Contacts of the helix formed by residues 270 - 282 (chain A) in PDB entry 4PED
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 VAL 270 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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266A THR 3.9 6.5 - - - +
267A LEU* 3.1 17.0 - - + +
269A LYS* 1.3 87.2 - - + +
271A ARG* 1.3 62.5 + - - +
272A GLY 3.2 3.2 + - - -
273A ALA* 3.2 5.1 + - + -
274A ALA* 3.0 18.9 + - - +
371A ASP* 3.6 45.8 - - + +
374A ASN* 3.6 30.3 - - + +
375A LEU* 4.2 23.3 - - + -
378A VAL* 5.8 0.4 - - + -
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Residues in contact with ARG 271 (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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267A LEU 3.0 9.4 + - - +
268A CYS* 3.3 28.5 + - - +
269A LYS 3.6 0.6 - - - -
270A VAL* 1.3 76.2 - - - +
272A GLY* 1.3 58.9 + - - +
274A ALA* 4.2 3.4 - - - -
275A LEU* 2.9 52.3 + - + +
300A VAL* 2.9 35.8 + - + +
301A ARG 3.5 4.6 + - - -
304A ALA* 3.5 32.4 - - - +
307A MSE 3.5 29.8 - - + +
338A ALA* 4.0 5.1 - - - +
340A SER 4.3 1.8 + - - -
361A TYR* 3.1 39.7 + - + -
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Residues in contact with GLY 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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270A VAL 3.2 1.2 - - - -
271A ARG* 1.3 81.5 - - - +
273A ALA* 1.3 61.5 + - - +
276A LYS* 3.1 26.7 + - - +
340A SER* 3.5 26.1 - - - -
341A ILE* 3.9 13.2 - - - -
361A TYR* 5.1 1.9 - - - -
364A VAL* 5.8 3.1 - - - -
402A LEU* 3.7 8.6 - - - +
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Residues in contact with ALA 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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270A VAL 3.2 7.8 + - - +
272A GLY* 1.3 77.3 - - - +
274A ALA* 1.3 63.2 + - - +
276A LYS* 3.9 1.0 - - - +
277A LEU* 3.0 25.3 + - - +
371A ASP* 4.4 20.5 + - + +
372A VAL* 4.3 11.4 - - + -
375A LEU* 3.5 16.9 - - + +
398A LEU* 3.9 3.5 - - + +
402A LEU* 3.7 30.0 - - + +
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Residues in contact with ALA 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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267A LEU* 4.2 19.1 - - + +
270A VAL 3.0 16.5 + - - +
271A ARG* 3.3 8.5 + - - +
273A ALA* 1.3 78.5 - - - +
275A LEU* 1.3 58.2 + - - +
277A LEU* 3.3 2.3 + - - +
278A GLY 2.9 22.9 + - - -
297A PHE* 3.2 18.7 - - + -
300A VAL* 4.8 6.5 - - + -
375A LEU* 3.7 27.7 - - + +
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Residues in contact with LEU 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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271A ARG* 2.9 49.5 + - - +
274A ALA* 1.3 69.1 - - - +
276A LYS* 1.3 66.4 + - - +
278A GLY* 3.2 2.1 + - - +
279A GLN* 3.0 34.0 + - - +
297A PHE* 4.2 17.9 - - + +
300A VAL* 3.9 19.3 - - + -
301A ARG* 3.6 30.7 - - + +
338A ALA* 4.2 15.0 - - + -
340A SER* 3.7 27.1 - - - +
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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 GLY 3.1 19.8 + - - +
273A ALA 3.9 2.0 - - - +
275A LEU* 1.3 76.3 - - - +
277A LEU* 1.3 62.2 + - - +
279A GLN* 3.1 22.9 + - + +
