Contacts of the helix formed by residues 249 - 267 (chain A) in PDB entry 4K71
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 ASP 249 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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67A HIS* 2.7 32.8 + - - -
244A GLU* 2.9 20.7 + - + +
245A CYS 4.3 0.2 + - - -
247A HIS* 2.5 35.5 + - - +
248A GLY* 1.3 75.2 - - - +
250A LEU* 1.3 57.2 + - - +
251A LEU 3.5 1.6 - - - -
252A GLU* 3.5 32.0 - - + +
253A CYS* 3.1 27.7 + - - +
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Residues in contact with LEU 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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22A LEU* 3.7 17.2 - - + +
25A ILE* 3.7 19.3 - - + -
26A ALA* 3.5 39.9 - - + +
29A GLN* 3.8 12.8 - - - +
70A PHE* 6.2 2.1 - - + -
106A LYS* 5.9 0.2 - - - +
149A PHE 5.7 1.3 - - - +
151A ALA* 4.0 22.4 - - + +
245A CYS* 3.8 29.1 - - - +
248A GLY* 3.1 17.4 + - - +
249A ASP* 1.3 73.9 - - - +
251A LEU* 1.3 63.0 + - + +
252A GLU* 4.0 0.2 + - - -
253A CYS* 3.4 5.1 - - - +
254A ALA* 2.8 31.7 + - - +
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Residues in contact with LEU 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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10A ARG* 4.1 14.6 - - + -
14A LEU* 3.6 26.3 - - + +
19A PHE* 3.7 40.2 - - + +
22A LEU* 3.7 28.5 - - + -
23A VAL* 4.3 4.9 - - + +
66A LEU* 3.7 23.8 - - + -
70A PHE* 4.0 24.0 - - + -
249A ASP 3.5 0.6 - - - -
250A LEU* 1.3 77.0 - - + +
252A GLU* 1.3 70.0 + - - +
254A ALA 3.5 0.2 + - - -
255A ASP* 3.1 25.1 + - - +
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Residues in contact with GLU 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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6A GLU* 4.1 10.4 - - - +
10A ARG* 3.6 29.6 + - - +
66A LEU* 3.8 26.6 - - - +
244A GLU* 3.7 20.9 - - + +
249A ASP* 3.5 47.7 - - + +
251A LEU* 1.3 81.4 + - - +
253A CYS* 1.3 52.4 + - - +
255A ASP* 3.3 1.2 + - - +
256A ASP* 2.9 41.0 + - - +
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Residues in contact with CYS 253 (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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150A TYR* 4.2 3.4 - - - -
152A PRO* 4.3 3.8 - - - -
241A VAL* 3.4 24.2 - - - +
244A GLU* 3.7 11.1 + - - -
245A CYS* 2.0 57.7 - - - +
249A ASP 3.1 19.0 + - - +
250A LEU 3.4 4.0 - - - +
252A GLU* 1.3 78.4 - - - +
254A ALA* 1.3 58.3 + - - +
256A ASP* 3.9 0.7 - - - -
257A ARG* 3.0 26.3 + - - +
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Residues in contact with ALA 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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14A LEU* 3.9 12.1 - - + +
22A LEU* 3.5 33.0 - - + -
152A PRO* 3.9 25.1 - - + -
155A LEU* 5.4 2.5 - - + -
250A LEU 2.8 14.3 + - - +
251A LEU 4.0 0.7 - - - +
253A CYS* 1.3 74.1 - - - +
255A ASP* 1.3 58.0 + - - +
257A ARG* 3.7 1.8 - - - +
258A ALA* 3.1 27.5 + - - +
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Residues in contact with ASP 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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9A HIS* 4.0 0.2 + - - -
10A ARG* 2.7 31.3 + - - +
13A ASP* 2.7 47.6 - - - +
14A LEU* 3.9 11.5 - - + +
251A LEU 3.1 18.4 + - - +
252A GLU 3.5 4.0 - - - +
253A CYS 3.2 0.2 - - - -
254A ALA* 1.3 75.3 - - - +
256A ASP* 1.3 66.5 + - - +
257A ARG 3.4 0.2 + - - -
258A ALA* 3.4 7.4 + - - +
259A ASP* 3.1 30.3 + - - +
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Residues in contact with ASP 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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10A ARG* 4.8 8.1 + - - -
240A LYS* 4.1 14.9 - - + +
241A VAL* 3.9 19.6 - - + +
244A GLU* 2.5 34.5 - - - +
252A GLU* 2.9 19.6 + - - +
253A CYS 4.0 0.7 - - - +
255A ASP* 1.3 70.5 - - - +
257A ARG* 1.3 60.4 + - - +
259A ASP* 3.2 15.2 + - - +
260A LEU* 2.8 26.9 + - - +
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Residues in contact with ARG 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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150A TYR* 3.1 39.8 + - - +
152A PRO* 3.4 33.6 + - - +
153A GLU* 3.2 29.4 + - - +
156A PHE* 6.0 0.2 - - - +
238A LEU* 6.4 1.6 - - + -
241A VAL* 3.9 13.9 - - + +
253A CYS 3.0 19.2 + - - +
254A ALA* 3.7 5.8 - - - +
255A ASP 3.2 0.2 - - - -
256A ASP* 1.3 74.7 - - - +
258A ALA* 1.3 61.2 + - - +
260A LEU* 3.1 9.2 + - + +
261A ALA* 2.9 28.5 + - + +
