Contacts of the helix formed by residues 304 - 316 (chain A) in PDB entry 1BRW
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 304 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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101A SER* 3.7 15.1 - - - +
299A ALA* 3.1 12.7 + - + +
302A SER* 3.2 14.8 + - - +
303A GLY* 1.3 80.3 - - - +
305A ALA* 1.3 59.4 + - - +
307A ALA* 3.4 6.7 + - - +
308A ALA* 3.0 28.6 + - - +
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Residues in contact with ALA 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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97A PRO* 4.4 7.6 - - - +
98A LEU* 4.0 22.4 - - + -
101A SER* 4.0 11.8 - - - +
260A LEU* 4.2 19.1 - - + +
299A ALA 3.0 22.6 + - - +
300A ILE* 4.0 10.5 - - + +
304A ALA* 1.3 75.5 - - - +
306A ILE* 1.3 65.8 + - - +
308A ALA* 3.5 4.7 + - - +
309A PHE* 3.3 18.4 + - - +
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Residues in contact with ILE 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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257A ILE* 4.1 13.9 - - + +
260A LEU* 3.8 30.6 + - + +
261A LYS* 4.0 19.7 - - + -
303A GLY* 3.3 21.7 - - - +
305A ALA* 1.3 77.5 - - - +
307A ALA* 1.3 66.9 + - + +
309A PHE* 3.3 17.9 + - + +
310A LYS* 3.3 32.2 + - - +
323A VAL* 3.7 29.6 - - + -
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Residues in contact with ALA 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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303A GLY 3.3 15.0 + - - +
304A ALA* 3.5 8.7 - - - +
305A ALA 3.2 0.2 - - - -
306A ILE* 1.3 81.0 - - + +
308A ALA* 1.3 63.6 + - - +
309A PHE 3.3 0.2 + - - -
310A LYS* 3.4 13.2 + - - +
311A THR* 3.2 25.1 + - - -
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Residues in contact with ALA 308 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97A PRO* 3.7 26.6 - - + +
100A ALA* 5.1 3.1 - - + -
101A SER* 3.8 14.1 - - - +
148A ILE* 5.2 4.6 - - + +
304A ALA 3.0 17.4 + - - +
305A ALA 3.8 1.6 - - - +
306A ILE 3.4 0.2 - - - -
307A ALA* 1.3 75.8 - - - +
309A PHE* 1.3 58.0 + - - +
311A THR* 3.7 7.5 + - - +
312A PHE* 3.0 27.9 + - - +
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Residues in contact with PHE 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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93A LEU* 3.8 23.3 - - + -
97A PRO* 3.6 23.1 - - + +
124A LEU* 5.8 1.3 - - + -
127A VAL* 5.7 0.4 - - + -
253A VAL* 4.8 13.0 - - + -
256A ALA* 5.1 6.7 - - + -
257A ILE* 3.6 27.6 - - + -
260A LEU* 3.8 17.0 - - + -
305A ALA 3.3 10.9 + - - +
306A ILE* 3.3 21.9 + - + +
307A ALA 3.1 0.4 - - - -
308A ALA* 1.3 77.0 - - - +
310A LYS* 1.3 59.4 + - - +
312A PHE* 3.1 21.0 + + - +
313A LEU* 2.8 56.2 + - + +
323A VAL* 3.9 16.6 - - + -
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Residues in contact with LYS 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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306A ILE* 3.3 23.8 + - - +
307A ALA* 3.7 10.1 - - - +
309A PHE* 1.3 77.4 - - - +
311A THR* 1.3 56.6 + - - +
313A LEU* 3.2 7.4 + - - +
314A ALA* 3.0 27.0 + - - +
320A ALA* 3.6 28.7 - - + +
323A VAL* 3.6 39.0 - - + -
324A ASP* 2.7 31.4 + - - -
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Residues in contact with THR 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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146A ASN* 2.9 35.7 - - + +
307A ALA 3.2 14.4 + - - -
308A ALA* 3.9 8.2 - - - +
310A LYS* 1.3 78.4 - - - +
312A PHE* 1.3 63.3 + - - +
314A ALA* 4.0 4.0 - - - +
315A ALA* 3.0 24.3 + - + +
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Residues in contact with PHE 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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93A LEU* 5.8 1.6 - - + -
97A PRO* 4.1 7.6 - - + -
124A LEU* 3.8 20.6 - - + -
130A PHE* 3.7 23.2 - + - -
146A ASN* 5.8 1.1 - - - -
148A ILE* 3.9 33.7 - - + -
150A ILE* 3.7 41.5 - - + -
308A ALA 3.0 16.1 + - - +
309A PHE* 3.2 27.6 - + - +
311A THR* 1.3 80.3 - - - +
313A LEU* 1.3 73.7 + - + +
315A ALA* 3.5 10.1 + - + +
316A GLN* 3.5 32.5 + - - +
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Residues in contact with LEU 313 (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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124A LEU* 5.1 3.1 - - + -
127A VAL* 4.2 30.5 - - + -
130A PHE* 3.9 16.8 - - + -
309A PHE* 2.8 48.0 + - + +
310A LYS* 3.2 7.4 + - - +
312A PHE* 1.3 92.8 - - + +
314A ALA* 1.3 57.4 + - - +
316A GLN* 3.2 8.7 + - - -
318A GLY* 2.8 32.6 + - - -
320A ALA* 4.3 16.2 - - - -
322A VAL* 4.4 6.1 - - + -
323A VAL* 4.0 18.2 - - + -
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Residues in contact with ALA 314 (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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310A LYS 3.0 18.2 + - - +
311A THR* 4.2 4.3 - - - +
313A LEU* 1.3 72.5 - - - +
315A ALA* 1.3 61.8 + - - +
317A GLY* 3.1 13.7 + - - -
318A GLY 3.3 15.8 + - - +
320A ALA* 4.4 9.2 - - + +
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Residues in contact with ALA 315 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142A LEU* 3.8 21.7 - - + +
146A ASN* 3.7 26.5 - - - +
311A THR 3.0 20.7 + - - +
312A PHE* 3.7 7.4 - - - +
313A LEU 3.2 0.4 - - - -
314A ALA* 1.3 77.0 - - - +
316A GLN* 1.3 59.6 + - + +
317A GLY 3.5 0.4 + - - -
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Residues in contact with GLN 316 (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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130A PHE* 3.7 21.2 - - + -
131A HIS* 2.8 64.5 + - + +
132A VAL* 4.5 0.2 - - - -
134A ILE* 3.9 6.2 - - + +
142A LEU* 4.1 23.4 - - + +
148A ILE 5.1 0.6 + - - -
149A ALA* 4.0 7.7 - - - +
150A ILE 3.2 30.1 + - - +
151A ILE* 3.7 9.8 - - - +
312A PHE* 3.5 32.5 + - - +
313A LEU 3.2 3.0 + - - -
314A ALA 3.1 0.8 - - - -
315A ALA* 1.3 81.3 - - + +
317A GLY* 1.3 55.1 + - - +
318A GLY 3.4 2.5 - - - -
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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