Contacts of the helix formed by residues 246 - 265 (chain B) in PDB entry 3K4H
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 ASN 246 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244B ASP* 3.2 18.5 + - - +
245B VAL* 1.3 79.3 - - - +
247B ILE* 1.3 65.8 + - - +
248B TYR* 3.6 11.4 - - - +
249B GLN* 3.0 52.0 + - + +
250B LEU 3.2 8.0 + - - -
274B ILE* 3.9 8.3 - - + +
275B PRO* 4.3 11.0 - - + +
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Residues in contact with ILE 247 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27B PHE* 3.6 51.8 - - + +
30B GLU* 3.8 16.1 - - + +
31B VAL* 3.6 21.0 - - + +
228B ASN* 2.9 36.3 - - - +
229B ASN 5.3 1.1 - - - +
230B ALA* 6.1 0.2 - - - -
244B ASP* 5.8 0.7 - - - +
245B VAL* 3.7 22.4 - - + -
246B ASN* 1.3 69.3 - - - +
248B TYR* 1.3 65.9 + - - +
250B LEU* 3.0 12.0 + - + +
251B GLY* 3.0 19.9 + - - -
1D GLC 5.6 0.2 - - - -
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Residues in contact with TYR 248 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30B GLU* 3.7 26.8 + - - +
33B ARG* 3.6 37.2 - - + +
34B GLY* 3.3 28.4 - - - -
37B SER* 2.4 35.7 + - - -
246B ASN* 3.6 9.9 - - - +
247B ILE* 1.3 79.6 - - - +
249B GLN* 1.3 80.1 + - - +
251B GLY 3.1 0.9 + - - -
252B TYR* 2.8 38.7 + + - +
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Residues in contact with GLN 249 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268A THR* 3.1 37.5 + - + +
269A ALA 6.0 1.8 - - - +
246B ASN* 3.0 35.3 + - + +
248B TYR* 1.3 98.4 - - - +
250B LEU* 1.3 58.9 + - - +
252B TYR* 3.7 19.2 - - - -
253B GLU* 2.8 52.4 + - - +
274B ILE* 3.9 15.5 - - + -
275B PRO* 5.9 3.1 - - + -
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Residues in contact with LEU 250 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27B PHE* 4.1 14.1 - - + -
31B VAL* 4.7 1.3 - - + -
98B ILE* 4.1 13.0 - - + -
111B VAL* 3.3 34.4 - - + +
112B ASP* 3.5 33.0 - - - +
113B ASN* 3.9 9.0 - - - +
246B ASN 3.2 5.6 + - - +
247B ILE* 3.0 18.8 + - + +
249B GLN* 1.3 74.1 - - - +
251B GLY* 1.3 59.1 + - - +
254B ALA* 2.8 33.3 + - - +
274B ILE* 3.9 15.5 - - + +
2D GLC 3.8 34.1 - - - +
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Residues in contact with GLY 251 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31B VAL* 3.4 35.2 - - - +
35B ILE* 3.4 22.1 - - - +
98B ILE* 4.3 2.0 - - - -
247B ILE 3.0 10.5 + - - -
248B TYR 3.4 2.2 - - - -
250B LEU* 1.3 77.1 - - - +
252B TYR* 1.3 60.6 + - - +
254B ALA* 3.4 1.0 + - - +
255B ALA 3.1 17.5 + - - -
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Residues in contact with TYR 252 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268A THR* 4.4 11.2 + - - -
34B GLY* 3.4 15.0 - - - +
37B SER* 3.8 16.8 - - - -
38B PHE* 3.5 54.7 - + + +
41B VAL* 4.5 10.4 - - + +
248B TYR* 2.8 29.2 + + + +
249B GLN* 3.6 30.3 - - - +
251B GLY* 1.3 70.8 - - - +
253B GLU* 1.3 67.6 + - - +
255B ALA* 3.3 4.9 + - - +
256B LYS* 3.1 37.5 + - + +
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Residues in contact with GLU 253 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268A THR* 4.6 7.5 + - - -
270A LYS* 3.3 35.7 - - + +
111B VAL* 4.1 4.3 - - + -
249B GLN* 2.8 47.1 + - - +
250B LEU 4.0 0.9 - - - +
252B TYR* 1.3 77.5 - - - +
254B ALA* 1.3 65.4 + - - +
256B LYS* 3.5 22.6 + - + +
257B ALA* 3.1 24.3 + - - +
272B ILE* 3.7 29.1 - - + +
274B ILE* 3.8 16.5 - - + +
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Residues in contact with ALA 254 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74B ILE* 4.7 10.3 - - + -
96B VAL* 3.7 18.3 - - + +
98B ILE* 3.4 26.2 - - + -
111B VAL* 3.7 17.8 - - + +
250B LEU 2.8 17.9 + - - +
251B GLY 3.5 4.5 - - - +
253B GLU* 1.3 76.5 - - - +
255B ALA* 1.3 61.9 + - - +
257B ALA* 3.3 3.5 + - - +
258B LEU* 3.0 21.1 + - - +
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Residues in contact with ALA 255 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B LEU* 4.8 8.7 - - + -
35B ILE* 4.0 27.6 - - + +
38B PHE* 3.7 18.8 - - + -
39B ALA 4.6 0.7 - - - +
74B ILE* 4.3 10.3 - - + +
251B GLY 3.1 12.8 + - - +
252B TYR 3.3 8.0 + - - +
254B ALA* 1.3 72.7 - - - +
256B LYS* 1.3 67.3 + - - +
258B LEU* 3.2 2.7 + - - +
259B VAL* 2.8 30.0 + - - +
