Contacts of the helix formed by residues 271 - 288 (chain A) in PDB entry 3QPV
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 SER 271 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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255A GLU* 2.9 37.6 + - - -
256A ASN* 3.8 5.0 - - - +
257A GLU* 4.0 11.2 - - - +
260A LEU* 3.7 22.7 - - - -
269A GLY 3.6 3.6 + - - -
270A LEU* 1.3 75.2 - - - +
272A SER* 1.3 63.3 + - - +
273A ARG* 3.1 4.2 + - - -
274A GLY 2.7 22.3 + - - -
275A LYS* 3.0 21.8 + - - +
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Residues in contact with SER 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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271A SER* 1.3 73.9 - - - +
273A ARG* 1.3 65.5 + - - +
275A LYS* 3.4 13.8 + - - +
276A LYS* 3.1 39.3 + - - +
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Residues in contact with ARG 273 (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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255A GLU* 2.7 44.0 + - - +
260A LEU* 3.3 17.2 - - - +
271A SER* 3.1 2.7 + - - -
272A SER* 1.3 77.4 + - - +
274A GLY* 1.4 54.7 + - - +
275A LYS 3.0 1.8 - - - -
276A LYS* 2.8 18.7 + - + +
277A PHE* 2.7 32.9 + - - +
414A HIS* 4.2 1.6 - - - +
435A VAL* 3.4 15.2 - - + +
436A GLU* 3.5 40.4 + - + +
437A SER* 3.4 17.5 + - - +
438A VAL* 3.5 6.1 - - - +
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Residues in contact with GLY 274 (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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254A GLY* 3.5 9.2 - - - -
255A GLU* 3.2 40.9 - - - +
270A LEU* 4.2 6.0 - - - +
271A SER* 2.7 16.0 + - - -
273A ARG* 1.4 69.5 - - - +
275A LYS* 1.3 57.3 + - - +
277A PHE* 3.2 5.5 + - - +
278A ALA* 3.0 24.6 + - - +
414A HIS* 4.0 1.1 - - - -
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Residues in contact with LYS 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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270A LEU* 3.8 35.9 - - + +
271A SER 3.0 22.1 + - - +
272A SER* 3.8 11.2 - - - +
273A ARG 3.0 0.4 - - - -
274A GLY* 1.3 74.1 - - - +
276A LYS* 1.3 65.8 + - + +
278A ALA* 3.1 14.8 + - + +
279A SER* 3.2 15.6 + - - -
305A GLN* 4.8 10.9 - - - +
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Residues in contact with LYS 276 (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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272A SER* 3.1 35.0 + - - +
273A ARG* 2.8 19.1 + - - +
275A LYS* 1.3 77.3 - - - +
277A PHE* 1.3 62.4 + - - +
278A ALA 3.3 0.2 + - - -
279A SER* 3.4 8.4 + - - -
280A ALA* 3.0 20.8 + - - +
435A VAL* 4.0 19.5 - - + +
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Residues in contact with PHE 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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251A CYS* 4.1 22.0 - - + -
252A ARG 3.5 20.4 - - - -
254A GLY* 3.4 22.4 - - - -
273A ARG 2.7 12.0 + - - +
274A GLY 3.2 6.7 + - - +
276A LYS* 1.3 72.2 - - - +
278A ALA* 1.3 53.7 + - - +
280A ALA* 3.0 2.8 + - - -
281A LEU* 2.7 46.6 + - + +
306A THR* 4.0 12.6 - - + -
414A HIS* 3.3 66.0 - - + +
415A THR* 4.1 0.7 - - - -
416A VAL* 5.1 0.9 - - + -
433A LEU* 3.5 28.5 - - + -
435A VAL* 3.8 9.4 - - + +
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Residues in contact with ALA 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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270A LEU* 4.7 3.6 - - + -
274A GLY 3.0 12.6 + - - +
275A LYS* 3.1 14.3 + - + +
277A PHE* 1.3 80.5 - - - +
279A SER* 1.3 58.0 + - - +
281A LEU* 2.9 9.9 + - - +
282A SER 2.9 22.9 + - - -
305A GLN 4.7 1.6 - - - +
306A THR* 4.1 22.9 - - + +
309A ALA* 3.2 29.4 - - + +
310A LEU* 4.2 1.0 - - - +
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Residues in contact with SER 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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275A LYS 3.2 9.8 + - - -
276A LYS* 3.5 10.4 - - - -
278A ALA* 1.3 75.1 - - - +
280A ALA* 1.3 66.0 + - - -
282A SER* 3.1 10.9 + - - -
283A LYS* 3.0 21.7 + - - +
309A ALA* 3.9 5.4 - - - +
