Contacts of the helix formed by residues 248 - 265 (chain A) in PDB entry 4BLV
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 248 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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28A SER* 6.1 1.8 - - - +
31A GLU* 5.9 1.6 - - - +
77A GLU* 5.7 2.9 - - - -
246A PRO* 3.3 2.5 - - + +
247A TRP* 1.3 122.5 - - + +
249A LEU* 1.3 59.2 + - - +
250A GLU 3.4 2.0 - - - -
251A GLN* 3.2 25.5 + - + +
252A GLN* 2.9 59.5 + - + +
255A ASN* 5.1 5.9 - - - +
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Residues in contact with LEU 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 VAL* 4.4 6.5 - - + -
24A LEU* 4.1 21.3 - - + -
25A ILE* 4.2 13.0 - - + +
220A LEU* 4.1 10.8 - - + -
222A ILE* 4.3 3.8 - - + -
242A VAL* 4.1 21.3 - - + -
245A PRO* 3.9 19.7 - - + -
246A PRO* 3.2 27.4 + - + +
248A LYS* 1.3 76.8 - - - +
250A GLU* 1.3 63.7 + - - +
252A GLN* 3.2 15.7 + - - +
253A MET* 2.9 47.6 + - + +
1295A EDO 3.4 8.2 + - - +
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Residues in contact with GLU 250 (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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220A LEU* 4.3 20.9 - - + +
249A LEU* 1.3 75.5 - - - +
251A GLN* 1.3 57.1 + - - +
253A MET* 3.4 4.2 + - - +
254A ASN* 2.9 42.1 + - - +
274A VAL* 4.7 12.0 - - + +
275A SER* 5.6 1.0 - - - -
276A TRP* 3.3 29.1 + - - -
1295A EDO 2.8 39.7 + - - +
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Residues in contact with GLN 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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247A TRP 5.8 0.4 - - - +
248A LYS* 3.2 26.6 + - + +
250A GLU* 1.3 76.8 - - - +
252A GLN* 1.3 62.2 + - - +
254A ASN* 3.1 18.4 + - - +
255A ASN* 2.8 57.0 + - - +
1295A EDO 4.8 0.6 - - - -
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Residues in contact with GLN 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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24A LEU* 3.8 46.6 + - + +
28A SER* 6.0 2.2 - - - -
31A GLU* 6.0 0.4 + - - -
77A GLU* 4.1 19.7 - - + +
246A PRO* 6.1 0.2 - - - +
248A LYS* 2.9 52.0 + - + +
249A LEU* 3.6 19.2 + - - +
251A GLN* 1.3 76.0 - - - +
253A MET* 1.3 58.4 + - - +
255A ASN* 3.1 12.3 + - - +
256A VAL* 3.0 31.8 + - - +
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Residues in contact with MET 253 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A LEU* 4.1 5.8 - - + -
20A THR* 4.5 5.2 - - + -
21A VAL* 4.1 19.1 - - + -
24A LEU* 3.9 25.6 - - - -
220A LEU* 5.5 0.2 - - + -
222A ILE* 3.6 42.6 - - + -
249A LEU* 2.9 25.4 + - + +
250A GLU* 3.8 2.9 - - - +
252A GLN* 1.3 72.8 - - - +
254A ASN* 1.3 60.7 + - - +
256A VAL* 3.9 10.5 - - + -
257A LEU* 2.8 57.0 + - + +
260A LEU* 5.3 0.4 - - + -
274A VAL* 3.5 19.7 - - + -
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Residues in contact with ASN 254 (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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250A GLU* 2.9 35.6 + - - +
251A GLN* 3.1 23.8 + - - +
253A MET* 1.3 77.1 - - - +
255A ASN* 1.3 62.1 + - - +
257A LEU* 5.3 0.4 - - - -
258A PRO* 3.4 20.5 - - - +
274A VAL* 3.1 22.9 - - - +
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Residues in contact with ASN 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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75A PRO* 5.5 2.8 - - - +
77A GLU* 3.0 29.4 + - - +
248A LYS* 5.1 6.7 - - - +
251A GLN* 2.8 42.9 + - - +
252A GLN* 3.2 12.0 - - - +
254A ASN* 1.3 79.5 - - - +
256A VAL* 1.3 58.3 + - - +
258A PRO* 4.4 4.7 - - - +
259A TRP* 5.1 5.2 + - - +
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Residues in contact with VAL 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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20A THR* 4.7 9.4 - - + -
24A LEU* 5.1 0.7 - - + -
75A PRO* 4.0 15.3 - - + -
77A GLU* 4.4 14.1 - - + +
78A LEU* 3.7 39.7 - - + -
252A GLN 3.0 18.8 + - - +
253A MET* 3.8 27.6 - - + +
255A ASN* 1.3 78.2 - - - +
257A LEU* 1.3 63.5 + - - +
258A PRO 3.5 2.2 - - - -
259A TRP* 3.4 5.7 + - + +
260A LEU* 2.9 32.1 + - + +
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Residues in contact with LEU 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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17A LEU* 4.1 16.8 - - + -
