Contacts of the helix formed by residues 242 - 257 (chain A) in PDB entry 4NZP
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 242 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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70A ASP* 2.7 28.9 + - - -
241A LEU* 1.3 75.3 - - - +
243A PRO* 1.3 62.5 - - - +
244A ALA* 4.2 0.5 - - - +
245A GLY* 2.9 17.2 + - - -
246A LEU* 2.7 31.2 + - - +
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Residues in contact with PRO 243 (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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70A ASP* 3.7 24.5 - - + +
73A VAL* 3.4 25.9 - - + +
74A LYS* 3.9 27.4 - - + +
78A PHE* 4.5 8.7 - - + -
241A LEU 4.4 1.6 - - - +
242A SER* 1.3 86.2 - - - +
244A ALA* 1.3 60.8 + - - +
246A LEU* 3.2 14.7 + - + +
247A LEU 3.1 18.4 + - - -
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Residues in contact with ALA 244 (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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69A ARG* 3.8 10.3 - - + -
70A ASP* 2.8 36.3 + - - +
73A VAL* 3.9 12.2 - - - +
186A LEU* 3.7 19.9 - - + +
242A SER* 4.2 0.7 - - - +
243A PRO* 1.3 73.7 - - - +
245A GLY* 1.3 57.0 + - - +
247A LEU* 3.3 1.4 + - - +
248A THR* 2.8 38.2 + - - +
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Residues in contact with GLY 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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241A LEU* 3.4 25.6 - - - +
242A SER* 2.9 20.7 + - - -
244A ALA* 1.3 78.0 - - - +
246A LEU* 1.3 54.6 + - - +
248A THR* 3.5 5.4 + - - -
249A LYS* 3.0 23.4 + - - +
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Residues in contact with LEU 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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78A PHE* 4.3 9.9 - - + -
233A LEU* 3.2 43.1 - - + +
234A VAL* 3.6 23.1 - - - +
235A ALA* 3.9 9.6 - - - +
236A ILE* 3.3 25.3 - - + +
239A GLU 4.1 3.1 - - - +
241A LEU* 3.6 37.2 - - + +
242A SER 2.7 18.4 + - - +
243A PRO* 3.6 9.2 - - + +
244A ALA 3.2 0.2 - - - -
245A GLY* 1.3 70.5 - - - +
247A LEU* 1.3 65.0 + - - +
249A LYS 3.3 1.6 + - - -
250A LEU* 3.1 19.9 + - - +
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Residues in contact with LEU 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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73A VAL* 3.7 29.2 - - + -
77A VAL* 4.2 20.0 - - + -
78A PHE* 5.1 3.1 - - + -
186A LEU* 3.5 34.5 - - + +
187A LEU* 4.3 9.6 - - + +
233A LEU* 5.6 0.2 - - - -
243A PRO 3.1 12.8 + - - +
244A ALA 4.0 2.5 - - - +
246A LEU* 1.3 79.0 - - - +
248A THR* 1.3 57.9 + - - +
250A LEU* 3.3 6.9 + - + +
251A ASN* 2.9 42.2 + - - +
282A GLY* 4.4 18.2 - - - +
283A GLY 4.4 2.9 - - - +
286A LEU* 4.9 14.8 - - + -
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Residues in contact with THR 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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69A ARG* 6.1 0.2 - - - -
186A LEU* 3.9 19.6 - - - +
244A ALA* 2.8 23.9 + - - +
245A GLY* 3.7 5.8 - - - -
247A LEU* 1.3 74.4 - - - +
249A LYS* 1.3 65.3 + - - +
251A ASN* 3.1 14.2 + - + +
252A GLU* 3.0 43.2 + - + +
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Residues in contact with LYS 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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236A ILE* 3.9 30.5 - - + -
237A ASN* 5.0 8.8 - - - +
239A GLU* 5.3 10.1 + - - +
241A LEU* 4.1 13.5 - - + -
245A GLY 3.0 14.6 + - - +
246A LEU 3.3 8.0 + - - +
248A THR* 1.3 78.5 - - - +
250A LEU* 1.3 61.9 + - - +
252A GLU* 3.3 19.8 + - + +
253A LEU* 3.1 50.4 + - + +
