Contacts of the helix formed by residues 265 - 280 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118A GLU* 3.2 11.6 + - - +
264A LEU* 1.3 72.3 - - - +
266A SER* 1.3 64.0 + - - +
267A LEU* 3.2 37.7 - - - -
268A ILE* 2.9 36.8 + - + +
269A VAL* 3.1 10.7 + - - +
312A ILE* 4.6 6.1 - - + -
314A HIS* 5.1 5.4 - - + +
325A SER* 3.8 23.6 - - - +
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Residues in contact with SER 266 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264A LEU 3.8 3.6 + - - -
265A CYS* 1.3 72.9 - - - +
267A LEU* 1.3 65.2 + - - +
269A VAL* 2.9 29.1 + - - +
270A GLU* 3.0 28.3 + - - +
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Residues in contact with LEU 267 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265A CYS* 3.7 22.2 - - - -
266A SER* 1.3 82.4 + - - +
268A ILE* 1.3 60.2 + - + +
270A GLU* 5.9 0.4 - - - -
271A PRO* 3.4 19.1 - - - +
310A LEU* 3.8 10.3 - - + +
312A ILE* 4.7 13.9 - - + -
325A SER* 4.2 23.8 - - - +
327A LEU* 4.9 15.3 - - + +
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Residues in contact with ILE 268 (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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118A GLU* 3.5 25.8 - - - +
122A LEU* 4.6 17.7 - - + -
265A CYS* 2.9 13.3 + - + +
267A LEU* 1.3 81.8 - - + +
269A VAL* 1.3 64.0 + - - +
270A GLU 3.5 0.7 - - - -
271A PRO* 3.3 3.8 - - - +
272A MET* 3.1 26.5 + - + +
307A ILE* 3.8 31.9 - - + -
310A LEU* 3.8 22.9 - - + +
312A ILE* 4.1 25.4 - - + -
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Residues in contact with VAL 269 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118A GLU* 5.2 0.4 - - - +
257A HIS* 5.1 4.9 - - + -
258A LEU* 3.7 21.0 - - + +
262A ASN* 4.8 4.0 - - - +
264A LEU* 3.7 36.8 - - + -
265A CYS 3.3 14.1 - - - +
266A SER* 2.9 18.4 + - - +
268A ILE* 1.3 78.3 - - - +
270A GLU* 1.3 53.7 + - + +
272A MET* 3.0 8.8 + - - +
273A GLU* 2.4 59.1 + - - +
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Residues in contact with GLU 270 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266A SER* 3.0 22.6 + - - +
267A LEU* 5.9 0.4 - - - -
269A VAL* 1.3 77.3 - - + +
271A PRO* 1.4 61.7 - - + +
273A GLU* 3.3 23.3 - - - +
274A ASN* 2.9 27.2 + - - +
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Residues in contact with PRO 271 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267A LEU 3.4 22.7 - - - +
268A ILE* 3.3 15.0 - - - +
270A GLU* 1.4 92.5 - - + +
272A MET* 1.3 56.3 + - - +
274A ASN* 3.5 6.4 + - + +
275A TRP* 2.9 27.8 + - - +
303A LEU* 4.0 21.2 - - + +
306A HIS* 5.6 5.6 - - + +
307A ILE* 3.7 20.0 - - + -
310A LEU* 4.3 6.1 - - + -
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Residues in contact with MET 272 (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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122A LEU* 5.6 7.2 - - + -
125A LEU* 3.8 18.4 - - + -
211A VAL* 4.4 11.7 - - + -
215A ILE* 4.8 10.5 - - + -
258A LEU* 5.5 5.2 - - + -
264A LEU* 6.5 1.1 - - + -
268A ILE* 3.1 22.4 + - + +
269A VAL* 3.0 11.7 + - - +
271A PRO* 1.3 74.3 - - - +
273A GLU* 1.3 59.9 + - - +
275A TRP* 3.5 42.2 - - + +
276A LEU* 2.9 38.6 + - + +
304A MET* 5.8 0.9 - - - -
307A ILE* 3.8 28.9 - - + -
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Residues in contact with GLU 273 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242A ILE* 3.8 14.5 - - + +
256A SER 4.5 8.5 - - - +
257A HIS* 2.5 40.6 + - - -
258A LEU* 4.1 13.9 + - + -
269A VAL* 2.4 43.5 + - + +
270A GLU* 3.3 27.0 - - - +
272A MET* 1.3 67.2 - - - +
274A ASN* 1.3 60.3 + - - +
276A LEU* 3.2 4.3 + - - +