284A LEU* 5.2 5.7 + - - +
287A SER* 3.5 40.5 + - - -
291A ALA* 4.3 10.9 - - - +
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Residues in contact with ALA 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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14A LEU* 5.7 3.1 - - + -
254A ALA 3.1 12.0 + - - +
255A ASP* 3.4 12.8 + - - +
257A ARG* 1.3 77.9 - - - +
259A ASP* 1.3 65.0 + - - +
261A ALA* 3.3 7.8 + - - +
262A LYS* 3.0 23.6 + - - +
283A LEU* 4.4 31.6 - - + +
286A LYS* 5.9 0.3 - - - -
287A SER* 5.0 4.0 + - - -
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Residues in contact with ASP 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 ASP* 3.1 22.8 + - - +
256A ASP* 3.4 18.9 - - - +
257A ARG 3.2 0.2 - - - -
258A ALA* 1.3 76.3 - - - +
260A LEU* 1.3 63.6 + - - +
262A LYS* 3.5 12.5 + - - +
263A TYR* 3.1 23.4 + - - +
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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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234A LEU* 3.9 29.6 - - + +
237A ASP* 3.9 27.1 - - + +
238A LEU* 3.9 46.9 - - + +
241A VAL* 4.9 3.8 - - + -
256A ASP 2.8 14.5 + - - +
257A ARG* 3.4 13.2 - - + +
259A ASP* 1.3 74.3 - - - +
261A ALA* 1.3 59.3 + - - +
263A TYR* 3.1 8.8 + - + +
264A ILE* 2.9 46.4 + - + +
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Residues in contact with ALA 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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257A ARG* 2.9 10.7 + - + +
258A ALA* 3.5 10.1 - - - +
260A LEU* 1.3 77.1 - - - +
262A LYS* 1.3 57.3 + - - +
264A ILE* 3.5 4.5 + - - +
265A CYS* 3.1 34.6 + - - -
283A LEU* 6.2 1.1 - - + -
286A LYS* 4.6 13.2 - - + -
287A SER* 3.5 26.5 - - - +
290A ILE* 3.7 18.1 - - + +
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Residues in contact with LYS 262 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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258A ALA 3.0 16.7 + - - +
259A ASP* 3.6 14.1 - - - +
260A LEU 3.2 0.2 - - - -
261A ALA* 1.3 73.4 - - - +
263A TYR* 1.3 65.3 + - - +
265A CYS* 3.2 7.2 + - - +
266A GLU* 3.1 51.8 + - + +
286A LYS* 4.8 12.1 - - - +
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Residues in contact with TYR 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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230A GLU* 2.8 35.0 + - - -
233A LYS* 3.9 35.7 - - - +
234A LEU* 4.0 20.4 - - + -
237A ASP* 5.5 0.9 - - - +
259A ASP 3.1 14.1 + - - +
260A LEU* 3.5 12.1 - - + +
262A LYS* 1.3 72.2 - - - +
264A ILE* 1.3 70.8 + - + +
266A GLU* 3.2 11.0 + - - -
267A ASN* 3.0 59.0 + - + +
271A ILE* 4.5 2.0 - - + -
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Residues in contact with ILE 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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219A LEU* 6.4 0.2 - - + -
223A PHE* 5.1 6.5 - - + -
234A LEU* 3.8 30.5 - - + -
260A LEU* 2.9 39.1 + - + +
261A ALA* 3.7 5.4 - - - +
263A TYR* 1.3 75.7 - - - +
265A CYS* 1.3 62.6 + - - +
267A ASN 3.2 13.2 + - - -
268A GLN* 3.3 13.2 + - - +
271A ILE* 3.7 20.3 - - + +
275A LEU* 3.8 22.0 - - + -
290A ILE* 3.9 35.4 - - + -
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Residues in contact with CYS 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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261A ALA 3.1 20.0 + - - +
262A LYS* 3.2 6.9 + - - +
264A ILE* 1.3 78.2 - - - +
266A GLU* 1.3 58.9 + - + +
267A ASN 3.4 0.4 - - - -
268A GLN* 3.0 22.8 + - - +
279A CYS* 2.0 57.6 - - + +
286A LYS* 3.9 14.6 - - - +
290A ILE* 3.6 16.6 - - - -
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Residues in contact with GLU 266 (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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262A LYS* 3.1 47.8 + - + +
263A TYR* 3.2 11.4 + - - +
265A CYS* 1.3 77.4 - - + +
267A ASN* 1.3 69.2 + - - +
268A GLN 3.7 1.6 - - - -
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Residues in contact with ASN 267 (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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230A GLU* 5.8 0.2 + - - -
263A TYR* 3.0 56.0 + - + +
264A ILE 3.2 6.5 + - - +
266A GLU* 1.3 88.9 + - - +
268A GLN* 1.3 61.8 + - - +
269A ASP* 3.3 3.4 - - - +
270A SER* 3.2 22.2 + - - +
271A ILE* 3.2 25.0 - - + +
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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