Contacts of the helix formed by residues 306 - 320 (chain A) in PDB entry 1W3U
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 306 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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303A ARG* 5.5 0.4 - - - -
304A LEU 3.1 2.2 - - - -
305A ALA* 1.3 83.8 - - - +
307A GLU* 1.3 65.8 + - - +
308A GLU* 3.4 10.2 + - - +
309A LEU* 3.0 29.5 + - - +
310A GLU* 3.0 28.1 + - - +
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Residues in contact with GLU 307 (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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303A ARG* 4.4 10.4 - - - +
306A SER* 1.3 75.1 - - - +
308A GLU* 1.3 62.4 + - - +
310A GLU* 3.2 18.9 + - + +
311A LYS* 2.9 24.3 + - - +
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Residues in contact with GLU 308 (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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306A SER* 3.0 8.8 + - - +
307A GLU* 1.3 80.2 - - - +
309A LEU* 1.3 65.0 + - + +
311A LYS* 3.2 9.3 + - - +
312A GLU* 2.4 63.7 + - - +
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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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285A PHE* 4.6 13.0 - - + -
304A LEU* 3.7 16.3 - - + +
305A ALA* 4.2 17.5 - - + +
306A SER* 3.0 33.2 + - - +
308A GLU* 1.3 81.6 - - + +
310A GLU* 1.3 57.3 + - - +
312A GLU* 3.2 17.0 + - - +
313A PHE* 2.9 28.2 + - - +
357A PHE* 3.8 9.2 - - + -
361A ARG* 3.6 32.1 - - + -
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Residues in contact with GLU 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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303A ARG* 2.8 47.0 + - - +
304A LEU* 2.8 39.5 + - + +
306A SER 3.0 17.5 + - - +
307A GLU* 3.6 15.1 - - + +
308A GLU 3.2 0.2 - - - -
309A LEU* 1.3 79.1 - - - +
311A LYS* 1.3 55.8 + - - +
313A PHE* 3.2 7.5 + - - +
314A VAL* 2.9 34.6 + - + +
333A GLY* 3.1 28.2 + - - +
334A LEU* 4.3 3.2 - - + +
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Residues in contact with LYS 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 GLU 2.9 13.1 + - - +
308A GLU* 3.2 14.1 + - - +
310A GLU* 1.3 75.3 - - - +
312A GLU* 1.3 59.6 + - + +
314A VAL* 3.4 7.1 + - - +
315A LYS* 3.0 28.8 + - - +
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Residues in contact with GLU 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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308A GLU* 2.4 49.1 + - - +
309A LEU* 3.5 20.5 - - - +
311A LYS* 1.3 74.7 - - + +
313A PHE* 1.3 60.3 + - - +
315A LYS* 3.9 6.1 - - - +
316A ALA* 2.8 34.3 + - - +
357A PHE* 3.7 8.1 - - + -
361A ARG* 2.9 35.2 + - - +
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Residues in contact with PHE 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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286A TYR* 3.4 33.0 - + - -
302A PHE* 4.2 11.0 - + - -
304A LEU* 4.4 2.9 - - + -
309A LEU 2.9 13.6 + - - +
310A GLU* 3.2 11.9 + - - +
312A GLU* 1.3 78.4 - - - +
314A VAL* 1.3 58.5 + - - +
317A SER* 2.8 35.8 + - - -
325A LEU* 4.0 20.6 - - + -
334A LEU* 3.5 33.2 - - + -
350A LEU* 4.5 3.1 - - + -
353A PHE* 3.6 32.5 - + - -
354A MET* 3.8 16.4 - - + -
357A PHE* 3.5 29.8 - + + -
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Residues in contact with VAL 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 GLU* 2.9 21.3 + - + +
311A LYS* 3.8 7.0 - - - +
313A PHE* 1.3 78.0 - - - +
315A LYS* 1.3 65.6 + - - +
317A SER* 2.9 22.2 + - - +
318A GLU* 2.9 39.1 + - + +
325A LEU* 5.8 0.7 - - + -
326A LYS* 3.7 41.3 - - + +
333A GLY 5.0 2.0 - - - +
334A LEU* 3.6 22.4 - - + -
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Residues in contact with LYS 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 LYS 3.0 17.1 + - - +
312A GLU* 4.1 5.4 - - - +
314A VAL* 1.3 77.8 - - - +
316A ALA* 1.3 66.1 + - + +
318A GLU* 3.2 13.5 + - - +
319A GLN* 3.0 51.0 + - + +
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Residues in contact with ALA 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 GLU 2.8 22.1 + - - +
315A LYS* 1.3 75.4 - - + +
317A SER* 1.3 63.1 + - - +
319A GLN* 3.2 14.8 + - - +
320A GLU* 3.1 28.6 + - + +
353A PHE* 3.8 17.5 - - + -
357A PHE* 4.4 11.0 - - + -
361A ARG* 5.3 6.3 - - - +
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Residues in contact with SER 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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313A PHE* 2.8 21.7 + - - -
314A VAL* 2.9 22.5 + - - +
316A ALA* 1.3 73.4 - - - +
318A GLU* 1.3 64.3 + - - +
320A GLU 3.0 7.8 + - - -
321A GLY 3.2 0.3 + - - -
322A PHE* 2.9 31.8 + - - +
325A LEU* 3.8 31.0 - - - +
353A PHE* 3.4 25.2 - - - -
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Residues in contact with GLU 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 VAL* 2.9 41.4 + - + +
315A LYS* 3.6 10.7 - - - +
317A SER* 1.3 78.7 + - - +
319A GLN* 1.3 64.8 + - + +
321A GLY* 3.1 14.6 + - - -
322A PHE 3.4 16.3 - - - +
323A VAL* 5.8 0.2 - - - -
324A GLY 5.6 5.2 + - - +
325A LEU 6.4 0.4 - - - +
326A LYS* 5.3 2.6 - - - +
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Residues in contact with GLN 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 LYS* 3.0 49.2 + - + +
316A ALA* 3.2 12.0 + - - +
318A GLU* 1.3 79.8 - - + +
320A GLU* 1.3 59.9 + - + +
321A GLY 3.2 1.5 + - - -
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Residues in contact with GLU 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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6A TYR* 4.3 9.9 - - - -
316A ALA* 3.1 14.6 + - - +
317A SER 3.0 5.9 + - - +
319A GLN* 1.3 77.2 - - + +
321A GLY* 1.3 59.2 + - - +
322A PHE* 3.5 20.3 - - + -
353A PHE* 3.5 29.8 - - + +
356A HIS* 5.4 6.2 + - - +
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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