Contacts of the helix formed by residues 265 - 280 (chain B) in PDB entry 5TQW
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 CYS 265 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118B GLU* 3.2 11.4 + - - +
264B LEU* 1.3 70.7 - - - +
266B SER* 1.3 63.9 + - - +
267B LEU* 3.7 36.8 - - - -
268B ILE* 2.9 37.2 + - + +
269B VAL* 3.1 11.3 + - - +
312B ILE* 4.6 4.7 - - + -
314B HIS* 5.1 4.9 - - - +
325B SER* 3.8 25.1 - - - +
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Residues in contact with SER 266 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264B LEU 3.8 3.4 + - - -
265B CYS* 1.3 73.7 - - - +
267B LEU* 1.3 63.8 + - - +
269B VAL* 2.9 28.1 + - - -
270B GLU* 3.0 29.2 + - - +
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Residues in contact with LEU 267 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265B CYS* 3.7 22.0 - - - -
266B SER* 1.3 81.3 + - - +
268B ILE* 1.3 61.3 + - + +
270B GLU* 5.9 0.4 - - - -
271B PRO* 3.4 18.4 - - - +
310B LEU* 3.8 10.2 - - + +
312B ILE* 4.7 14.1 - - + -
325B SER* 4.2 24.5 - - - +
327B LEU* 4.9 14.8 - - + +
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Residues in contact with ILE 268 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118B GLU* 3.5 26.0 - - - +
122B LEU* 4.6 18.2 - - + -
265B CYS* 2.9 14.5 + - + +
267B LEU* 1.3 82.0 - - + +
269B VAL* 1.3 65.3 + - - +
270B GLU 3.5 0.7 - - - -
271B PRO* 3.3 3.9 - - - +
272B MET* 3.1 26.7 + - + +
307B ILE* 3.8 31.4 - - + -
310B LEU* 3.8 22.4 - - + +
312B ILE* 4.1 26.0 - - + -
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Residues in contact with VAL 269 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118B GLU* 5.2 0.7 - - - +
257B HIS* 5.1 5.2 - - + -
258B LEU* 3.7 20.9 - - + -
262B ASN* 4.8 4.7 - - - +
264B LEU* 3.7 37.0 - - + -
265B CYS 3.3 13.9 - - - +
266B SER* 2.9 17.8 + - - +
268B ILE* 1.3 77.2 - - - +
270B GLU* 1.3 53.8 + - + +
272B MET* 3.0 8.5 + - - +
273B GLU* 2.4 59.6 + - - +
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Residues in contact with GLU 270 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266B SER* 3.0 22.0 + - - +
267B LEU* 5.6 0.8 - - - -
269B VAL* 1.3 76.5 - - + +
271B PRO* 1.4 61.4 - - + +
273B GLU* 3.1 24.1 + - - +
274B ASN* 2.9 27.0 + - - +
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Residues in contact with PRO 271 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267B LEU 3.4 22.9 - - - +
268B ILE* 3.3 14.4 - - - +
270B GLU* 1.4 91.4 - - + +
272B MET* 1.3 55.2 + - - -
274B ASN* 3.5 7.0 + - + +
275B TRP* 2.9 27.9 + - - +
303B LEU* 4.0 20.4 - - + +
306B HIS* 5.6 5.2 - - + +
307B ILE* 3.7 20.4 - - + -
310B LEU* 4.3 5.6 - - + -
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Residues in contact with MET 272 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122B LEU* 5.6 6.5 - - + -
125B LEU* 3.8 18.8 - - + -
211B VAL* 4.4 11.4 - - + -
215B ILE* 4.8 10.5 - - + -
258B LEU* 5.5 5.2 - - + -
264B LEU* 6.5 1.3 - - + -
268B ILE* 3.1 22.8 + - + +
269B VAL* 3.0 11.5 + - - +
271B PRO* 1.3 73.2 - - - +
273B GLU* 1.3 61.2 + - - +
275B TRP* 3.5 41.4 - - + +
276B LEU* 2.9 39.7 + - + +
304B MET* 5.8 0.4 - - - -
307B ILE* 3.8 29.2 - - + -
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Residues in contact with GLU 273 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242B ILE* 3.8 13.6 - - + +
256B SER 4.5 9.3 - - - +
257B HIS* 2.5 40.6 + - - -
258B LEU* 4.1 14.2 + - + -
269B VAL* 2.4 43.6 + - + +
270B GLU* 3.1 27.0 + - - +
