Contacts of the helix formed by residues 248 - 264 (chain B) in PDB entry 6T2C
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 ILE 248 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221B ALA 5.1 6.9 + - - +
222B LEU* 5.6 4.7 - - + -
223B THR 5.7 0.4 - - - +
224B LEU* 5.0 9.0 - - + -
244B PRO* 3.7 13.6 - - + +
245B GLY* 3.5 28.7 - - - +
247B GLN* 1.3 77.4 - - - +
249B ARG* 1.3 63.1 + - - +
250B GLY 3.5 1.6 - - - -
251B PHE* 4.4 7.2 - - + -
252B VAL* 3.3 27.3 + - + +
340B ALA* 5.3 2.7 - - - +
343B MET* 3.7 47.8 - - + +
344B PHE* 4.0 29.4 - - + -
347B LYS* 6.0 1.8 - - + -
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Residues in contact with ARG 249 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122B LEU* 4.1 13.1 - - + +
126B ARG* 4.1 26.6 + - - +
127B GLN 2.4 32.7 + - - -
128B THR* 2.7 28.1 + - - +
243B THR* 3.9 4.6 - - - +
244B PRO* 3.4 34.4 - - - +
245B GLY 3.3 13.8 + - - -
246B MET* 3.5 28.0 + - + +
247B GLN 3.3 2.0 - - - -
248B ILE* 1.3 79.2 - - - +
250B GLY* 1.3 60.6 + - - +
252B VAL* 3.5 7.8 + - + +
253B TYR* 2.9 28.2 + - - +
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Residues in contact with GLY 250 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122B LEU* 4.0 20.3 - - - +
163B LEU* 5.2 5.6 - - - -
166B PHE* 6.0 0.2 - - - -
167B LEU* 4.1 21.9 - - - +
246B MET 4.6 2.0 + - - -
247B GLN 4.3 3.6 + - - -
248B ILE 3.5 0.4 - - - -
249B ARG* 1.3 77.0 - - - +
251B PHE* 1.3 60.1 + - - +
253B TYR* 3.2 6.2 + - - +
254B PHE* 3.0 32.1 + - - -
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Residues in contact with PHE 251 (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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205A PHE* 4.4 1.3 - + - -
167B LEU* 3.6 43.1 - - + -
170B VAL* 3.9 11.9 - - + -
171B LEU* 3.6 24.0 - - + -
247B GLN 3.3 25.8 - - - -
248B ILE* 4.4 8.3 - - + +
249B ARG 3.4 0.2 - - - -
250B GLY* 1.3 75.0 - - - +
252B VAL* 1.3 58.4 + - - +
254B PHE* 3.3 5.6 + - - +
255B VAL* 3.0 33.8 + - - +
336B LEU* 4.0 19.1 - - + +
337B LEU* 5.4 0.2 - - - +
339B VAL* 3.6 33.0 - - + -
340B ALA* 3.7 22.9 - - + +
343B MET* 4.8 9.9 - - + -
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Residues in contact with VAL 252 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244B PRO* 6.0 6.7 - - + -
248B ILE* 3.3 24.3 + - + +
249B ARG* 3.5 8.2 + - + +
250B GLY 3.3 0.4 - - - -
251B PHE* 1.3 77.9 - - - +
253B TYR* 1.3 58.4 + - - +
255B VAL* 3.9 3.0 - - - +
256B GLU* 2.9 44.0 + - + +
340B ALA* 4.4 7.4 - - + -
344B PHE* 3.6 32.8 - - + -
411B MET* 4.3 15.9 - - + +
412B PHE* 4.3 9.6 - - + -
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Residues in contact with TYR 253 (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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117B THR* 4.2 18.1 + - + +
121B LYS* 3.7 42.3 + - + +
122B LEU* 5.0 7.6 - - + -
163B LEU* 4.3 12.6 - - + -
249B ARG 2.9 18.0 + - - +
250B GLY* 3.2 6.7 + - - +
252B VAL* 1.3 77.4 - - - +
254B PHE* 1.3 83.8 + + - +
256B GLU* 3.8 4.9 - - + +
257B LEU* 2.9 47.9 + - + +
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Residues in contact with PHE 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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110B THR* 4.4 4.8 - - + +
113B ALA 4.5 1.3 - - - -
114B ILE* 3.7 48.9 - - + -
117B THR* 4.3 7.2 - - - -
163B LEU* 3.9 27.6 - - + -
164B ILE* 5.0 4.3 - - - -
167B LEU* 3.6 28.5 - - + -
250B GLY 3.0 19.2 + - - +
251B PHE* 3.3 5.8 + - - +
253B TYR* 1.3 95.2 - + - +
255B VAL* 1.3 64.0 + - - +
257B LEU* 3.2 14.1 + - + +
258B LEU* 3.1 22.0 + - - +
336B LEU* 4.3 16.2 - - + +
337B LEU* 3.9 20.3 - - + +
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Residues in contact with VAL 255 (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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251B PHE 3.0 20.2 + - - +
252B VAL 4.0 2.9 - - - +
254B PHE* 1.3 75.2 - - - +
256B GLU* 1.3 60.2 + - - +
258B LEU* 3.2 8.1 + - + +
259B ALA* 2.9 26.9 + - + +
322B VAL* 4.6 9.6 - - + -
336B LEU 5.3 0.2 - - - +
337B LEU* 3.5 39.9 - - + +
340B ALA* 3.9 13.2 - - + -
341B PRO* 5.0 2.2 - - + -
412B PHE* 3.8 26.5 - - + -
415B LEU* 4.3 21.5 - - + +
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Residues in contact with GLU 256 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252B VAL* 2.9 29.5 + - + +
