Contacts of the helix formed by residues 245 - 263 (chain A) in PDB entry 3BRS
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 LYS 245 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111A THR* 5.0 0.2 + - - -
227A MET* 6.5 0.9 - - - -
243A VAL* 5.5 1.1 - - + +
244A GLN* 1.3 81.4 - - - +
246A PRO* 1.3 66.7 - - - +
247A PHE* 3.1 3.6 - - + -
248A ASN* 2.9 32.1 + - - +
249A ILE* 3.0 11.6 + - - +
272A SER* 3.4 23.7 + - - +
273A GLY* 3.7 32.1 + - - +
274A CYS* 4.3 10.9 + - - +
275A ALA* 5.3 4.2 - - - +
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Residues in contact with PRO 246 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A PHE* 3.6 39.0 - - + +
24A VAL* 3.6 18.2 - - + -
25A LEU* 3.4 15.6 - - + +
225A SER 3.4 24.0 - - - +
226A SER* 3.8 12.3 - - - -
244A GLN* 3.5 6.5 - - + +
245A LYS* 1.3 87.3 - - - +
247A PHE* 1.3 65.7 + - - +
249A ILE* 3.2 15.3 + - + +
250A GLY 3.1 15.9 + - - -
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Residues in contact with PHE 247 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A VAL* 3.4 25.7 - - + +
27A GLU* 3.7 13.5 - - + -
28A GLY* 3.4 34.6 - - - -
31A MET* 3.9 32.3 - - + -
245A LYS* 3.0 1.7 + - + -
246A PRO* 1.3 83.4 - - - +
248A ASN* 1.3 70.7 + - - +
250A GLY 3.2 0.5 + - - -
251A TYR* 2.9 45.0 + + - +
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Residues in contact with ASN 248 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245A LYS* 2.9 31.3 + - + +
247A PHE* 1.3 91.1 - - - +
249A ILE* 1.3 64.3 + - - +
251A TYR* 4.2 8.7 - - - +
252A LEU* 2.9 46.1 + - + +
272A SER* 4.1 11.7 - - - +
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Residues in contact with ILE 249 (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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21A PHE* 3.9 29.2 - - + -
25A LEU* 3.5 20.0 - - + -
96A ILE* 3.8 18.1 - - + +
97A ASP* 3.8 6.7 - - - +
109A VAL* 3.6 31.9 - - + +
110A ALA* 4.6 1.8 - - - -
111A THR* 4.1 19.7 - - - +
244A GLN* 4.8 0.2 - - - +
245A LYS 3.0 16.2 + - - +
246A PRO* 3.2 6.3 + - + +
248A ASN* 1.3 75.2 - - - +
250A GLY* 1.3 57.9 + - - +
252A LEU 4.1 0.2 - - - -
253A GLY* 3.1 23.7 + - - -
272A SER* 3.1 30.0 + - - +
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Residues in contact with GLY 250 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A LEU* 3.7 29.6 - - - +
29A ALA* 3.4 22.9 - - - +
70A LEU* 5.0 1.6 - - - +
96A ILE* 5.3 2.9 - - - -
246A PRO 3.1 8.5 + - - -
247A PHE 3.8 0.4 - - - -
249A ILE* 1.3 77.7 - - - +
251A TYR* 1.3 68.0 + - - +
253A GLY* 3.4 1.1 + - - -
254A VAL* 3.3 14.9 + - - +
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Residues in contact with TYR 251 (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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28A GLY* 3.3 24.0 - - - +
31A MET* 4.0 13.0 - - + -
32A ALA* 3.6 27.5 - - + +
35A GLU* 3.7 23.8 + - + +
36A TYR* 3.9 5.4 + + - -
247A PHE* 2.9 36.6 + + + +
248A ASN* 4.0 11.4 - - - +
250A GLY* 1.3 77.2 - - - +
252A LEU* 1.3 76.1 + - + +
254A VAL 3.2 0.3 + - - -
255A GLU* 3.0 49.0 + - + -
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Residues in contact with LEU 252 (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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109A VAL* 4.0 26.0 - - + -
248A ASN* 2.9 41.0 + - + +
251A TYR* 1.3 81.8 - - + +
253A GLY* 1.3 67.3 + - - +
255A GLU* 3.9 22.0 - - - +
256A LYS* 2.9 42.7 + - + +
270A LEU* 4.8 11.7 - - + -
271A ASP 5.4 2.5 - - - +
272A SER* 5.1 8.7 - - - -
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Residues in contact with GLY 253 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A LEU* 3.9 13.0 - - - -
94A ILE* 3.9 27.4 - - - +
96A ILE* 4.3 1.1 - - - -
109A VAL* 4.1 6.7 - - - +
249A ILE 3.1 19.0 + - - -
250A GLY 3.4 2.0 + - - -
251A TYR 3.2 0.4 - - - -
252A LEU* 1.3 75.3 - - - +
254A VAL* 1.3 63.0 + - - +
256A LYS* 4.0 1.0 - - - +
257A ALA* 3.0 24.3 + - - +
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Residues in contact with VAL 254 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A MET* 3.9 15.3 - - - +
29A ALA* 3.7 25.4 - - + +
32A ALA* 3.7 15.7 - - + -
33A ALA* 4.1 7.4 - - + +
38A ILE* 3.4 32.3 - - + -
40A LEU* 4.5 9.9 - - + -
70A LEU* 4.1 12.6 - - + -
