Contacts of the helix formed by residues 308 - 324 (chain D) in PDB entry 4EOZ
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 ASN 308 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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273D MSE 3.2 13.8 - - + +
306D VAL* 3.6 4.8 - - - +
307D PRO* 1.3 86.8 - - + +
309D GLY* 1.3 61.4 + - - +
310D LEU 3.6 2.0 - - - -
311D LYS* 3.5 37.7 + - + +
312D THR* 3.2 27.5 + - - +
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Residues in contact with GLY 309 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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273D MSE 3.8 16.3 - - - -
303D PHE* 3.2 48.1 - - - +
306D VAL* 3.6 8.8 + - - -
307D PRO 3.4 3.4 + - - -
308D ASN* 1.3 76.8 - - - +
310D LEU* 1.3 63.5 + - - +
312D THR* 3.9 1.9 + - - -
313D MSE 3.6 9.4 + - - +
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Residues in contact with LEU 310 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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300D TYR* 3.6 46.7 - - + +
303D PHE* 3.6 7.4 + - + -
304D SER* 3.5 44.9 - - - +
306D VAL 5.0 1.3 + - - +
309D GLY* 1.3 75.3 - - - +
311D LYS* 1.3 65.7 + - - +
312D THR 3.2 0.7 - - - -
313D MSE 3.3 10.1 + - - +
314D CYS* 3.1 29.7 + - - +
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Residues in contact with LYS 311 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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307D PRO 5.5 0.9 - - - +
308D ASN* 3.5 40.3 + - - +
309D GLY 3.3 0.4 - - - -
310D LEU* 1.3 80.5 - - - +
312D THR* 1.3 58.9 + - - +
314D CYS* 3.6 8.0 + - + +
315D GLU* 3.2 44.2 + - - +
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Residues in contact with THR 312 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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273D MSE 2.8 37.5 - - + +
274D LYS* 4.4 27.0 + - + +
277D VAL* 3.9 26.9 - - + -
278D GLU* 5.9 0.7 - - - +
308D ASN* 3.2 9.1 + - - +
309D GLY 4.0 2.7 - - - -
311D LYS* 1.3 76.7 - - - +
313D MSE 1.3 66.5 + - - +
314D CYS 3.1 1.6 - - - -
315D GLU* 3.0 19.4 + - + +
316D CYS* 3.1 12.5 + - - +
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Residues in contact with MSE 313 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277D VAL* 4.0 5.4 - - + -
284D LEU* 3.4 18.2 - - + +
296D LEU* 4.5 15.7 - - + +
299D MSE 3.5 61.2 - - + +
300D TYR* 4.1 20.6 - - + +
303D PHE* 3.6 24.7 - - + -
309D GLY 3.6 2.1 + - - +
310D LEU* 3.3 17.1 + - - +
312D THR* 1.3 77.8 - - - +
314D CYS* 1.3 57.9 + - - +
316D CYS* 3.6 0.6 + - - -
317D MSE 3.1 40.8 + - + +
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Residues in contact with CYS 314 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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310D LEU* 3.1 20.7 + - - +
311D LYS* 3.7 8.7 - - + +
312D THR 3.1 0.2 - - - -
313D MSE 1.3 77.3 - - - +
315D GLU* 1.3 65.7 + - - +
317D MSE 4.1 16.3 - - - +
318D SER* 3.0 27.7 + - - -
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Residues in contact with GLU 315 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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311D LYS* 3.2 32.8 + - - +
312D THR* 3.0 12.0 + - + +
314D CYS* 1.3 81.9 - - - +
316D CYS* 1.3 60.4 + - - +
318D SER* 2.3 32.8 + - - -
319D SER* 3.3 5.4 + - - -
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Residues in contact with CYS 316 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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277D VAL* 3.3 47.3 - - + -
278D GLU* 4.6 10.5 - - + +
284D LEU* 4.3 9.2 - - + -
285D VAL* 4.2 20.0 - - - +
312D THR 3.1 8.8 + - - +
313D MSE 4.1 3.1 - - - +
315D GLU* 1.3 74.0 - - - +
317D MSE 1.3 64.8 + - - +
319D SER* 3.3 16.6 + - - +
320D TYR* 3.5 11.3 + - - +
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Residues in contact with MSE 317 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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284D LEU* 3.9 18.1 - - + +
288D LEU* 3.7 28.7 - - + -
296D LEU* 6.5 0.4 - - + -
313D MSE 3.1 29.3 + - + +
314D CYS* 4.1 16.4 - - - +
316D CYS* 1.3 75.9 - - - +
318D SER* 1.3 65.1 + - - +
320D TYR* 3.1 6.0 + - - +
321D LEU* 3.0 27.7 + - + +
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Residues in contact with SER 318 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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314D CYS 3.0 16.4 + - - -
315D GLU* 2.3 31.4 + - - -
317D MSE 1.3 75.6 - - - +
319D SER* 1.3 59.2 + - - +
321D LEU* 3.2 9.8 + - - +
322D ARG* 2.8 49.0 + - - +
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Residues in contact with SER 319 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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315D GLU 4.1 6.5 - - - -
316D CYS* 3.3 13.5 + - - -
317D MSE 3.2 1.0 - - - -
318D SER* 1.3 80.9 + - - +
320D TYR* 1.3 59.8 + - - +
322D ARG* 3.4 28.7 - - - +
323D GLU* 3.9 12.0 + - - +
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Residues in contact with TYR 320 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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285D VAL* 3.6 37.6 - - + +
288D LEU* 4.8 21.3 - - + -
289D LYS* 2.9 47.5 - - + +
316D CYS 3.5 3.7 + - - +
317D MSE 3.1 9.8 + - - +
319D SER* 1.3 74.7 - - - +
321D LEU* 1.3 69.8 + - + +
322D ARG 3.1 1.9 + - - -
323D GLU* 3.3 18.4 + - - +
324D GLN* 2.7 63.8 + - + +
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Residues in contact with LEU 321 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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317D MSE 3.0 18.3 + - + +
318D SER* 3.6 11.0 - - - +
320D TYR* 1.3 80.2 - - + +
322D ARG* 1.3 65.8 + - - +
324D GLN* 3.2 29.1 - - + +
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Residues in contact with ARG 322 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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318D SER* 2.8 25.7 + - - +
319D SER* 3.4 26.4 - - - +
320D TYR 3.1 0.2 - - - -
321D LEU* 1.3 77.1 - - - +
323D GLU* 1.3 65.4 + - + +
324D GLN 4.0 2.9 - - - +
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Residues in contact with GLU 323 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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319D SER 4.0 13.9 - - - +
320D TYR* 3.3 16.6 + - - +
322D ARG* 1.3 80.1 - - + +
324D GLN* 1.3 85.7 + - - +
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Residues in contact with GLN 324 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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289D LYS* 5.5 0.4 - - - +
320D TYR* 2.7 55.3 + - + +
321D LEU* 3.2 26.3 + - + +
322D ARG 4.0 2.9 - - - +
323D GLU* 1.3 98.7 + - - +
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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