Contacts of the helix formed by residues 245 - 257 (chain A) in PDB entry 4X5O
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 SER 245 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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241A LEU* 3.9 6.3 - - - -
244A VAL* 1.3 79.2 - - - +
246A TRP* 1.3 59.3 + - - +
247A GLU* 3.9 12.5 + - - +
248A GLU* 2.9 35.0 + - - +
249A VAL* 2.9 29.1 + - - +
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Residues in contact with TRP 246 (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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238A VAL* 5.4 1.3 - - + -
241A LEU* 3.6 19.7 - - + +
245A SER* 1.3 71.4 - - - +
247A GLU* 1.3 73.1 + - + +
249A VAL* 4.2 12.1 - - + -
250A LYS* 2.7 64.2 + - + +
253A MET* 3.9 20.4 - - + -
264A ALA 3.0 28.5 - - - -
265A ASP* 3.6 18.0 + - - -
267A ILE* 4.8 4.3 - - + -
268A GLY* 3.5 22.4 - - - -
271A VAL* 4.9 9.6 - - + -
272A GLN* 3.0 45.6 + - + +
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Residues in contact with GLU 247 (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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245A SER* 4.0 13.7 - - - +
246A TRP* 1.3 88.7 - - + +
248A GLU* 1.3 60.2 + - + +
250A LYS* 3.7 7.1 - - - +
251A ASN* 2.8 31.0 + - - +
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Residues in contact with GLU 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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244A VAL* 3.3 31.9 - - + +
245A SER* 2.9 21.8 + - - +
246A TRP 3.3 0.2 - - - -
247A GLU* 1.3 75.0 - - + +
249A VAL* 1.3 58.1 + - - +
251A ASN* 4.0 6.3 - - - +
252A GLU* 2.7 36.6 + - - +
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Residues in contact with VAL 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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237A SER* 3.9 29.8 - - - +
238A VAL* 4.2 10.8 - - - -
240A LYS* 4.4 7.9 - - + +
241A LEU* 4.0 27.4 - - + +
244A VAL* 4.7 5.2 - - + -
245A SER 2.9 19.4 + - - +
246A TRP* 3.5 18.8 - - + +
248A GLU* 1.3 77.0 - - - +
250A LYS* 1.3 57.0 + - - +
251A ASN 3.0 0.5 + - - -
252A GLU* 3.7 4.9 - - - +
253A MET* 2.8 50.4 + - + +
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Residues in contact with LYS 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 TRP* 2.7 58.3 + - + +
247A GLU* 3.8 5.6 - - - +
249A VAL* 1.3 73.8 - - - +
251A ASN* 1.3 55.9 + - - +
253A MET* 3.2 12.7 - - - +
254A VAL* 3.0 47.7 + - + +
261A PRO* 5.2 5.4 - - - -
264A ALA* 4.5 9.2 - - + -
265A ASP* 2.6 35.2 + - - +
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Residues in contact with ASN 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 GLU 2.8 21.4 + - - +
248A GLU* 3.6 8.0 - - - +
249A VAL 3.0 0.6 + - - -
250A LYS* 1.3 73.9 - - - +
252A GLU* 1.3 69.9 + - - +
253A MET 3.1 1.2 + - - -
254A VAL* 3.5 3.7 + - - +
255A GLY* 3.2 17.3 + - - -
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Residues in contact with GLU 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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237A SER* 2.5 34.9 + - - -
240A LYS* 2.8 32.8 + - - +
248A GLU 2.7 20.9 + - - +
249A VAL* 3.7 3.6 - - - +
251A ASN* 1.3 71.3 - - - +
253A MET* 1.3 67.6 + - - +
255A GLY* 3.4 1.2 + - - -
256A GLU* 3.0 36.3 + - + +
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Residues in contact with MET 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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234A ILE* 4.3 15.7 - - + -
237A SER* 3.2 23.8 - - - +
238A VAL* 4.3 18.4 - - + -
246A TRP* 3.9 25.4 - - + -
249A VAL* 2.8 22.4 + - + +
250A LYS* 3.2 26.9 - - - +
252A GLU* 1.3 76.5 - - - +
254A VAL* 1.3 56.7 + - - +
256A GLU* 2.6 31.2 + - - +
257A LYS* 2.7 49.6 + - + +
259A LEU* 5.0 0.4 - - - -
264A ALA* 4.2 8.3 - - + +
267A ILE* 5.3 3.6 - - + -
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Residues in contact with VAL 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 LYS* 3.0 26.7 + - + +
251A ASN* 4.4 2.9 - - - +
253A MET* 1.3 76.4 - - - +
255A GLY* 1.3 63.1 + - - +
257A LYS* 3.4 24.1 - - - +
258A GLY* 3.6 15.0 + - - -
259A LEU 4.4 12.1 - - - +
261A PRO* 4.7 20.9 - - + -
264A ALA* 4.4 8.5 - - + -
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Residues in contact with GLY 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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251A ASN* 3.2 12.3 + - - -
252A GLU 3.8 2.7 - - - -
253A MET 2.7 5.7 + - - -
254A VAL* 1.3 76.6 - - - +
256A GLU* 1.3 58.2 + - - +
257A LYS 5.1 0.2 - - - -
258A GLY* 4.9 0.7 + - - -
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Residues in contact with GLU 256 (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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233A THR* 4.2 24.1 - - - +
234A ILE* 5.3 3.1 - - - +
237A SER* 4.8 1.2 - - - -
240A LYS* 5.8 0.2 + - - -
252A GLU* 3.0 34.0 + - + +
253A MET* 2.6 17.2 + - - +
255A GLY* 1.3 73.3 - - - +
257A LYS* 1.3 73.7 + - + +
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Residues in contact with LYS 257 (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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230A LYS* 5.7 4.4 + - + -
234A ILE* 3.6 22.2 - - + -
253A MET* 2.7 60.3 + - + +
254A VAL* 3.4 19.9 - - - +
255A GLY 5.1 0.2 - - - -
256A GLU* 1.3 81.5 - - + +
258A GLY* 1.3 56.3 + - - +
259A LEU* 3.3 53.7 + - + +
264A ALA* 3.0 33.5 - - - +
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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