272B MET* 1.3 68.0 - - - +
274B ASN* 1.3 60.7 + - - +
276B LEU* 3.2 4.5 + - - +
277B GLN* 2.9 33.7 + - + +
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Residues in contact with ASN 274 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270B GLU 2.9 15.1 + - - +
271B PRO* 3.9 6.3 - - + +
273B GLU* 1.3 76.5 - - - +
275B TRP* 1.3 57.6 + - - +
277B GLN* 3.2 22.1 + - - +
278B LEU* 2.9 33.5 + - - +
299B ARG* 4.4 17.6 + - - +
303B LEU* 4.3 11.6 - - + +
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Residues in contact with TRP 275 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125B LEU* 3.6 8.1 - - + -
207B PHE* 3.4 27.8 - + - -
208B GLY* 4.3 4.0 - - - -
211B VAL* 4.4 7.4 - - + -
271B PRO 2.9 20.0 + - - +
272B MET* 3.5 41.1 - - + +
273B GLU 3.2 0.2 - - - -
274B ASN* 1.3 77.0 - - - +
276B LEU* 1.3 77.7 + - + +
278B LEU* 3.1 6.1 + - - +
279B MET* 2.9 51.1 + - + +
300B CYS* 3.0 50.6 + - - +
303B LEU* 3.8 18.1 - - + +
304B MET* 3.4 28.6 - - + +
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Residues in contact with LEU 276 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208B GLY* 3.9 27.1 - - - +
211B VAL* 5.7 1.6 - - + -
212B PHE* 4.4 17.3 - - + +
215B ILE* 5.4 6.5 - - + -
242B ILE* 3.6 19.5 - - + +
258B LEU* 3.8 32.1 - - + -
272B MET* 2.9 23.2 + - + +
273B GLU 3.2 4.0 + - - +
275B TRP* 1.3 93.5 - - + +
277B GLN* 1.3 56.8 + - - +
279B MET* 3.9 6.3 - - + +
280B LEU* 2.6 48.3 + - + +
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Residues in contact with GLN 277 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239B PRO 4.2 7.2 - - - +
240B LYS* 3.2 40.5 + - + +
242B ILE* 3.7 9.9 - - + -
256B SER* 3.3 34.2 + - - -
273B GLU* 2.9 19.4 + - - +
274B ASN* 3.2 25.6 + - - +
276B LEU* 1.3 76.6 - - - +
278B LEU* 1.3 62.9 + - - +
281B ASN* 3.8 18.2 + - - +
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Residues in contact with LEU 278 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274B ASN* 2.9 20.9 + - - +
275B TRP* 3.1 6.9 + - - +
277B GLN* 1.3 78.8 - - - +
279B MET* 1.3 62.7 + - - +
281B ASN* 3.8 11.7 - - - +
286B GLN 5.8 1.6 - - - +
288B GLY 3.2 28.1 + - - +
289B GLY* 4.4 13.7 - - - +
290B PRO* 5.2 2.5 - - + -
299B ARG* 3.8 34.1 - - + +
300B CYS* 3.7 23.1 - - - +
303B LEU* 3.7 29.2 - - + -
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Residues in contact with MET 279 (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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132B ILE* 6.0 0.7 - - + -
204B TYR* 3.1 54.5 - - + +
205B TRP* 3.7 10.7 - - - -
207B PHE* 4.6 4.5 - - + -
208B GLY* 4.4 6.7 - - - -
275B TRP* 2.9 57.5 + - + +
276B LEU* 3.0 15.0 + - + +
278B LEU* 1.3 77.9 - - - +
280B LEU* 1.3 61.0 + - + +
281B ASN 3.2 5.6 + - - -
287B ARG* 3.4 21.4 - - - +
288B GLY* 5.3 0.2 - - - -
300B CYS* 3.7 30.1 - - + -
301B PHE* 5.9 2.9 - - + -
304B MET* 5.2 1.6 - - - -
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Residues in contact with LEU 280 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205B TRP* 3.5 30.0 + - + +
208B GLY 6.0 0.7 - - - +
209B THR* 4.1 15.5 - - - +
212B PHE* 6.2 1.3 - - + -
220B PRO* 4.5 13.5 - - + -
221B PHE* 4.0 19.3 - - + -
234B ILE* 5.7 4.5 - - - +
239B PRO* 3.0 19.3 - - - +
241B CYS 4.8 2.9 - - - +
242B ILE* 3.5 48.0 - - + +
276B LEU* 2.6 31.0 + - + +
277B GLN 4.4 0.2 - - - -
279B MET* 1.3 74.8 - - + +
281B ASN* 1.3 62.0 + - - +
282B TRP* 3.3 5.2 + - - +
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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