253B TYR* 4.0 4.7 - - + +
255B VAL* 1.3 77.5 - - - +
257B LEU* 1.3 57.1 + - - +
259B ALA* 3.8 4.2 - - - +
260B ARG* 2.9 31.2 + - - +
411B MET 3.4 18.8 - - - +
412B PHE* 3.2 30.3 - - + +
413B ASN* 3.5 12.2 + - - +
414B MET* 3.3 29.4 + - + +
415B LEU* 4.6 4.2 + - - +
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Residues in contact with LEU 257 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110B THR* 4.4 15.3 - - + +
113B ALA* 3.8 29.6 - - + +
117B THR* 6.0 0.2 - - - +
253B TYR* 2.9 40.0 + - + +
254B PHE* 3.4 21.1 - - + +
255B VAL 3.2 0.4 - - - -
256B GLU* 1.3 75.0 - - - +
258B LEU* 1.3 60.3 + - - +
260B ARG* 3.4 15.1 + - - +
261B ASN* 3.0 37.6 + - - +
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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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106B ALA* 3.9 22.7 - - + +
107B CYS* 4.0 13.5 - - - -
110B THR* 3.4 32.7 - - + +
254B PHE 3.1 13.7 + - - +
255B VAL* 3.6 7.9 - - + +
257B LEU* 1.3 76.7 - - - +
259B ALA* 1.3 60.0 + - + +
261B ASN* 3.1 3.9 + - - +
262B ILE* 3.0 31.6 + - + +
322B VAL* 5.3 10.5 - - + -
325B ILE* 4.1 23.8 - - + -
326B THR* 4.4 5.8 - - + -
333B PHE* 4.9 1.1 - - + -
337B LEU* 3.6 24.7 - - + -
415B LEU* 6.0 2.2 - - + -
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Residues in contact with ALA 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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255B VAL* 2.9 16.5 + - + +
256B GLU* 4.1 5.8 - - - +
258B LEU* 1.3 78.0 - - - +
260B ARG* 1.3 58.0 + - - +
262B ILE* 3.3 9.9 + - - +
263B CYS* 2.9 32.7 + - - +
414B MET* 3.7 24.2 - - + +
415B LEU* 3.7 31.0 - - + +
418B VAL* 4.6 1.7 - - + +
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Residues in contact with ARG 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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256B GLU 2.9 20.1 + - - +
257B LEU* 3.6 16.8 - - - +
258B LEU 3.2 0.2 - - - -
259B ALA* 1.3 76.4 - - - +
261B ASN* 1.3 65.8 + - - +
263B CYS* 4.1 0.3 - - - +
264B GLU* 3.3 41.7 + - + +
272B PRO* 3.4 43.6 + - + +
414B MET* 4.1 18.6 - - + +
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Residues in contact with ASN 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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106B ALA* 4.1 21.6 + - + +
109B GLU* 3.3 45.0 + - - +
110B THR* 4.5 2.7 + - - +
257B LEU* 3.0 25.1 + - - +
258B LEU* 3.1 10.1 + - - +
260B ARG* 1.3 79.2 - - - +
262B ILE* 1.3 61.8 + - - +
264B GLU* 4.3 11.3 + - - +
265B ARG* 3.8 25.5 + - - +
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Residues in contact with ILE 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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95B LEU* 5.7 0.4 - - + -
102B LEU* 4.2 18.0 - - + +
103B PHE* 3.9 23.1 - - + -
106B ALA* 3.7 19.1 - - + -
258B LEU* 3.0 22.8 + - + +
259B ALA* 3.7 10.8 - - - +
260B ARG 3.2 0.2 - - - -
261B ASN* 1.3 77.9 - - - +
263B CYS* 1.3 59.2 + - - +
265B ARG* 3.0 23.7 + - - +
266B LEU* 3.6 27.5 + - + +
325B ILE* 3.8 37.5 - - + -
415B LEU* 6.1 0.2 - - + -
418B VAL* 4.0 14.1 - - + -
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Residues in contact with CYS 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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259B ALA 2.9 15.6 + - - +
260B ARG 3.4 1.1 + - - +
262B ILE* 1.3 75.5 - - - +
264B GLU* 1.3 60.6 + - - +
265B ARG 3.2 0.9 + - - -
266B LEU* 3.7 14.5 - - - +
269B SER* 3.2 28.8 + - - +
271B LEU 3.6 4.8 - - - +
281B LYS* 5.2 0.9 + - - -
414B MET* 3.5 48.2 - - + -
417B THR* 3.9 23.8 - - - -
418B VAL* 3.7 15.9 - - - -
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Residues in contact with GLU 264 (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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260B ARG* 3.3 33.0 + - - +
261B ASN* 4.7 12.7 - - - +
262B ILE 3.1 1.8 + - - -
263B CYS* 1.3 76.4 - - - +
265B ARG* 1.3 63.3 + - + +
266B LEU 4.7 1.9 - - - +
271B LEU 4.8 0.4 - - - -
272B PRO* 3.7 32.2 - - + +
273B VAL* 4.8 11.9 - - + +
281B LYS* 5.7 3.9 + - - +
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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
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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