280A MSE 3.1 30.0 + - - +
340A SER* 3.9 6.1 - - - +
398A LEU* 3.9 14.8 - - + -
401A GLU* 3.9 31.2 + - - -
402A LEU* 3.8 19.5 - - + +
405A GLU* 2.9 33.7 + - + +
488A ASP* 4.8 16.5 + - - +
509A GLY 4.8 2.2 + - - -
510A ALA* 4.1 14.5 - - - +
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Residues in contact with LEU 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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273A ALA 3.0 18.4 + - - +
274A ALA 3.6 3.8 - - - +
276A LYS* 1.3 76.8 - - - +
278A GLY* 1.3 57.3 + - - +
280A MSE 3.1 15.4 + - + +
281A LEU* 2.9 58.8 + - + +
283A ILE* 6.1 0.2 - - + -
297A PHE* 5.7 2.5 - - + -
375A LEU* 3.9 2.7 - - + -
376A MSE 3.8 20.2 - - + -
379A LEU* 3.6 31.2 - - + -
394A LEU* 4.5 16.4 - - + -
398A LEU* 3.9 27.7 - - + +
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Residues in contact with GLY 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 ALA 2.9 13.8 + - - -
275A LEU 3.5 4.7 - - - -
276A LYS 3.2 0.4 - - - -
277A LEU* 1.3 77.8 - - - +
279A GLN* 1.3 55.9 + - - +
281A LEU 3.5 0.2 + - - -
282A SER* 3.0 9.9 + - - -
283A ILE* 2.9 48.8 + - - +
297A PHE* 3.9 13.1 - - - -
301A ARG* 5.9 2.5 - - - -
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Residues in contact with GLN 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 LEU* 3.0 24.7 + - - +
276A LYS* 3.1 25.5 + - + +
278A GLY* 1.3 74.8 - - - +
280A MSE 1.3 62.8 + - - +
282A SER* 3.5 13.6 + - - +
301A ARG* 6.2 0.4 - - - +
339A ALA 5.0 0.2 - - - -
340A SER* 4.2 18.5 + - - +
405A GLU* 5.0 2.8 - - - +
488A ASP* 3.8 32.4 - - + +
490A ASN* 3.5 49.6 + - - +
507A ASP* 5.0 1.9 - - - +
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Residues in contact with MSE 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* 3.1 20.1 + - - +
277A LEU* 3.6 15.3 - - + +
279A GLN* 1.3 79.5 - - - +
281A LEU* 1.3 66.1 + - + +
282A SER* 3.7 1.4 + - - -
394A LEU* 6.4 0.7 - - + -
397A VAL* 3.9 31.0 - - + +
398A LEU* 3.7 33.7 - - - +
401A GLU* 4.0 19.3 - - + -
488A ASP* 3.4 29.7 - - + +
591A ILE* 4.2 6.1 - - - +
595A LEU* 6.4 1.1 - - + -
611A ARG* 3.5 41.0 - - - +
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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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277A LEU* 2.9 46.9 + - + +
280A MSE 1.3 81.1 - - + +
282A SER* 1.3 70.5 + - - +
283A ILE* 3.8 24.9 - - + +
289A ILE* 4.7 0.5 - - - +
385A LEU* 4.9 7.6 - - + -
386A PRO* 5.8 0.9 - - + +
389A LEU* 3.9 28.9 - - + -
394A LEU* 4.3 22.9 - - + -
588A HIS* 3.8 12.8 + - - -
591A ILE* 3.8 32.4 - - + +
595A LEU* 4.5 2.9 - - + -
611A ARG* 5.9 0.2 - - - -
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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 GLY 3.0 7.2 + - - -
279A GLN* 3.5 8.7 + - - +
280A MSE 3.4 4.1 + - - -
281A LEU* 1.3 79.2 - - - +
283A ILE* 1.3 63.5 + - - +
284A GLN* 3.2 16.5 + - - +
289A ILE* 3.8 0.9 - - - +
491A TRP* 5.6 3.3 + - - -
588A HIS* 3.2 17.6 - - - -
591A ILE* 4.8 2.7 - - - +
615A GLY* 4.2 14.7 + - - -
618A LEU* 3.6 37.1 - - - +
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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