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Residues in contact with LYS 256 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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260A ASP* 3.3 31.6 + - - +
264A ASN* 3.9 13.3 - - - +
268A THR* 5.8 2.0 - - - -
270A LYS* 4.3 14.8 - - - +
38B PHE* 3.5 41.5 - - + -
252B TYR* 3.1 27.0 + - + +
253B GLU* 3.5 28.3 - - + +
255B ALA* 1.3 75.9 - - - +
257B ALA* 1.3 63.7 + - - +
259B VAL* 3.4 2.6 + - - +
260B ASP* 3.1 23.5 + - + +
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Residues in contact with ALA 257 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96B VAL* 4.0 14.8 - - + -
109B THR* 4.4 7.2 - - + -
253B GLU 3.1 18.6 + - - +
254B ALA 3.5 5.8 - - - +
255B ALA 3.2 0.2 - - - -
256B LYS* 1.3 76.2 - - - +
258B LEU* 1.3 63.3 + - - +
260B ASP* 3.1 9.8 + - - +
261B LYS* 2.9 22.3 + - - +
270B LYS* 5.5 6.3 - - - +
272B ILE* 3.5 24.7 - - + -
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Residues in contact with LEU 258 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11B LEU* 4.0 19.5 - - + -
72B GLY* 3.6 8.3 - - - +
73B ILE 3.4 30.7 - - - +
74B ILE* 3.7 13.7 - - + -
94B PRO* 3.5 28.7 - - + +
95B PHE* 3.5 23.1 - - - -
96B VAL* 3.5 11.6 - - + +
254B ALA 3.0 14.1 + - - +
255B ALA* 3.8 5.2 - - - +
257B ALA* 1.3 71.9 - - - +
259B VAL* 1.3 55.8 + - - +
261B LYS* 2.9 7.0 + - + +
262B VAL* 2.7 44.3 + - + +
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Residues in contact with VAL 259 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11B LEU* 4.3 18.2 - - + -
38B PHE* 3.7 19.1 - - + -
39B ALA* 5.6 1.3 - - - -
42B GLU* 4.1 15.7 - - + -
44B TYR* 3.8 28.9 - - + -
255B ALA 2.8 25.4 + - - +
256B LYS 3.9 3.6 - - - +
258B LEU* 1.3 72.3 - - - +
260B ASP* 1.3 61.5 + - - +
262B VAL* 3.3 7.2 + - - +
263B GLU* 3.1 49.4 + - - +
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Residues in contact with ASP 260 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256A LYS* 2.6 38.3 + - - -
256B LYS* 3.1 14.5 + - + +
257B ALA* 3.4 11.2 - - - +
259B VAL* 1.3 76.3 - - - +
261B LYS* 1.3 63.2 + - - +
262B VAL 3.2 0.2 + - - -
263B GLU* 3.2 1.0 + - - -
264B ASN* 2.4 60.0 + - - +
265B ALA 4.2 0.2 + - - -
266B GLU* 3.6 9.4 + - - +
270B LYS* 4.4 9.5 + - - -
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Residues in contact with LYS 261 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94B PRO* 4.1 23.2 - - + +
95B PHE* 3.3 34.3 - - - +
96B VAL* 4.4 10.5 - - + -
107B GLU 5.8 2.0 + - - -
108B ILE* 6.1 0.2 - - - +
109B THR* 3.8 27.5 + - + +
257B ALA 2.9 10.8 + - - +
258B LEU* 2.9 12.1 + - + +
260B ASP* 1.3 79.4 + - - +
262B VAL* 1.3 61.7 + - - +
265B ALA* 3.4 18.9 + - - -
266B GLU* 3.5 33.3 + - + +
267B SER* 3.9 13.3 + - - +
268B THR 4.4 1.9 + - - +
269B ALA* 5.5 0.8 - - - +
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Residues in contact with VAL 262 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11B LEU* 5.1 3.6 - - + -
44B TYR* 4.1 20.4 - - + +
71B GLY* 3.4 42.8 - - - +
72B GLY* 3.7 11.7 - - - +
94B PRO* 3.9 14.3 - - + +
258B LEU* 2.7 28.0 + - + +
259B VAL* 3.8 7.9 - - - +
260B ASP 3.2 0.4 - - - -
261B LYS* 1.3 73.0 - - - +
263B GLU* 1.3 62.4 + - + +
265B ALA 4.6 1.2 + - - -
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Residues in contact with GLU 263 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9B LYS* 4.4 6.9 - - - -
42B GLU* 4.7 10.1 - - - +
44B TYR* 2.7 39.8 + - - +
259B VAL* 3.1 24.7 + - - +
260B ASP* 5.7 0.3 - - - -
262B VAL* 1.3 81.5 - - + +
264B ASN* 1.3 74.9 + - - +
265B ALA 3.6 0.7 - - - -
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Residues in contact with ASN 264 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256A LYS* 5.4 1.2 - - - +
260B ASP* 2.4 43.7 + - - +
263B GLU* 1.3 94.5 + - - +
265B ALA* 1.3 75.5 + - - +
266B GLU* 3.3 5.2 + - + +
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Residues in contact with ALA 265 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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261B LYS 3.4 12.0 + - - -
262B VAL 4.6 1.2 + - - -
263B GLU 3.6 1.8 - - - -
264B ASN* 1.3 82.3 - - - +
266B GLU* 1.3 61.5 + - - +
267B SER* 3.4 6.2 + - - -
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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
------------------------------------------------------------
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