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Residues in contact with ALA 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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276A LYS 3.0 10.0 + - - +
277A PHE* 3.0 11.5 + - - +
279A SER* 1.3 80.3 - - - +
281A LEU* 1.4 52.3 + - - +
283A LYS* 3.0 12.0 + - + +
284A PHE* 2.6 37.1 + - - +
433A LEU* 3.9 33.6 - - + +
435A VAL* 4.6 3.8 - - + -
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Residues in contact with LEU 281 (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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251A CYS* 4.1 15.3 - - - -
277A PHE* 2.7 24.9 + - + +
278A ALA* 2.9 10.1 + - - +
280A ALA* 1.4 73.6 - - - +
282A SER* 1.3 57.7 + - - +
284A PHE* 3.7 5.3 - - + -
285A VAL* 2.8 46.1 + - + +
306A THR* 3.9 23.8 - - + -
310A LEU* 3.7 18.4 - - + -
383A LEU* 4.1 10.3 - - + -
385A ILE* 4.1 15.9 - - + -
416A VAL* 4.1 26.2 - - + -
433A LEU* 3.6 12.5 - - + +
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Residues in contact with SER 282 (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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278A ALA 2.9 10.2 + - - -
279A SER* 3.1 12.8 + - - -
281A LEU* 1.3 77.9 - - - +
283A LYS* 1.3 62.0 + - - +
285A VAL* 3.1 5.2 + - - +
286A GLU* 2.9 27.9 + - - +
309A ALA 3.6 19.2 + - - -
310A LEU* 3.7 15.7 + - - +
311A ARG* 3.1 28.8 + - - -
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Residues in contact with LYS 283 (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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279A SER 3.0 11.9 + - - +
280A ALA* 3.4 13.5 - - + +
282A SER* 1.3 73.3 - - - +
284A PHE* 1.3 66.2 + - - +
286A GLU* 3.1 14.2 + - - +
287A GLU* 3.1 35.6 + - + +
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Residues in contact with PHE 284 (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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249A TYR* 3.8 23.6 - + - -
280A ALA 2.6 20.2 + - - +
281A LEU* 3.7 16.6 - - + +
283A LYS* 1.3 74.0 - - - +
285A VAL* 1.3 70.7 + - + +
287A GLU* 3.4 22.2 + - - +
288A GLN* 3.2 64.0 + - + +
416A VAL* 4.1 10.3 - - + -
418A LYS* 5.0 0.2 - - + -
431A ILE* 3.9 40.2 - - + -
433A LEU* 3.9 30.5 - - + -
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Residues in contact with VAL 285 (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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249A TYR* 6.5 1.8 - - + -
281A LEU* 2.8 33.7 + - + +
282A SER* 3.1 5.1 + - - +
284A PHE* 1.3 79.2 - - + +
286A GLU* 1.3 64.6 + - - +
288A GLN* 3.1 18.7 + - - +
289A ASN* 4.0 2.3 + - - -
290A LEU* 5.1 7.5 + - + +
293A LEU* 3.6 27.1 - - + -
310A LEU* 4.7 7.4 - - + -
312A LEU* 4.3 13.9 - - + -
383A LEU* 4.1 25.8 - - + -
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Residues in contact with GLU 286 (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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282A SER* 2.9 16.6 + - - +
283A LYS* 3.1 14.5 + - - +
285A VAL* 1.3 76.8 - - - +
287A GLU* 1.3 63.1 + - - +
289A ASN* 3.1 19.6 + - - +
311A ARG* 4.5 15.2 + - - +
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Residues in contact with GLU 287 (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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283A LYS* 3.1 26.2 + - + +
284A PHE* 3.7 26.5 - - - +
285A VAL 3.3 0.2 - - - -
286A GLU* 1.3 79.3 - - - +
288A GLN* 1.3 79.0 + - - +
289A ASN* 3.2 3.9 + - - +
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Residues in contact with GLN 288 (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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249A TYR* 3.1 23.0 + - + +
284A PHE* 3.2 53.8 - - + +
285A VAL* 3.1 12.8 + - - +
287A GLU* 1.3 92.2 + - - +
289A ASN* 1.3 68.0 + - - +
290A LEU* 3.4 17.0 + - + +
418A LYS* 3.0 29.4 + - - +
431A ILE* 5.8 0.2 - - - +
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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
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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