Contacts of the helix formed by residues 308 - 321 (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 PRO 308 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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306A PHE 3.6 5.8 - - - +
307A MSE 1.3 98.8 - - + +
309A LEU* 1.3 79.1 + - + +
310A LYS* 4.3 1.6 - - + +
311A GLN* 3.2 39.4 + - + +
312A MSE 3.6 8.1 + - - +
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Residues in contact with LEU 309 (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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307A MSE 3.2 5.2 + - - -
308A PRO* 1.3 79.7 - - + +
310A LYS* 1.3 90.3 + - + +
312A MSE 3.0 25.6 + - - +
313A MSE 3.3 23.0 + - + +
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Residues in contact with LYS 310 (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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308A PRO* 3.2 1.3 - - + +
309A LEU* 1.3 96.7 - - + +
311A GLN* 1.3 63.9 + - - +
313A MSE 3.2 51.6 + - + +
314A LYS* 3.0 35.4 + - - +
317A ASN* 5.5 2.8 - - - +
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Residues in contact with GLN 311 (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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307A MSE 6.2 1.6 - - + -
308A PRO* 3.2 35.5 + - + +
310A LYS* 1.3 76.3 - - - +
312A MSE 1.3 76.6 + - + +
314A LYS* 2.6 51.6 + - - +
315A THR* 3.3 3.8 + - - -
361A TYR* 5.5 1.8 - - + -
362A PRO* 3.3 39.4 + - + +
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Residues in contact with MSE 312 (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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307A MSE 5.3 3.8 - - + +
308A PRO 3.6 6.3 + - - +
309A LEU* 3.0 12.7 + - - +
311A GLN* 1.3 87.1 - - + +
313A MSE 1.3 65.8 + - + +
315A THR* 3.0 16.2 + - - -
316A LEU* 3.0 24.1 + - + +
331A PHE* 5.5 4.7 - - + -
333A GLU 5.7 0.2 - - - +
343A GLN* 3.7 30.5 - - - +
345A HIS* 3.6 25.1 - - + +
359A ILE* 3.8 32.4 - - + +
360A GLN 4.8 0.9 - - - +
361A TYR* 3.5 34.1 - - + -
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Residues in contact with MSE 313 (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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309A LEU* 3.3 19.7 + - + +
310A LYS* 3.2 58.6 + - + +
311A GLN 3.3 0.6 - - - -
312A MSE 1.3 77.7 - - + +
314A LYS* 1.3 55.6 + - - +
316A LEU* 3.9 8.4 - - + +
317A ASN* 2.8 36.7 + - - +
324A TRP* 3.9 23.9 + - + +
325A ARG* 4.1 24.5 - - - +
331A PHE* 6.0 2.5 - - + -
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Residues in contact with LYS 314 (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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310A LYS* 3.0 34.7 + - - +
311A GLN* 2.6 43.4 + - - +
313A MSE 1.3 76.7 - - - +
315A THR* 1.3 57.5 + - - +
317A ASN* 3.4 6.8 - - - +
318A ASN* 2.8 44.5 + - - +
362A PRO* 4.0 13.9 - - + -
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Residues in contact with THR 315 (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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311A GLN 3.3 1.2 + - - -
312A MSE 3.0 9.8 + - - -
314A LYS* 1.3 76.8 - - - +
316A LEU* 1.3 58.2 + - - +
318A ASN* 3.2 7.0 + - - +
319A ASP* 2.9 35.0 + - - +
359A ILE* 3.7 15.0 - - + -
360A GLN 2.8 28.5 + - - +
361A TYR 3.9 0.2 - - - -
362A PRO* 3.5 22.9 - - - +
441A HIS* 3.8 32.8 - - + +
442A VAL* 4.1 4.9 - - + -
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Residues in contact with LEU 316 (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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312A MSE 3.0 20.8 + - + +
313A MSE 3.9 9.0 - - + +
315A THR* 1.3 75.5 - - - +
317A ASN* 1.3 57.8 + - - +
319A ASP* 4.8 2.9 - - - -
320A LEU* 2.9 39.2 + - + +
321A GLY 3.3 5.4 + - - +
324A TRP* 3.6 53.3 - - + +
331A PHE* 4.3 8.1 - - + -
357A MSE 3.8 29.2 - - + -
359A ILE* 4.1 27.6 - - + -
442A VAL* 4.4 9.9 - - + -
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Residues in contact with ASN 317 (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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310A LYS* 5.5 2.9 - - - +
313A MSE 2.8 22.7 + - - +
314A LYS* 3.4 6.6 + - - +
316A LEU* 1.3 69.8 - - - +
318A ASN* 1.3 77.5 + - - +
321A GLY* 2.6 40.1 + - - -
322A PRO* 4.0 18.9 - - + +
324A TRP* 4.1 4.3 - - - +
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Residues in contact with ASN 318 (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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314A LYS* 2.8 35.3 + - - +
315A THR* 3.8 6.2 - - - +
317A ASN* 1.3 90.9 + - - +
319A ASP* 1.3 68.1 + - - +
321A GLY 4.5 0.7 + - - -
362A PRO* 5.5 5.1 - - - +
441A HIS* 5.9 0.2 - - - +
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Residues in contact with ASP 319 (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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315A THR* 2.9 19.0 + - - +
316A LEU 4.3 0.4 - - - +
318A ASN* 1.3 84.8 - - - +
320A LEU* 1.3 63.5 + - + +
321A GLY 3.6 0.4 - - - -
439A SER* 2.2 44.3 + - - +
440A PRO* 3.6 4.4 - - - +
441A HIS* 2.8 51.5 + - - +
442A VAL* 4.3 8.3 - - + -
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Residues in contact with LEU 320 (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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316A LEU* 2.9 30.3 + - + +
319A ASP* 1.3 85.6 - - + +
321A GLY* 1.3 61.1 + - - +
322A PRO 3.6 0.9 - - - +
323A ASN* 2.8 27.6 + - - +
324A TRP* 3.3 31.0 - - + -
327A LYS* 6.1 0.4 - - + -
357A MSE 5.4 0.9 - - + -
436A GLU 4.8 7.4 - - - +
437A LEU* 4.3 29.2 - - + +
438A CYS 5.8 0.7 - - - +
439A SER* 4.7 6.7 - - - +
442A VAL* 4.6 12.8 - - + -
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Residues in contact with GLY 321 (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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316A LEU 3.3 1.9 + - - +
317A ASN* 2.6 32.4 + - - -
318A ASN 4.3 0.6 + - - -
319A ASP 3.6 1.4 - - - -
320A LEU* 1.3 75.3 - - - +
322A PRO* 1.3 76.8 - - - +
324A TRP* 3.2 18.9 - - - -
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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