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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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224A ILE* 4.5 1.3 - - + -
226A LEU* 3.9 29.4 - - + -
233A LEU* 3.6 22.7 - - + -
236A ILE* 3.8 14.8 - - + -
246A LEU 3.1 9.6 + - - +
247A LEU* 3.6 11.7 - - + +
249A LYS* 1.3 74.8 - - - +
251A ASN* 1.3 57.5 + - - +
253A LEU* 3.4 15.6 + - + +
254A GLY* 2.8 25.3 + - - -
282A GLY* 3.6 32.9 - - - +
285A ILE* 3.9 21.7 - - + +
286A LEU* 4.2 20.6 - - + +
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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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186A LEU* 2.8 35.4 + - - +
187A LEU 4.7 2.1 - - - +
210A TRP* 3.5 31.9 - - + +
247A LEU* 2.9 28.3 + - - +
248A THR* 3.1 13.9 + - + +
250A LEU* 1.3 75.5 - - - +
252A GLU* 1.3 52.7 + - + +
254A GLY* 3.2 1.4 + - - -
255A CYS* 2.7 41.9 + - - -
281A PRO* 3.6 5.4 - - + +
282A GLY* 3.0 27.2 + - - +
283A GLY 4.5 0.5 + - - -
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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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248A THR* 3.0 37.2 + - + +
249A LYS* 3.6 23.2 + - + +
251A ASN* 1.3 76.7 - - + +
253A LEU* 1.3 58.9 + - + +
255A CYS* 4.0 6.3 - - - +
256A LYS* 3.0 30.1 + - - +
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Residues in contact with LEU 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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222A GLU* 3.5 32.8 - - - +
224A ILE* 3.8 24.9 - - + -
236A ILE* 4.4 10.8 - - + -
237A ASN* 5.3 1.8 - - - +
249A LYS* 3.1 50.5 + - + +
250A LEU* 3.6 17.0 - - + +
251A ASN 3.2 0.2 - - - -
252A GLU* 1.3 78.6 - - + +
254A GLY* 1.3 62.1 + - - +
256A LYS* 3.4 7.9 + - + +
257A HIS* 3.2 30.4 + - - +
285A ILE* 4.6 2.2 - - + -
349A LEU* 4.1 14.5 - - + +
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Residues in contact with GLY 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 2.8 15.9 + - - -
251A ASN 3.6 2.9 - - - -
253A LEU* 1.3 76.6 - - - +
255A CYS* 1.3 55.0 + - - +
257A HIS 3.4 0.9 + - - -
258A GLY 3.0 8.3 + - - -
259A ILE* 2.8 42.7 + - - +
281A PRO* 3.7 17.0 - - - -
285A ILE* 4.0 10.2 - - - +
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Residues in contact with CYS 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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210A TRP* 3.5 53.6 - - - +
211A SER* 3.9 9.4 - - - -
212A LYS* 3.0 25.8 + - - +
251A ASN 2.7 27.9 + - - +
252A GLU* 4.0 5.8 - - - +
254A GLY* 1.3 69.2 - - - +
256A LYS* 1.3 65.7 + - - +
258A GLY 3.1 6.4 + - - -
281A PRO* 3.7 18.2 - - - -
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Residues in contact with LYS 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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212A LYS* 4.0 10.9 - - - +
217A ALA* 3.8 4.5 - - - +
218A PRO* 3.1 36.2 - - + +
222A GLU* 2.9 34.5 + - - +
252A GLU 3.0 19.8 + - - +
253A LEU* 3.5 10.5 - - + +
255A CYS* 1.3 77.7 - - - +
257A HIS* 1.3 70.5 + - + +
258A GLY 3.8 0.2 + - - -
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Residues in contact with HIS 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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217A ALA* 3.5 9.9 - - - -
218A PRO* 4.0 15.1 + - + +
220A GLU 3.7 23.1 + - - -
222A GLU* 2.8 39.9 + - + +
253A LEU* 3.2 24.1 + - - +
255A CYS 3.2 0.6 - - - -
256A LYS* 1.3 92.1 - - + +
258A GLY* 1.3 58.3 + - - +
259A ILE* 3.3 17.2 - - + +
349A LEU* 3.9 30.7 + - + -
350A TYR* 4.6 3.8 - - - -
351A LYS* 3.3 12.5 + - - +
352A GLY 2.8 26.2 + - - -
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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