + +
334C LEU* 3.9 16.7 - - + +
335C CYS* 3.6 24.2 - - + +
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Residues in contact with VAL 293 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68C ARG* 5.9 0.2 - - - +
98C VAL* 4.2 16.6 - - + +
101C GLY* 3.5 27.8 - - - +
102C LEU* 4.0 11.3 - - + +
109C TYR* 3.8 21.1 - - + +
289C ILE* 2.8 38.9 + - + +
290C ARG 3.8 3.1 - - - +
292C MET* 1.3 75.2 - - - +
294C SER* 1.3 58.2 + - - +
296C SER* 2.8 20.9 + - - -
334C LEU* 4.1 18.6 - - + -
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Residues in contact with SER 294 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109C TYR* 4.5 9.4 - - - -
110C ASP* 4.4 8.5 - - - -
130C GLU* 4.8 2.6 + - - -
135C ARG* 3.4 29.7 + - - -
270C PHE* 5.4 0.2 - - - -
290C ARG* 2.8 28.0 + - - +
291C ILE* 3.5 6.1 + - - -
293C VAL* 1.3 74.7 - - - +
295C ARG* 1.3 70.6 + - - +
296C SER* 3.3 0.4 - - - -
297C GLU 4.7 1.1 + - - -
298C VAL* 3.5 18.7 - - - +
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Residues in contact with ARG 295 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134C SER* 4.6 3.8 + - - -
135C ARG* 3.7 17.5 - - - +
139C GLU* 4.5 13.7 + - - -
266C LYS* 4.4 15.0 - - - +
270C PHE* 3.4 44.5 - - + -
291C ILE* 2.8 30.4 + - + +
294C SER* 1.3 85.6 + - - +
296C SER* 1.3 59.5 + - - +
297C GLU 3.2 3.6 - - - -
298C VAL* 2.9 53.0 + - - +
299C ASP* 2.6 34.3 + - - +
300C MET* 3.2 20.7 + - + -
303C ILE* 3.7 14.4 - - + -
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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