250A GLY 3.3 12.5 + - - +
251A TYR 3.2 6.3 + - - +
252A LEU 3.1 0.4 - - - -
253A GLY* 1.3 75.0 - - - +
255A GLU* 1.3 69.7 + - - +
257A ALA* 2.9 23.8 + - - +
258A LEU* 3.2 4.9 + - - +
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Residues in contact with GLU 255 (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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32A ALA* 4.3 1.0 - - + +
36A TYR* 2.7 44.0 + - + +
251A TYR* 3.0 37.0 + - + +
252A LEU* 3.9 17.0 - - - +
254A VAL* 1.3 76.6 - - - +
256A LYS* 1.3 83.7 + - + +
258A LEU* 2.8 29.5 - - - +
259A LYS* 3.7 8.0 + - - +
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Residues in contact with LYS 256 (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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107A ILE* 4.1 13.1 - - + +
252A LEU* 2.9 33.3 + - + +
253A GLY* 4.5 1.1 - - - +
255A GLU* 1.3 95.9 + - + +
257A ALA* 1.3 60.6 + - - +
258A LEU 2.9 4.9 - - - -
259A LYS* 3.1 35.4 + - + +
260A LEU* 3.4 14.8 + - - +
266A VAL* 4.1 25.1 - - + +
267A PRO* 5.8 1.8 - - - -
270A LEU* 3.8 32.5 - - + -
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Residues in contact with ALA 257 (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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8A MET* 3.5 25.8 - - + -
68A VAL* 3.9 21.0 - - + +
70A LEU* 5.6 0.4 - - + -
94A ILE* 4.0 5.8 - - + +
253A GLY 3.0 14.6 + - - +
254A VAL 2.9 12.9 + - - +
256A LYS* 1.3 76.6 - - - +
258A LEU* 1.3 59.6 + - - +
260A LEU* 3.4 16.7 + - - +
261A LEU* 3.2 25.1 + - - +
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Residues in contact with LEU 258 (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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6A TYR* 3.8 33.2 - - + -
8A MET* 3.9 15.3 - - + -
36A TYR* 3.4 47.8 - - + +
38A ILE* 3.9 13.7 - - + -
254A VAL 3.2 4.1 + - - +
255A GLU* 2.8 17.9 + - - +
257A ALA* 1.3 78.3 - - - +
259A LYS* 1.3 64.3 + - + +
261A LEU* 3.4 4.5 + - + +
262A LYS* 3.0 43.7 + - + +
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Residues in contact with LYS 259 (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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255A GLU* 4.3 6.3 - - - +
256A LYS* 3.1 40.0 + - + +
258A LEU* 1.3 75.0 - - + +
260A LEU* 1.3 64.7 + - - +
262A LYS* 3.1 9.6 + - - +
263A LYS 2.9 17.5 + - - -
264A GLU* 3.1 53.2 + - + +
265A TYR 4.1 15.0 + - - +
266A VAL* 4.3 9.6 - - + -
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Residues in contact with LEU 260 (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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92A LYS* 3.7 34.6 + - + -
94A ILE* 3.4 33.9 - - + -
106A ASP* 3.8 25.4 - - + +
107A ILE* 3.9 4.3 - - + -
256A LYS 3.7 8.3 - - - +
257A ALA* 3.6 9.2 - - - +
258A LEU 3.2 0.4 - - - -
259A LYS* 1.3 78.7 - - - +
261A LEU* 1.3 57.5 + - - +
263A LYS* 2.9 22.1 + - - +
264A GLU 4.6 5.2 - - - +
266A VAL* 3.3 30.1 - - + -
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Residues in contact with LEU 261 (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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6A TYR* 3.6 52.1 + - + -
8A MET* 4.2 9.0 - - + -
67A ASP* 3.9 23.3 - - + +
68A VAL* 3.8 14.1 - - + -
92A LYS* 3.5 34.3 - - + +
257A ALA 3.2 17.0 + - - +
258A LEU* 3.8 7.0 - - + +
260A LEU* 1.3 80.1 - - - +
262A LYS* 1.3 59.0 - - - +
263A LYS* 3.2 10.5 + - - +
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Residues in contact with LYS 262 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A TYR* 4.7 20.0 - - + +
258A LEU* 3.0 39.8 + - + +
259A LYS 3.4 8.3 - - - +
261A LEU* 1.3 73.4 - - - +
263A LYS* 1.3 73.4 + - - +
264A GLU* 3.3 25.9 + - - +
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Residues in contact with LYS 263 (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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92A LYS* 5.4 9.0 - - - +
259A LYS 2.9 3.8 + - - -
260A LEU 2.9 15.4 + - - +
261A LEU 4.1 9.6 + - - +
262A LYS* 1.3 82.9 - - - +
264A GLU* 1.3 58.6 + - - +
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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
------------------------------------------------------------
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