Contacts of the helix formed by residues 253 - 267 (chain B) in PDB entry 5TQB
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 PRO 253 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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109A LYS* 5.0 3.8 - - - +
302A EDO 3.6 26.9 - - - +
251B VAL 3.7 0.6 - - - -
252B PRO* 1.3 87.9 - - + +
254B PHE* 1.3 67.3 + - - +
255B PRO* 3.8 10.3 - - + -
256B SER* 3.0 19.0 + - - +
257B ARG* 3.1 9.7 + - - -
404B EDO 3.4 21.5 - - - +
405B EDO 3.4 24.9 - - - +
407B EDO 3.6 16.6 - - - +
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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
----------------------------------------------------------
40A HIS* 3.4 29.6 - - + +
51A TYR* 3.5 37.9 - + - -
302A EDO 3.2 16.8 + - - +
252B PRO 3.7 0.2 + - - -
253B PRO* 1.3 69.4 - - - +
255B PRO* 1.3 71.4 - - + +
257B ARG* 2.9 20.5 + - - +
258B VAL* 3.0 18.9 + - + +
280B LEU* 3.4 46.8 - - + +
283B GLU* 3.7 12.3 - - + -
284B ASP* 4.0 21.1 - - + -
287B SER* 4.1 5.8 - - - -
290B VAL* 3.8 23.8 - - + -
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Residues in contact with PRO 255 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A HIS 4.6 0.2 - - - +
41A THR 4.2 0.9 - - - +
42A GLY* 4.2 22.2 - - - -
51A TYR* 4.0 37.6 - - + +
106A ILE* 3.9 8.4 - - + +
107A TRP 3.5 25.4 - - - +
109A LYS* 4.1 15.7 - - - +
253B PRO* 3.4 13.5 - - + -
254B PHE* 1.3 93.4 - - + +
256B SER* 1.3 60.5 + - - +
258B VAL* 3.3 13.2 + - + +
259B SER* 3.3 10.6 + - - -
406B EDO 4.6 0.9 + - - -
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Residues in contact with SER 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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106A ILE* 3.9 16.8 - - - +
108A ARG* 6.4 0.4 - - - -
212B GLU* 2.7 27.9 + - - +
215B GLN* 2.8 37.0 + - - -
252B PRO* 4.2 5.0 - - - +
253B PRO* 3.0 27.0 + - - -
255B PRO* 1.3 79.2 - - - +
257B ARG* 1.3 57.6 + - - +
259B SER* 3.5 1.6 + - - -
260B LEU 3.2 8.5 + - - -
404B EDO 3.7 6.0 - - - -
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Residues in contact with ARG 257 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302A EDO 3.9 12.9 + - - -
241B TRP* 4.0 27.3 - - + -
251B VAL* 3.8 14.2 - - - +
252B PRO* 3.0 51.9 + - + -
253B PRO 3.1 4.5 + - - -
254B PHE* 2.9 13.7 + - - +
256B SER* 1.3 74.9 - - - +
258B VAL* 1.3 64.1 + - - +
260B LEU* 3.4 11.9 - - + +
261B VAL* 3.1 27.4 + - - +
276B VAL* 4.2 4.4 - - + +
279B ARG* 3.5 19.2 - - - +
280B LEU* 3.4 32.1 - - + +
283B GLU* 3.0 40.6 + - - -
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Residues in contact with VAL 258 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A TYR* 4.0 24.5 - - + -
254B PHE* 3.0 37.0 + - + +
255B PRO 3.4 7.6 - - - +
257B ARG* 1.3 75.5 - - - +
259B SER* 1.3 66.1 + - - +
261B VAL* 3.1 16.9 + - - +
262B ARG* 3.3 13.3 + - - +
280B LEU* 4.7 3.8 - - + -
289B GLU* 4.3 5.6 - - + +
290B VAL* 4.2 11.0 - - + -
293B LEU* 3.8 20.6 - - + +
406B EDO 3.8 24.5 - - - +
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Residues in contact with SER 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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104A THR* 4.4 6.6 + - - -
106A ILE* 3.6 31.2 - - - +
215B GLN* 3.8 5.5 + - - +
219B ASN* 4.8 8.0 + - - -
255B PRO 3.3 4.3 + - - -
256B SER 3.6 9.4 - - - -
257B ARG 3.4 0.2 - - - -
258B VAL* 1.3 77.7 - - - +
260B LEU* 1.3 63.1 + - - +
262B ARG* 3.2 9.1 + - - +
263B LEU* 3.1 30.4 + - - +
406B EDO 3.3 19.4 + - - -
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Residues in contact with LEU 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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215B GLN* 3.6 30.3 - - - +
234B LEU* 3.6 27.8 - - + -
237B SER* 4.4 8.3 - - - +
238B LEU* 3.9 25.4 - - + -
241B TRP* 3.9 20.6 - - + +
252B PRO* 5.9 0.2 - - + -
256B SER 3.2 7.3 + - - +
257B ARG* 3.4 12.8 - - + +