222A ILE* 3.9 5.4 - - + -
223A GLU 4.7 0.9 - - - +
224A LEU* 4.2 21.1 - - + -
253A MET* 2.8 42.0 + - + +
254A ASN* 5.3 0.4 - - - -
256A VAL* 1.3 73.1 - - - +
258A PRO* 1.3 62.6 - - + +
260A LEU* 3.6 6.8 - - + +
261A HIS* 2.9 33.5 + - - +
272A ALA* 4.4 12.1 - - + +
273A THR 3.8 24.5 - - - +
274A VAL* 3.5 34.1 - - + -
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Residues in contact with PRO 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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254A ASN* 3.4 21.8 - - - +
255A ASN 4.4 3.1 - - - +
256A VAL 3.7 2.2 - - - -
257A LEU* 1.3 93.1 - - + +
259A TRP* 1.3 61.6 + - - +
261A HIS* 3.9 4.5 - - + +
262A SER* 3.0 25.1 + - - -
272A ALA* 5.9 0.7 - - + -
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Residues in contact with TRP 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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68A ILE* 4.0 20.4 - - + -
71A GLN* 3.7 25.6 - - + -
73A ASP* 3.1 41.5 + - - -
74A LEU* 3.9 8.7 - - + -
75A PRO* 3.5 42.8 - - + -
78A LEU* 3.7 17.7 - - + -
255A ASN 5.1 3.5 + - - +
256A VAL* 3.4 9.5 + - - +
257A LEU 3.3 0.4 - - - -
258A PRO* 1.3 78.9 - - - +
260A LEU* 1.3 72.0 + - + +
262A SER* 3.1 6.9 + - - -
263A LYS* 3.0 53.5 + - + +
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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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16A VAL* 3.8 27.1 - - + -
17A LEU* 4.7 8.3 - - + -
20A THR* 4.2 23.8 - - + +
68A ILE* 4.0 16.8 - - + -
78A LEU* 4.0 18.4 - - + -
224A LEU* 4.3 12.1 - - + -
256A VAL* 2.9 33.1 + - + +
257A LEU* 3.6 21.3 - - + +
259A TRP* 1.3 79.1 - - + +
261A HIS* 1.3 59.7 + - - +
263A LYS* 3.2 2.7 + - - +
264A LEU* 2.9 38.5 + - + +
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Residues in contact with HIS 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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224A LEU* 4.0 15.7 - - + +
225A ALA 3.1 13.4 + - - -
257A LEU 2.9 17.7 + - - +
258A PRO* 4.0 4.5 - - + +
260A LEU* 1.3 76.8 - - - +
262A SER* 1.3 60.0 + - - +
264A LEU* 4.7 2.2 - - - -
265A VAL* 2.8 52.1 + - + +
268A GLY* 3.9 16.7 - - - -
269A THR 3.0 27.9 + - - -
270A GLY 4.5 1.1 - - - -
271A HIS* 3.3 29.3 + - - -
272A ALA* 4.0 12.6 - - + -
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Residues in contact with SER 262 (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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258A PRO 3.0 20.0 + - - -
259A TRP* 3.1 7.8 + - - -
261A HIS* 1.3 78.8 + - - +
263A LYS* 1.3 69.2 - - - +
265A VAL 4.5 3.8 - - - +
266A PRO* 3.6 22.0 - - - -
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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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67A ARG* 3.4 30.7 - - - +
68A ILE* 3.8 20.4 - - + -
71A GLN* 3.6 20.2 + - - +
73A ASP* 4.4 8.2 + - - -
259A TRP* 3.0 65.3 + - + +
260A LEU 3.8 0.9 - - - +
262A SER* 1.3 85.5 + - - +
264A LEU* 1.3 63.1 + - - +
265A VAL 3.6 0.2 + - - -
266A PRO* 3.9 7.3 - - - +
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Residues in contact with LEU 264 (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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13A HIS* 4.2 23.5 - - + +
16A VAL* 4.2 22.9 - - + -
17A LEU 5.6 0.4 - - - +
63A GLU 3.8 6.0 - - - +
64A GLY* 3.4 40.2 - - - +
67A ARG* 2.8 24.9 + - + +
68A ILE* 4.3 12.1 - - + -
224A LEU* 3.8 24.7 - - + -
226A VAL* 5.2 0.3 - - - +
260A LEU* 2.9 27.1 + - + +
261A HIS* 4.2 0.4 - - - +
263A LYS* 1.3 77.1 - - - +
265A VAL* 1.3 70.2 + - + +
266A PRO* 3.5 1.6 - - - -
1285A EDO 3.9 8.5 + - - -
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Residues in contact with VAL 265 (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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224A LEU* 4.5 0.4 - - + -
226A VAL* 3.7 32.1 - - + +
261A HIS* 2.8 41.6 + - + +
262A SER* 3.7 5.5 - - - +
264A LEU* 1.3 86.3 - - + +
266A PRO* 1.3 61.4 - - - +
267A ALA 3.2 0.2 - - - -
268A GLY* 2.9 20.2 + - - +
269A THR* 3.4 42.8 - - - +
1286A EDO 3.7 12.3 - - - +
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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