Contacts of the helix formed by residues 242 - 255 (chain A) in PDB entry 4CSC
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 242 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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238A HIS 2.7 29.6 + - - +
239A GLU* 2.9 15.9 + - - +
240A GLY 3.3 0.2 - - - -
241A GLY* 1.3 78.4 - - - +
243A VAL* 1.3 65.0 + - - +
244A SER* 3.2 5.4 + - - -
245A ALA* 3.1 22.1 + - - +
246A HIS* 2.9 23.2 + - - +
274A HIS* 3.7 0.4 + - + -
401A ARG* 3.2 21.2 + - - +
702A MLT 3.1 49.3 + - + +
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Residues in contact with VAL 243 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241A GLY 3.8 1.9 + - - +
242A ASN* 1.3 71.5 + - - +
244A SER* 1.3 58.3 + - - +
246A HIS* 4.0 3.5 - - - +
247A THR* 2.8 40.5 + - - +
268A GLY* 3.9 27.4 - - - +
274A HIS* 3.6 22.0 + - + +
702A MLT 5.0 0.6 + - - -
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Residues in contact with SER 244 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242A ASN* 3.2 5.2 + - - -
243A VAL* 1.3 76.1 - - - +
245A ALA* 1.3 64.6 + - - +
247A THR* 3.1 2.7 + - - -
248A SER* 3.0 18.7 + - - -
265A ALA* 3.4 39.1 - - - +
266A MET* 4.7 1.1 - - - -
269A LEU* 3.9 11.1 - - - +
274A HIS* 3.0 27.7 + - - -
401A ARG* 3.6 25.5 + - - +
405A VAL* 4.7 0.4 - - - -
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Residues in contact with ALA 245 (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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53A TYR* 3.7 19.8 - - + +
237A ASP* 4.9 1.3 - - - +
239A GLU 3.7 15.7 - - - +
240A GLY 3.8 3.8 - - - +
242A ASN* 3.1 19.2 + - - +
244A SER* 1.3 74.3 + - - +
246A HIS* 1.3 65.2 + - - +
248A SER* 2.7 18.2 + - - -
249A HIS* 3.0 11.8 + - - +
401A ARG* 5.1 1.8 - - - +
405A VAL* 3.4 26.7 - - + +
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Residues in contact with HIS 246 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A MET* 4.8 18.8 - - + -
51A LEU* 3.9 21.0 - - + +
240A GLY 3.1 17.1 + - - +
241A GLY* 4.2 8.7 + - - +
242A ASN 2.9 21.2 + - - +
243A VAL* 4.0 3.8 - - - +
245A ALA* 1.3 74.5 - - - +
247A THR* 1.4 56.1 + - - +
249A HIS* 3.1 7.0 + + - +
250A LEU* 2.8 35.7 + - + +
420A GLU* 2.7 41.9 + - - -
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Residues in contact with THR 247 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243A VAL* 2.8 34.4 + - - +
244A SER* 3.1 5.1 + - - -
246A HIS* 1.4 74.7 - - - +
248A SER* 1.3 65.6 + - - +
250A LEU* 3.6 9.1 - - + +
251A VAL* 2.9 30.0 + - + +
264A ALA* 3.5 38.1 + - + +
265A ALA* 4.1 7.0 - - - -
268A GLY* 5.0 2.8 - - - -
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Residues in contact with SER 248 (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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53A TYR* 5.7 0.7 - - - -
244A SER 3.0 9.5 + - - -
245A ALA* 2.7 19.6 + - - -
247A THR* 1.3 78.0 - - - +
249A HIS* 1.3 58.3 + - - +
252A GLY* 2.9 27.0 + - - -
261A SER* 3.6 33.3 + - - -
262A PHE* 5.1 0.2 - - - -
265A ALA* 4.2 6.5 - - - -
405A VAL* 3.4 32.7 + - - +
409A LEU* 4.4 11.2 - - - +
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Residues in contact with HIS 249 (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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51A LEU* 3.4 33.1 - - + +
52A VAL 3.7 16.9 + - - -
53A TYR* 4.4 13.7 - + + -
245A ALA 3.0 17.0 + - - +
246A HIS* 3.5 7.2 - + - +
247A THR 3.1 0.2 - - - -
248A SER* 1.3 76.7 + - - +
250A LEU* 1.3 63.2 + - - +
252A GLY* 3.9 0.7 - - - -
253A SER* 3.0 28.0 + - - -
408A GLN* 4.7 2.0 - - + +
409A LEU* 5.3 5.4 - - - -
412A SER* 3.8 23.1 + - - -
413A ARG* 5.2 1.6 + - - -
417A PHE* 4.1 14.4 - + + +
420A GLU* 3.4 27.5 + - + +
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Residues in contact with LEU 250 (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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246A HIS* 2.8 22.1 + - + +
247A THR* 3.6 11.4 - - + +
249A HIS* 1.3 77.4 - - - +
251A VAL* 1.3 66.8 + - + +
253A SER* 2.9 20.7 + - - -
254A ALA* 3.9 5.4 + - - +
419A LEU* 5.7 0.3 - - - +
420A GLU* 3.6 52.7 - - + +
422A PRO* 5.7 2.0 - - + -
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Residues in contact with VAL 251 (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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247A THR* 2.9 35.2 + - + +
250A LEU* 1.3 81.5 - - + +
252A GLY* 1.3 64.6 + - - +
254A ALA* 3.3 20.0 + - - +
256A SER* 3.5 23.9 + - - +
260A LEU* 4.1 6.5 - - + +
261A SER* 3.6 29.4 - - - +
264A ALA* 3.9 10.3 - - + -
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Residues in contact with GLY 252 (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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248A SER 2.9 18.8 + - - -
249A HIS 3.9 0.7 - - - -
251A VAL* 1.3 77.5 - - - +
253A SER* 1.4 53.2 + - - +
255A LEU* 2.8 26.9 + - - +
256A SER 3.9 13.5 - - - +
261A SER* 3.8 6.0 - - - -
409A LEU* 4.2 12.8 - - - -
413A ARG* 3.4 18.3 + - - -
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Residues in contact with SER 253 (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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249A HIS* 3.0 19.2 + - - -
250A LEU 2.9 17.8 + - - -
252A GLY* 1.4 74.5 - - - +
254A ALA* 1.4 56.8 + - - +
255A LEU* 3.1 9.4 + - - +
413A ARG* 3.9 16.2 + - - +
417A PHE* 5.0 0.7 - - - +
418A PRO 3.5 12.5 - - - -
419A LEU* 3.7 18.6 + - - +
420A GLU* 2.9 36.8 + - - +
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Residues in contact with ALA 254 (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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250A LEU 3.9 3.1 + - - +
251A VAL* 3.3 14.3 + - - +
252A GLY 3.1 0.8 - - - -
253A SER* 1.4 77.7 + - - +
255A LEU* 1.3 69.3 + - - +
256A SER* 4.4 8.2 + - - +
419A LEU* 4.0 18.6 - - + -
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Residues in contact with LEU 255 (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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154A PHE* 3.4 26.4 - - + -
158A TYR* 3.9 30.6 - - + +
167A TYR* 3.8 26.2 - - + +
252A GLY 2.8 11.2 + - - +
253A SER 4.3 6.3 - - - +
254A ALA* 1.3 82.6 - - - +
256A SER* 1.3 63.9 + - - +
257A ASP 3.6 0.5 + - - -
413A ARG* 3.5 35.9 - - - +
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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