258B VAL 3.1 0.4 - - - -
259B SER* 1.3 79.7 - - - +
261B VAL* 1.3 56.7 + - - +
263B LEU* 3.0 9.0 + - - +
264B LEU* 2.9 40.5 + - + +
276B VAL* 4.3 14.1 - - + -
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Residues in contact with VAL 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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257B ARG 3.1 13.7 + - - +
258B VAL* 3.1 9.4 + - - +
260B LEU* 1.3 76.4 - - - +
262B ARG* 1.3 62.7 + - - +
264B LEU* 3.2 7.9 + - - +
265B ILE* 3.0 43.7 + - + +
273B ALA* 4.4 7.2 - - + +
276B VAL* 3.7 25.4 - - + -
277B THR* 3.8 31.4 - - + -
280B LEU* 4.2 7.0 - - + -
293B LEU* 3.8 18.4 - - + -
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Residues in contact with ARG 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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65A SER* 4.1 9.3 + - - -
68A THR 4.1 6.5 + - - -
69A GLY* 3.6 27.1 + - - -
70A ARG 5.1 0.2 + - - -
101A PHE* 3.4 55.0 - - + +
102A ALA* 3.0 39.6 + - - +
104A THR* 3.7 18.7 + - - +
258B VAL* 3.3 10.1 + - - +
259B SER* 3.2 8.4 + - - +
260B LEU 3.2 0.4 - - - -
261B VAL* 1.3 77.1 - - - +
263B LEU* 1.3 64.1 + - + +
265B ILE* 3.6 0.4 + - - -
266B GLU* 3.1 24.7 + - - +
289B GLU* 4.2 1.3 + - - -
293B LEU* 4.1 15.2 - - + +
406B EDO 3.5 34.2 + - - -
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Residues in contact with LEU 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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99A ARG* 3.7 18.4 - - - +
215B GLN* 3.5 46.2 - - + +
218B ALA* 4.7 0.2 - - + -
219B ASN* 3.8 20.0 - - - +
222B ILE* 3.6 22.9 - - + -
234B LEU* 3.8 20.3 - - + +
259B SER* 3.1 21.4 + - - +
260B LEU* 3.0 7.9 + - - +
262B ARG* 1.3 78.0 - - + +
264B LEU* 1.3 60.6 + - - +
266B GLU* 3.4 6.3 - - - +
267B VAL* 3.2 28.1 + - - +
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Residues in contact with LEU 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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234B LEU* 4.1 10.5 - - + -
238B LEU* 4.2 19.3 - - + -
260B LEU* 2.9 35.9 + - + +
261B VAL* 3.2 10.7 + - - +
263B LEU* 1.3 74.6 - - - +
265B ILE* 1.3 63.4 + - - +
267B VAL* 3.6 1.8 + - - -
268B ASP 3.3 2.8 + - - -
269B MSE 2.8 69.6 + - + +
272B GLU* 4.0 8.3 - - + +
273B ALA* 3.7 30.1 - - + +
276B VAL* 4.1 11.2 - - + -
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Residues in contact with ILE 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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100A MSE 3.2 21.1 - - + +
101A PHE* 4.2 16.8 - - + -
261B VAL* 3.0 32.9 + - + +
262B ARG 4.1 2.9 - - - +
264B LEU* 1.3 72.9 - - - +
266B GLU* 1.3 66.9 + - - +
268B ASP* 3.3 12.0 + - - +
270B GLU* 4.3 16.5 - - + +
273B ALA* 4.2 7.0 - - + -
293B LEU* 3.8 24.2 - - + +
296B TYR* 4.1 22.0 - - + -
297B ALA* 3.8 19.3 - - + +
300B ARG* 4.2 13.8 + - + +
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Residues in contact with GLU 266 (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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74A ARG* 2.9 49.1 + - - +
77A ARG* 3.1 8.2 + - - +
99A ARG* 3.7 15.8 - - - +
100A MSE 3.2 25.4 + - - +
101A PHE* 2.8 37.5 + - - +
222B ILE* 3.8 27.3 - - + +
262B ARG 3.1 18.7 + - - +
263B LEU* 3.4 11.0 - - + +
265B ILE* 1.3 79.4 - - - +
267B VAL* 1.3 58.6 + - + +
268B ASP* 3.4 2.8 + - - +
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Residues in contact with VAL 267 (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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77A ARG* 4.0 4.9 - - - +
222B ILE* 3.6 35.4 - - + -
227B THR* 4.2 12.8 - - + +
230B ALA* 4.0 10.5 - - + -
231B ARG* 2.8 36.6 + - + -
234B LEU* 3.6 5.6 - - + -
263B LEU 3.3 12.6 - - - +
264B LEU 4.0 1.8 - - - +
266B GLU* 1.3 79.7 - - + +
268B ASP* 1.3 68.2 + - - +
269B MSE 3.1 32.4 + - + +
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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