277A GLN* 2.9 34.6 + - - +
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Residues in contact with ASN 274 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270A GLU 2.9 13.8 + - - +
271A PRO* 3.9 7.2 - - + +
273A GLU* 1.3 76.3 - - - +
275A TRP* 1.3 57.1 + - - +
277A GLN* 3.2 22.8 + - - +
278A LEU* 2.9 33.9 + - - +
299A ARG* 4.4 17.2 + - - +
303A LEU* 4.3 11.7 - - + +
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Residues in contact with TRP 275 (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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125A LEU* 3.6 8.5 - - + -
207A PHE* 3.4 26.9 - + - -
208A GLY* 4.3 5.6 - - - -
211A VAL* 4.4 7.0 - - + -
271A PRO 2.9 19.1 + - - +
272A MET* 3.5 41.5 - - + +
273A GLU 3.2 0.2 - - - -
274A ASN* 1.3 78.8 - - - +
276A LEU* 1.3 76.7 + - + +
278A LEU* 3.1 6.4 + - - +
279A MET* 2.9 52.5 + - + +
300A CYS* 3.0 50.5 + - + +
303A LEU* 3.8 19.5 - - + +
304A MET* 3.4 27.8 - - + +
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Residues in contact with LEU 276 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208A GLY* 3.9 27.6 - - - +
211A VAL* 5.7 2.0 - - + -
212A PHE* 4.4 16.8 - - + +
215A ILE* 5.4 6.3 - - + -
242A ILE* 3.6 18.2 - - + +
258A LEU* 3.8 33.0 - - + -
272A MET* 2.9 23.1 + - + +
273A GLU 3.7 4.5 - - - +
275A TRP* 1.3 92.8 - - + +
277A GLN* 1.3 58.0 + - - +
279A MET* 3.9 6.1 - - + +
280A LEU* 2.6 48.7 + - + +
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Residues in contact with GLN 277 (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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239A PRO 4.2 7.3 - - - +
240A LYS* 3.2 43.1 + - + +
242A ILE* 3.7 9.4 - - + -
256A SER* 3.3 34.6 + - - -
273A GLU* 2.9 20.1 + - - +
274A ASN* 3.4 25.5 + - - +
276A LEU* 1.3 76.0 - - - +
278A LEU* 1.3 62.5 + - - +
281A ASN* 3.8 18.0 + - - +
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Residues in contact with LEU 278 (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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274A ASN* 2.9 20.5 + - - +
275A TRP* 3.1 7.6 + - - +
277A GLN* 1.3 80.3 - - - +
279A MET* 1.3 62.0 + - - +
281A ASN* 3.8 11.1 - - - +
286A GLN 4.9 1.5 - - - +
288A GLY 3.2 28.0 + - - +
289A GLY* 4.4 13.2 - - - +
290A PRO* 5.2 2.7 - - + -
299A ARG* 3.8 33.7 - - + +
300A CYS* 3.7 23.1 - - - +
303A LEU* 3.7 28.7 - - + -
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Residues in contact with MET 279 (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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132A ILE* 6.0 0.9 - - + -
204A TYR* 3.1 54.3 - - + +
205A TRP* 3.7 10.6 - - - -
207A PHE* 4.6 4.9 - - + -
208A GLY* 4.4 6.5 - - - -
275A TRP* 2.9 57.6 + - + +
276A LEU* 3.0 15.0 + - + +
278A LEU* 1.3 77.5 - - - +
280A LEU* 1.3 61.5 + - + +
281A ASN 3.2 5.8 + - - -
287A ARG* 3.4 21.7 - - - +
300A CYS* 3.7 30.3 - - + -
301A PHE* 5.9 2.0 - - + -
304A MET* 5.2 2.2 - - - -
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Residues in contact with LEU 280 (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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205A TRP* 3.5 30.0 + - + +
208A GLY 6.0 0.4 - - - +
209A THR* 4.1 14.1 - - - +
212A PHE* 6.2 1.1 - - + -
220A PRO* 4.5 13.5 - - + -
221A PHE* 4.0 19.5 - - + -
234A ILE* 5.7 4.7 - - - +
239A PRO* 3.0 19.4 - - - +
241A CYS 4.8 3.4 - - - +
242A ILE* 3.5 48.0 - - + +
276A LEU* 2.6 30.4 + - + +
279A MET* 1.3 74.5 - - + +
281A ASN* 1.3 61.3 + - - +
282A TRP* 3.3 4.7 + - - +
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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