Contacts of the helix formed by residues 296 - 312 (chain A) in PDB entry 1R00
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 ALA 296 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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297A ASP* 1.3 73.0 - - + +
298A ARG* 3.3 3.0 - - - +
299A PHE* 3.0 27.9 + - - +
300A PHE* 4.0 14.9 - - - -
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Residues in contact with ASP 297 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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296A ALA* 1.3 81.4 - - - +
298A ARG* 1.3 67.8 + - - +
299A PHE 3.4 0.5 + - - -
300A PHE* 3.5 19.1 + - - +
301A SER* 3.7 10.7 + - - -
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Residues in contact with ARG 298 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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296A ALA 3.0 2.3 + - - +
297A ASP* 1.3 85.3 + - - +
299A PHE* 1.3 63.0 + - - +
301A SER* 3.1 19.3 + - - +
302A THR* 3.3 24.3 + - + +
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Residues in contact with PHE 299 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296A ALA* 3.0 18.1 + - - +
298A ARG* 1.3 78.0 - - - +
300A PHE* 1.3 86.3 + + + +
302A THR* 3.0 21.9 + - - -
303A LEU* 3.0 54.0 + - + +
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Residues in contact with PHE 300 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296A ALA* 4.0 22.0 - - - -
297A ASP* 3.5 9.8 + - - +
298A ARG 3.4 1.0 - - - -
299A PHE* 1.3 99.9 - + - +
301A SER* 1.3 62.1 + - - +
303A LEU* 3.6 10.2 - - + +
304A LEU* 3.2 22.2 + - - +
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Residues in contact with SER 301 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297A ASP 3.7 8.5 + - - -
298A ARG* 3.1 16.5 + - - +
300A PHE* 1.3 78.6 - - - +
302A THR* 1.3 60.5 + - - +
304A LEU* 3.3 8.5 + - - +
305A ASP* 2.9 28.8 + - - +
316A VAL* 5.9 1.8 - - - +
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Residues in contact with THR 302 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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298A ARG* 3.3 28.1 + - + +
299A PHE* 3.0 20.0 + - - -
301A SER* 1.3 76.2 - - - +
303A LEU* 1.3 64.6 + - - +
305A ASP* 3.6 8.7 - - + +
306A LEU* 3.1 34.6 + - - +
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Residues in contact with LEU 303 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123A PHE* 5.9 3.8 - - + -
299A PHE* 3.0 50.9 + - + +
300A PHE* 3.6 13.5 - - + +
302A THR* 1.3 79.2 + - - +
304A LEU* 1.3 60.7 + - - +
306A LEU* 3.4 6.9 + - + +
307A ARG* 3.1 56.9 + - + +
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Residues in contact with LEU 304 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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259A LEU* 6.2 2.7 - - + -
300A PHE 3.2 14.7 + - - +
301A SER* 3.8 8.3 - - - +
302A THR 3.3 0.2 - - - -
303A LEU* 1.3 76.1 - - - +
305A ASP* 1.3 55.5 + - - +
307A ARG* 3.3 15.4 + - + +
308A MET* 2.7 59.4 + - + +
316A VAL* 4.5 18.2 - - + -
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Residues in contact with ASP 305 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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301A SER 2.9 18.9 + - - +
302A THR* 3.6 10.7 - - - +
304A LEU* 1.3 78.1 - - - +
306A LEU* 1.3 68.9 + - - +
308A MET* 3.2 8.0 + - - +
