Contacts of the helix formed by residues 332 - 344 (chain H) 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 H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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45D GLN* 3.1 25.7 - - + +
46D LYS* 2.9 27.5 + - + +
47D LEU 4.3 1.0 - - - +
49D THR* 3.2 27.6 + - - -
330H GLY 3.7 1.4 + - - -
331H CYS* 1.3 76.2 - - - +
333H GLU* 1.3 64.7 + - - +
334H ALA* 3.1 2.3 + - - +
335H LEU* 2.8 38.2 + - - +
336H MET* 3.1 27.5 + - - +
427I GLU* 4.3 6.7 - - - -
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Residues in contact with GLU 333 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45D GLN* 2.9 17.9 + - - +
51D TYR* 2.8 28.5 + - - -
332H ASN* 1.3 74.3 - - - +
334H ALA* 1.3 57.0 + - - +
336H MET* 3.1 6.3 + - - +
337H LYS* 2.9 36.6 + - + +
397I ASP* 4.5 3.5 - - - +
399I TRP* 3.7 27.1 - - + -
419I ARG* 2.7 41.0 + - + +
420I GLY* 3.9 14.2 - - - -
427I GLU* 4.0 20.3 + - - +
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Residues in contact with ALA 334 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45D GLN* 3.1 15.0 + - - +
49D THR* 4.0 19.5 - - + -
51D TYR* 4.2 22.4 - - + -
57D SER* 4.8 7.9 - - - +
207H LEU* 4.8 0.8 - - - +
332H ASN* 3.1 4.5 + - - +
333H GLU* 1.3 78.8 - - - +
335H LEU* 1.3 63.2 + - + +
337H LYS* 3.4 11.7 + - - +
338H LEU* 3.0 31.8 + - + +
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Residues in contact with LEU 335 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47D LEU 6.2 0.2 - - - +
49D THR* 4.1 15.9 - - + +
57D SER* 6.0 0.9 - - - +
324H VAL* 3.6 17.9 - - + +
325H GLY* 3.9 17.9 - - - +
330H GLY 3.7 17.9 - - - +
332H ASN* 2.8 37.1 + - - +
334H ALA* 1.3 72.4 - - - +
336H MET* 1.3 57.4 + - - +
338H LEU* 3.4 14.9 - - + +
339H GLU* 2.9 30.0 + - - +
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Residues in contact with MET 336 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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324H VAL* 4.4 3.1 - - + -
331H CYS* 3.4 30.7 - - - -
332H ASN 3.1 16.6 + - - +
333H GLU 3.3 7.2 - - - +
335H LEU* 1.3 73.8 - - - +
337H LYS* 1.3 60.8 + - - +
339H GLU 3.3 0.5 + - - -
340H LEU* 2.8 32.1 + - - +
346H MET* 3.4 13.2 - - - +
348H VAL* 3.8 14.1 - - + -
385I LEU* 3.7 24.0 - - + -
399I TRP* 3.8 21.3 - - + +
426I ILE* 3.7 19.3 - - + +
427I GLU* 3.8 23.3 - - + -
430I ALA* 3.9 9.4 - - + -
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Residues in contact with LYS 337 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51D TYR* 4.5 19.5 - - + -
55D GLY* 5.6 5.5 - - - -
207H LEU* 4.0 19.5 - - + +
208H PRO 5.0 1.6 + - - -
333H GLU* 2.9 33.0 + - + +
334H ALA* 3.8 9.0 - - - +
336H MET* 1.3 71.2 - - - +
338H LEU* 1.3 57.8 + - - +
340H LEU* 3.3 6.5 + - - +
341H VAL* 2.9 35.2 + - - +
388I TYR* 3.8 39.8 - - + -
399I TRP* 3.8 20.4 - - + -
419I ARG* 3.9 22.4 - - - +
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Residues in contact with LEU 338 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55D GLY 5.6 1.8 - - - +
57D SER* 3.4 28.7 - - - +
207H LEU* 3.8 23.2 - - + +
334H ALA* 3.0 23.7 + - + +
335H LEU* 3.4 20.6 - - + +
337H LYS* 1.3 77.6 - - - +
339H GLU* 1.3 62.7 + - - +
342H HIS* 3.0 63.2 + - + +
343H HIS* 5.4 0.2 - - - -
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Residues in contact with GLU 339 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246H ARG* 2.7 34.7 + - - +
322H HIS* 3.6 20.8 + - - -
324H VAL* 4.1 12.0 - - + +
335H LEU 2.9 18.3 + - - +
336H MET 3.8 3.1 - - - +
338H LEU* 1.3 73.6 - - - +
340H LEU* 1.3 58.5 + - - +
343H HIS* 2.8 61.7 + - - +
344H GLY 3.3 4.3 + - - -
346H MET* 3.7 15.3 - - + -
432I ALA* 3.3 19.8 - - + +
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Residues in contact with LEU 340 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211H TRP* 4.6 4.7 - - + -
213H TRP* 2.8 39.0 + - + +
336H MET 2.8 17.3 + - - +
337H LYS 3.5 4.5 - - - +
339H GLU* 1.3 77.6 - - - +
341H VAL* 1.3 57.7 + - + +
344H GLY 3.0 14.0 + - - +
345H PRO* 3.7 15.9 - - + -
346H MET* 3.2 14.0 - - + +
385I LEU* 3.6 37.9 - - + +
386I VAL 4.0 2.0 - - - -
387I GLY* 3.7 34.1 - - - +
388I TYR* 4.0 16.2 - - + -
399I TRP* 4.6 3.4 - - + -
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Residues in contact with VAL 341 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207H LEU* 4.5 13.5 - - + -
208H PRO* 4.3 13.2 - - + -
211H TRP* 3.8 42.7 - - + +
213H TRP* 3.6 16.1 - - - -
337H LYS 2.9 20.8 + - - +
338H LEU 4.2 1.1 - - - +
340H LEU* 1.3 78.4 - - + +
342H HIS* 1.3 66.8 + - + +
388I TYR* 3.7 33.0 - - + +
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Residues in contact with HIS 342 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342B HIS* 6.2 3.6 - + - -
207H LEU* 3.7 16.9 - - + +
213H TRP* 5.4 0.9 - - - -
338H LEU* 3.0 53.7 + - + +
341H VAL* 1.3 80.9 - - + +
343H HIS* 1.3 81.8 + - + +
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Residues in contact with HIS 343 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213H TRP* 4.9 1.6 - - - -
246H ARG* 3.2 26.9 + - - +
249H ILE* 4.6 7.9 - - - +
339H GLU* 2.8 48.9 + - - +
342H HIS* 1.3 98.6 + - + +
344H GLY* 1.3 59.6 - - - +
434I THR* 6.1 0.2 - - - +
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Residues in contact with GLY 344 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213H TRP* 3.5 7.9 - - - -
246H ARG* 3.0 12.0 + - - -
249H ILE* 3.7 9.6 - - - -
339H GLU 3.3 0.4 + - - -
340H LEU* 3.0 32.3 + - - -
342H HIS 3.9 0.2 - - - -
343H HIS* 1.3 78.8 - - - +
345H PRO* 1.3 80.2 - - - +
346H MET* 3.7 1.2 + - - +
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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