Contacts of the helix formed by residues 310 - 322 (chain A) in PDB entry 4WMB
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 GLU 310 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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306A SER* 3.8 8.4 - - - +
307A HIS* 3.0 44.4 + - - +
309A LEU* 1.3 78.6 - - + +
311A PRO* 1.4 75.3 - - + +
312A SER* 4.6 7.6 + - - +
313A TRP* 3.0 27.4 + - + +
314A VAL* 3.0 11.5 + - - +
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Residues in contact with PRO 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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182A PRO 6.0 2.7 - - - +
183A VAL 5.8 1.8 - - - +
186A ALA* 3.7 31.2 - - + +
190A TYR* 5.8 0.2 - - - -
309A LEU 3.6 6.0 - - - +
310A GLU* 1.4 84.8 - - + +
312A SER* 1.3 57.4 + - - +
314A VAL* 3.4 5.0 + - + +
315A GLN* 3.0 30.4 + - - +
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Residues in contact with SER 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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310A GLU* 3.2 7.1 + - - +
311A PRO* 1.3 79.5 - - - +
313A TRP* 1.3 66.0 + - - +
315A GLN* 3.8 11.3 - - - +
316A GLN* 2.9 46.0 + - - +
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Residues in contact with TRP 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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307A HIS* 3.4 44.5 - - + +
308A LEU* 4.1 20.2 - - + -
310A GLU* 3.0 17.8 + - - +
312A SER* 1.3 81.9 + - - +
314A VAL* 1.3 65.3 + - - +
316A GLN* 3.3 34.8 + - + +
317A LEU* 3.1 49.6 + - + +
339A GLU* 5.9 2.0 - - + -
340A HIS* 6.1 4.5 - + - -
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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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186A ALA* 4.2 2.5 - - + +
187A MET* 3.8 41.5 - - + +
190A TYR* 3.8 20.6 - - + -
191A PHE* 4.5 8.5 - - + -
308A LEU 3.3 21.1 + - - +
309A LEU 4.1 4.9 - - - +
310A GLU 3.0 12.7 + - - +
311A PRO* 3.7 10.1 - - + +
313A TRP* 1.3 74.2 - - - +
315A GLN* 1.3 58.4 - - - +
317A LEU* 4.0 1.8 - - - +
318A ALA* 3.0 28.1 + - - +
332A PHE* 4.1 14.4 - - + -
335A MET* 4.1 7.6 - - + +
336A ILE* 6.5 0.2 - - - -
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Residues in contact with GLN 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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190A TYR* 3.2 30.1 - - + +
311A PRO 3.0 18.4 + - - +
312A SER* 3.8 12.5 - - - +
314A VAL* 1.3 75.8 - - - +
316A GLN* 1.3 72.3 + - - +
318A ALA* 3.6 1.0 + - - +
319A ASP* 3.0 47.2 + - - +
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Residues in contact with GLN 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 SER* 2.9 37.5 + - - +
313A TRP* 3.3 41.0 + - + +
315A GLN* 1.3 83.4 - - - +
317A LEU* 1.3 59.3 + - + +
319A ASP* 3.4 7.3 + - - +
320A LYS* 2.9 28.5 + - - +
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Residues in contact with LEU 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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308A LEU* 3.8 28.5 - - + -
313A TRP* 3.1 35.0 + - + +
314A VAL* 5.8 0.2 - - - -
316A GLN* 1.3 76.5 - - + +
318A ALA* 1.3 61.0 + - - +
320A LYS* 3.3 7.6 + - + -
321A TYR* 2.9 42.8 + - + +
335A MET* 3.7 19.1 - - + +
336A ILE* 4.0 20.2 - - + -
339A GLU* 3.7 46.0 - - + +
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Residues in contact with ALA 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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190A TYR* 3.6 42.0 - - + -
314A VAL 3.0 18.8 + - - +
315A GLN 4.0 1.3 - - - +
317A LEU* 1.3 74.8 - - - +
319A ASP* 1.3 57.8 + - - +
322A HIS* 2.9 24.1 + - - -
323A PHE* 2.9 19.8 + - + +
335A MET* 3.5 16.0 - - + -
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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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190A TYR* 4.9 7.4 + - - -
315A GLN* 3.0 46.8 + - - +
316A GLN* 3.5 7.2 - - - +
318A ALA* 1.3 74.0 - - - +
320A LYS* 1.3 67.1 + - - +
322A HIS* 3.2 25.7 + - - +
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Residues in contact with LYS 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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267A PHE* 3.4 30.3 - - + -
316A GLN 2.9 18.6 + - - +
317A LEU* 3.6 10.8 - - + +
319A ASP* 1.3 76.6 - - - +
321A TYR* 1.3 82.0 + - + +
322A HIS* 3.6 9.8 + - - -
339A GLU* 2.8 35.1 + - - +
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Residues in contact with TYR 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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264A PHE* 3.7 36.0 - + + -
267A PHE* 3.6 53.5 + + - +
276A VAL* 4.2 5.4 - - + +
317A LEU* 2.9 37.8 + - + +
320A LYS* 1.3 92.9 + - + +
322A HIS* 1.3 72.0 + - - +
323A PHE* 3.3 10.7 + - + -
335A MET* 4.2 21.1 - - + -
338A MET* 3.7 20.4 + - + +
339A GLU* 2.7 39.8 + - + -
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Residues in contact with HIS 322 (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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263A THR 4.4 8.8 - - - +
266A GLN* 3.2 48.6 + - + +
267A PHE* 4.0 15.5 - - - -
270A GLU* 2.9 27.0 + - - -
318A ALA 2.9 8.4 + - - -
319A ASP* 3.2 17.7 + - - +
320A LYS* 3.7 10.7 + - - -
321A TYR* 1.3 81.6 - - - +
323A PHE* 1.3 60.8 + - - +
324A ARG* 3.8 6.1 + - - +
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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