309A LEU* 2.9 29.9 + - - +
314A GLY 4.4 1.2 - - - +
315A ARG* 3.9 21.5 - - - +
316A VAL* 4.2 15.5 + - + +
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Residues in contact with LEU 306 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123A PHE* 3.6 20.6 - - + -
126A LEU* 5.2 16.2 - - + -
302A THR* 3.1 24.8 + - - +
303A LEU* 4.0 7.0 - - + +
305A ASP* 1.3 83.5 - - - +
307A ARG* 1.3 61.7 + - - +
309A LEU* 3.1 19.2 + - + +
310A THR* 2.8 34.8 + - - +
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Residues in contact with ARG 307 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34A ARG* 3.8 8.3 - - - +
109A TRP* 4.5 15.7 + - - +
116A VAL* 4.0 19.1 - - - +
120A ASP* 2.7 38.5 + - - -
123A PHE* 3.6 23.3 - - + -
303A LEU* 3.1 47.7 + - + +
304A LEU* 3.3 16.1 + - + +
306A LEU* 1.3 75.0 - - - +
308A MET* 1.3 57.8 + - + +
311A PHE* 2.8 56.5 + - + -
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Residues in contact with MET 308 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159A PHE* 6.5 0.4 - - - -
259A LEU* 3.1 40.2 - - + +
260A ASN* 3.4 20.0 - - - +
304A LEU* 2.7 42.8 + - + +
305A ASP* 3.5 9.0 - - - +
306A LEU 3.2 0.2 - - - -
307A ARG* 1.3 73.4 - - + +
309A LEU* 1.3 59.3 + - - +
311A PHE* 4.8 0.7 - - - -
312A MET* 3.2 54.2 + - + +
313A GLY 3.1 19.6 + - - -
314A GLY* 3.2 16.0 + - - +
315A ARG* 4.5 4.9 - - - -
316A VAL* 5.3 3.6 - - + -
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Residues in contact with LEU 309 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126A LEU* 5.4 3.1 - - + -
129A VAL* 3.5 29.9 - - + +
130A VAL* 5.7 4.7 - - + -
133A GLY* 4.0 24.2 - - - +
135A PRO* 3.6 8.7 - - - +
305A ASP* 2.9 15.3 + - - +
306A LEU* 3.4 24.5 - - + +
308A MET* 1.3 78.1 - - - +
310A THR* 1.3 58.7 + - - +
313A GLY* 3.1 25.7 + - - +
314A GLY 3.5 12.9 + - - +
315A ARG* 6.1 0.7 - - + -
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Residues in contact with THR 310 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122A ALA* 3.8 32.9 - - + +
123A PHE* 3.4 33.1 - - + +
126A LEU* 3.8 15.2 - - + +
129A VAL* 4.0 11.4 - - + +
135A PRO* 4.2 0.2 - - - -
136A ALA* 3.0 35.3 + - + +
137A TYR* 3.4 5.9 + - - -
306A LEU 2.8 19.9 + - - -
307A ARG 4.2 0.7 - - - -
309A LEU* 1.3 73.2 - - - +
311A PHE* 1.3 65.5 + - + +
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Residues in contact with PHE 311 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116A VAL* 3.7 19.5 - - + -
119A ALA* 3.3 48.9 - - + -
120A ASP* 3.4 23.8 - - - -
123A PHE* 3.9 12.8 - + - -
135A PRO* 3.8 4.4 - - - +
137A TYR* 3.1 27.8 - + - +
145A PHE* 3.6 20.8 + + + +
159A PHE* 5.2 5.6 - + - -
307A ARG* 2.8 40.6 + - + +
308A MET* 6.3 0.2 - - - -
310A THR* 1.3 83.5 - - - +
312A MET* 1.3 83.0 + - + +
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Residues in contact with MET 312 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135A PRO* 3.6 13.9 - - - +
145A PHE* 3.3 44.9 - - + +
146A TRP* 3.6 22.9 - - + +
159A PHE* 4.8 6.3 - - + -
260A ASN* 3.5 32.5 - - - +
261A TRP* 4.6 13.9 - - + -
262A SER 5.1 0.3 + - - -
265A ASP* 5.6 0.5 - - - +
308A MET* 3.2 43.0 + - + +
311A PHE* 1.3 101.8 - - + +
313A GLY* 1.3 61.2 + - - +
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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
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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