Contacts of the helix formed by residues 332 - 344 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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330B GLY 3.7 1.6 + - - -
331B CYS* 1.3 77.8 - - - +
333B GLU* 1.3 64.4 + - - +
334B ALA* 3.1 8.1 + - - +
335B LEU* 2.9 37.5 + - - +
336B MET* 3.0 27.7 + - - +
427C GLU* 4.3 6.5 - - - -
45J GLN* 3.1 19.8 - - + +
46J LYS* 2.7 28.0 + - + +
47J LEU 4.3 0.8 - - - +
49J THR* 3.1 26.4 + - - -
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Residues in contact with GLU 333 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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332B ASN* 1.3 74.5 - - - +
334B ALA* 1.3 56.6 + - - +
336B MET* 3.1 8.0 + - - +
337B LYS* 2.8 39.6 + - + +
397C ASP* 4.9 2.3 - - - +
399C TRP* 3.6 27.1 - - + -
419C ARG* 2.8 40.2 + - + +
420C GLY* 4.1 12.5 - - - +
427C GLU* 4.2 17.7 + - - +
45J GLN* 2.8 28.0 + - - +
51J TYR* 3.0 19.7 + - - -
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Residues in contact with ALA 334 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207B LEU* 4.7 3.4 - - + +
332B ASN* 3.1 8.3 + - - +
333B GLU* 1.3 78.5 - - - +
335B LEU* 1.3 60.1 + - + +
337B LYS* 3.3 13.9 + - + +
338B LEU* 3.0 28.8 + - - +
45J GLN* 3.1 8.6 + - - +
49J THR* 3.9 20.4 - - + -
51J TYR* 3.9 23.3 - - + -
57J SER* 5.4 5.2 - - - -
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Residues in contact with LEU 335 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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324B VAL* 3.6 16.1 - - + +
325B GLY* 3.7 30.7 - - - +
330B GLY 3.7 12.1 - - - +
332B ASN* 2.9 28.9 + - - +
334B ALA* 1.3 77.0 - - - +
336B MET* 1.3 56.6 + - - +
338B LEU* 3.7 17.2 - - + +
339B GLU* 2.9 30.8 + - - +
49J THR* 4.1 15.0 - - + +
57J SER* 6.4 1.3 - - - -
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Residues in contact with MET 336 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324B VAL* 4.4 3.4 - - + -
331B CYS* 3.5 30.1 - - - -
332B ASN 3.0 17.2 + - - +
333B GLU 3.4 7.2 - - - +
335B LEU* 1.3 74.3 - - - +
337B LYS* 1.3 64.9 + - - +
340B LEU* 3.0 26.0 + - - +
346B MET* 3.5 12.3 - - - +
348B VAL* 3.8 14.8 - - + -
385C LEU* 3.7 23.6 - - + -
399C TRP* 3.8 19.7 - - + +
426C ILE* 3.5 21.8 - - + +
427C GLU* 3.7 24.9 - - + -
430C ALA* 3.9 9.9 - - + -
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Residues in contact with LYS 337 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207B LEU* 3.9 23.2 - - + +
208B PRO 5.2 1.8 + - - -
333B GLU* 2.8 37.2 + - - +
334B ALA* 3.6 10.5 - - - +
336B MET* 1.3 74.5 - - - +
338B LEU* 1.3 63.5 + - - +
340B LEU* 3.3 6.6 + - - +
341B VAL* 3.0 27.5 + - - +
388C TYR* 3.9 37.2 - - + -
399C TRP* 3.8 19.5 - - + -
419C ARG* 4.0 13.5 - - - +
51J TYR* 4.3 21.2 + - + +
55J GLY* 5.4 5.3 - - - -
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Residues in contact with LEU 338 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207B LEU* 4.1 19.0 - - + +
334B ALA 3.0 15.9 + - - +
335B LEU* 3.7 19.5 - - + +
337B LYS* 1.3 74.4 - - - +
339B GLU* 1.3 66.5 + - - +
342B HIS* 3.0 67.9 + - + +
343B HIS* 6.2 1.1 - - + -
57J SER* 5.4 11.0 - - - +
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Residues in contact with GLU 339 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246B ARG* 2.8 30.9 + - - +
322B HIS* 3.6 20.3 + - - -
324B VAL* 4.1 10.5 - - + +
335B LEU 2.9 16.8 + - - +
336B MET 3.9 3.4 - - - +
338B LEU* 1.3 77.9 - - - +
340B LEU* 1.3 58.6 + - - +
343B HIS* 2.8 55.4 + - - +
344B GLY 3.3 4.7 + - - -
346B MET* 3.9 15.9 - - + -
432C ALA* 3.2 22.0 - - + +
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Residues in contact with LEU 340 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211B TRP* 4.5 4.0 - - + -
213B TRP* 2.8 38.1 + - + +
336B MET 3.0 17.8 + - - +
337B LYS 3.5 3.6 - - - +
339B GLU* 1.3 77.7 - - - +
341B VAL* 1.3 58.5 - - - +
344B GLY 3.0 14.8 + - - +
345B PRO* 3.8 13.0 - - + -
346B MET* 3.3 17.4 - - + +
385C LEU* 3.4 36.6 - - + +
386C VAL 3.9 2.7 - - - +
387C GLY* 3.6 31.6 - - - +
388C TYR* 3.8 22.2 - - + -
399C TRP* 4.8 2.2 - - + -
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Residues in contact with VAL 341 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207B LEU* 4.2 18.8 - - + -
208B PRO* 4.5 6.7 - - + -
211B TRP* 3.9 45.3 - - + +
213B TRP* 3.7 13.7 - - - -
337B LYS 3.0 16.2 + - - +
338B LEU 4.3 0.7 - - - +
340B LEU* 1.3 77.4 - - + +
342B HIS* 1.3 72.1 + - + +
388C TYR* 3.6 32.3 - - + +
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Residues in contact with HIS 342 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206B HIS 5.2 3.6 + - - -
207B LEU* 4.4 13.3 - - + +
213B TRP* 5.5 0.9 - - - -
338B LEU* 3.0 49.6 + - + +
341B VAL* 1.3 88.9 - - + +
343B HIS* 1.3 82.9 + - + +
342H HIS* 6.2 3.8 - + - -
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Residues in contact with HIS 343 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213B TRP* 4.9 1.6 - - - -
246B ARG* 3.2 28.5 + - - +
249B ILE* 4.8 7.1 - - - +
338B LEU* 5.3 0.9 - - + -
339B GLU* 2.8 51.5 + - - +
342B HIS* 1.3 98.0 + - + +
344B GLY* 1.3 54.9 - - - +
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Residues in contact with GLY 344 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213B TRP* 3.4 11.6 - - - -
246B ARG* 3.1 10.8 + - - -
249B ILE* 3.8 6.3 - - - -
339B GLU 3.3 0.8 + - - -
340B LEU* 3.0 32.4 + - - -
342B HIS 4.0 0.2 - - - -
343B HIS* 1.3 77.5 - - - +
345B PRO* 1.3 79.8 - - - +
346B MET* 3.6 1.9 + - - +
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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