Contacts of the helix formed by residues 332 - 344 (chain E) in PDB entry 4CDC
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 332 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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330E GLY 3.7 1.6 + - - -
331E CYS* 1.3 76.5 - - - +
333E GLU* 1.3 64.7 + - - +
334E ALA* 3.1 7.6 + - - +
335E LEU* 2.8 48.7 + - - +
336E MET* 3.0 28.7 + - - +
427F GLU* 4.3 7.9 - - - -
45G GLN* 3.4 18.6 - - + +
46G LYS* 2.8 29.3 + - + +
47G LEU 4.3 0.4 - - - +
49G THR* 3.1 25.8 + - - -
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Residues in contact with GLU 333 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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332E ASN* 1.3 75.0 - - - +
334E ALA* 1.3 57.0 + - - +
336E MET* 3.2 6.0 + - - +
337E LYS* 2.9 37.9 + - + +
397F ASP* 5.0 1.4 - - - +
399F TRP* 3.6 27.8 - - + -
419F ARG* 2.7 40.8 + - + +
420F GLY* 3.3 16.5 - - - +
427F GLU* 4.1 17.9 + - - +
45G GLN* 3.1 24.7 + - - +
51G TYR* 3.2 18.2 + - - -
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Residues in contact with ALA 334 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207E LEU* 4.6 2.7 - - - +
332E ASN* 3.1 6.9 + - - +
333E GLU* 1.3 74.9 - - - +
335E LEU* 1.3 60.4 + - + +
337E LYS* 3.2 11.5 + - - +
338E LEU* 3.0 29.6 + - - +
45G GLN* 3.1 13.8 + - - +
49G THR* 3.8 21.8 - - + -
51G TYR* 4.0 22.7 - - + -
57G SER* 5.7 3.8 - - - -
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Residues in contact with LEU 335 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324E VAL* 3.5 19.1 - - + +
325E GLY* 3.9 16.8 - - - +
330E GLY 3.6 17.9 - - - +
332E ASN* 2.8 38.7 + - - +
334E ALA* 1.3 73.9 - - + +
336E MET* 1.3 58.1 + - - +
338E LEU* 3.5 18.5 + - + +
339E GLU* 3.0 30.8 + - - +
47G LEU 6.1 0.2 - - - +
49G THR* 4.1 13.2 - - + +
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Residues in contact with MET 336 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324E VAL* 4.5 2.7 - - + -
331E CYS* 3.5 31.0 - - - -
332E ASN 3.0 16.0 + - - +
333E GLU 3.2 6.7 + - - +
335E LEU* 1.3 75.0 - - - +
337E LYS* 1.3 64.3 + - - +
340E LEU* 3.0 25.8 + - - +
346E MET* 3.4 13.1 - - - +
348E VAL* 3.8 22.4 - - + -
385F LEU* 4.0 14.1 - - + +
399F TRP* 3.9 23.8 - - + +
426F ILE* 3.4 21.3 - - + +
427F GLU* 3.7 22.7 - - + -
430F ALA* 3.8 11.0 - - + -
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Residues in contact with LYS 337 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207E LEU* 3.6 26.1 + - + +
208E PRO 5.0 2.0 + - - -
333E GLU* 2.9 39.8 + - - +
334E ALA* 3.6 10.5 - - - +
336E MET* 1.3 74.4 - - - +
338E LEU* 1.3 63.7 + - - +
340E LEU* 3.5 4.0 - - - +
341E VAL* 3.1 29.5 + - - +
388F TYR* 3.7 42.8 - - + -
399F TRP* 3.9 15.9 - - + -
419F ARG* 3.8 11.9 - - - +
51G TYR* 4.8 15.2 - - + +
55G GLY* 5.2 8.1 - - - -
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Residues in contact with LEU 338 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207E LEU* 3.7 17.9 - - + +
334E ALA 3.0 16.7 + - - +
335E LEU* 3.7 20.4 - - + +
337E LYS* 1.3 77.0 - - - +
339E GLU* 1.3 64.4 + - - +
341E VAL 3.5 0.2 + - - -
342E HIS* 3.0 64.6 + - + +
343E HIS* 6.4 0.4 - - + -
57G SER* 5.1 10.5 - - - +
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Residues in contact with GLU 339 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246E ARG* 2.8 34.3 + - - +
322E HIS* 4.0 14.4 + - - -
324E VAL* 4.2 10.1 - - + +
335E LEU 3.0 18.0 + - - +
338E LEU* 1.3 75.7 - - - +
340E LEU* 1.3 56.2 + - - +
343E HIS* 2.8 56.3 + - - +
344E GLY 3.3 4.5 + - - -
346E MET* 3.5 25.4 - - + -
432F ALA* 3.2 23.0 - - + +
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Residues in contact with LEU 340 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211E TRP* 4.7 4.3 - - + -
213E TRP* 2.7 41.3 + - + +
336E MET 3.0 18.3 + - - +
337E LYS 3.5 2.9 - - - +
339E GLU* 1.3 78.4 - - - +
341E VAL* 1.3 55.1 + - - +
344E GLY 3.0 13.7 + - - +
345E PRO* 3.7 15.9 - - + -
346E MET* 3.3 12.3 - - + -
385F LEU* 3.4 38.1 - - + +
386F VAL 4.0 2.7 - - - +
387F GLY* 3.7 29.2 - - - +
388F TYR* 3.9 23.6 - - + -
399F TRP* 4.6 2.2 - - + -
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Residues in contact with VAL 341 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207E LEU* 4.6 4.5 - - + -
208E PRO* 4.4 12.1 - - + -
211E TRP* 4.0 41.2 - - + +
213E TRP* 3.6 19.7 - - - -
337E LYS 3.1 16.5 + - - +
340E LEU* 1.3 78.6 - - + +
342E HIS* 1.3 83.1 + - + +
388F TYR* 3.8 31.6 - - + +
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Residues in contact with HIS 342 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206E HIS 6.1 0.4 - - - -
207E LEU* 3.6 28.7 - - + +
213E TRP* 5.5 0.4 - - - -
338E LEU* 3.0 34.9 + - + +
341E VAL* 1.3 93.5 - - + +
343E HIS* 1.3 79.7 + - + +
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Residues in contact with HIS 343 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213E TRP* 4.8 2.0 - - - -
246E ARG* 3.5 26.5 + - - +
249E ILE* 4.5 9.3 - - - +
338E LEU* 5.4 0.7 - - + -
339E GLU* 2.8 56.5 + - - +
342E HIS* 1.3 92.7 + - + +
344E GLY* 1.3 56.9 + - - +
434F THR* 5.9 1.7 + - - +
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Residues in contact with GLY 344 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213E TRP* 3.5 6.4 - - - -
246E ARG* 2.8 14.3 + - - -
249E ILE* 3.7 8.5 - - - -
339E GLU 3.3 0.8 + - - -
340E LEU* 3.0 32.5 + - - -
342E HIS 4.0 0.2 - - - -
343E HIS* 1.3 78.4 - - - +
345E PRO* 1.3 79.4 - - - +
346E MET* 3.5 1.4 + - - +
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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