Contacts of the helix formed by residues 248 - 259 (chain A) in PDB entry 4WNP
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 248 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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112A GLU* 2.6 35.2 + - - -
116A ARG* 5.7 0.7 + - - -
246A GLU 3.5 2.9 + - - -
247A THR* 1.3 74.6 - - - +
249A ALA* 1.3 65.2 + - - +
250A PRO* 3.7 10.9 - - - +
251A LEU* 3.5 12.8 + - - +
252A ARG* 3.0 20.4 + - - +
277A PHE* 4.7 2.8 - - - -
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Residues in contact with ALA 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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247A THR 3.6 1.6 + - - -
248A SER* 1.3 70.1 - - - +
250A PRO* 1.3 65.9 - - + +
252A ARG* 3.3 15.3 + - - +
253A GLN* 2.9 31.1 + - - +
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Residues in contact with PRO 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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248A SER* 3.5 13.2 - - - +
249A ALA* 1.3 94.9 - - + +
251A LEU* 1.3 59.8 + - - +
253A GLN* 3.4 5.8 + - + +
254A LEU 3.1 17.0 + - - -
275A HIS* 3.2 22.7 - - + -
276A PRO* 5.3 7.0 - - + -
277A PHE* 4.5 20.6 - - + +
280A ALA 6.2 2.5 - - - +
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Residues in contact with LEU 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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112A GLU* 3.8 25.1 - - + +
115A ILE* 4.5 9.0 - - + -
211A VAL* 3.9 24.2 - - + -
215A LEU* 3.8 20.6 - - + -
247A THR* 3.8 13.2 - - + -
248A SER* 3.2 19.4 + - - +
250A PRO* 1.3 75.2 - - - +
252A ARG* 1.3 65.7 + - - +
254A LEU* 3.3 8.6 + - + +
255A LEU* 2.9 28.2 + - + +
277A PHE* 3.7 40.2 - - + -
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Residues in contact with ARG 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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243A ILE* 3.9 28.1 + - + +
244A PRO 2.9 27.7 + - - -
245A ARG* 3.2 23.4 + - - +
247A THR* 3.2 30.6 + - + +
248A SER 3.0 10.7 + - - +
249A ALA* 3.6 15.9 - - - +
251A LEU* 1.3 76.5 - - - +
253A GLN* 1.3 62.5 + - - +
255A LEU* 3.3 6.4 + - - +
256A LEU* 3.0 37.3 + - + +
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Residues in contact with GLN 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 ALA 2.9 17.8 + - - +
250A PRO* 3.7 6.2 - - + +
252A ARG* 1.3 76.4 - - - +
254A LEU* 1.3 62.9 + - - +
256A LEU* 3.4 8.2 + - + +
257A ALA* 3.0 25.8 + - + +
275A HIS* 2.9 26.7 + - - +
276A PRO* 5.1 3.6 - - - +
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Residues in contact with LEU 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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119A LEU* 3.7 30.3 - - + -
211A VAL* 5.7 0.9 - - + -
250A PRO 3.1 13.3 + - - +
251A LEU* 3.5 13.7 - - + +
253A GLN* 1.3 76.7 - - - +
255A LEU* 1.3 63.4 + - + +
257A ALA* 3.2 2.4 + - - +
258A LEU* 3.0 42.7 + - + +
267A MET* 3.4 35.4 - - + -
272A PHE* 4.4 7.6 - - + -
275A HIS* 3.8 23.9 + - + +
277A PHE* 3.8 24.5 - - + -
278A LEU* 5.2 2.0 - - + -
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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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208A GLY* 3.5 28.5 - - - +
211A VAL* 3.8 18.4 - - + -
212A TYR* 3.7 23.6 - - + +
215A LEU* 3.7 30.3 - - + -
243A ILE* 4.0 25.8 - - + -
251A LEU* 2.9 26.6 + - + +
252A ARG* 3.7 4.5 - - - +
254A LEU* 1.3 75.8 - - + +
256A LEU* 1.3 59.2 + - - +
258A LEU* 3.3 5.0 + - + +
259A LEU* 2.8 42.6 + - + +
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Residues in contact with LEU 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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240A VAL* 4.2 15.7 - - + -
241A PRO* 3.9 21.5 - - + -
243A ILE* 3.7 20.9 - - + -
252A ARG* 3.0 36.3 + - + +
253A GLN* 3.9 6.3 - - - +
255A LEU* 1.3 77.4 - - - +
257A ALA* 1.3 60.4 + - - +
258A LEU 3.7 0.2 + - - -
259A LEU* 3.7 7.4 + - - +
260A GLN* 2.8 32.1 + - - +
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Residues in contact with ALA 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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253A GLN* 3.0 19.5 + - + +
254A LEU 3.6 4.3 - - - +
256A LEU* 1.3 78.3 - - - +
258A LEU* 1.3 60.2 + - - +
260A GLN* 3.4 16.0 - - - +
265A ASP 5.8 0.4 - - - -
266A ARG* 3.6 0.9 - - - +
267A MET* 3.0 51.5 + - + +
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Residues in contact with LEU 258 (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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119A LEU* 5.6 0.2 - - + -
204A LEU* 3.6 31.6 - - + +
205A TRP* 3.7 10.4 - - - -
207A ILE* 4.5 11.4 - - + +
208A GLY* 3.8 29.8 - - - +
211A VAL* 5.1 5.2 - - + -
254A LEU* 3.0 42.6 + - + +
255A LEU* 3.9 5.6 - - + +
257A ALA* 1.3 75.2 - - - +
259A LEU* 1.3 59.2 + - - +
260A GLN 3.2 5.9 + - - -
266A ARG* 3.3 23.7 + - - -
267A MET* 3.8 22.4 - - + -
272A PHE* 4.3 14.8 - - + -
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Residues in contact with LEU 259 (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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205A TRP* 3.5 34.2 - - + +
208A GLY* 3.8 17.0 - - - +
209A THR* 3.8 36.8 - - + +
212A TYR* 4.3 7.6 - - + -
220A PRO* 4.2 14.8 - - + -
221A PHE* 4.8 1.9 - - + -
239A LEU* 3.9 16.6 - - - +
241A PRO* 3.7 38.0 - - + +
255A LEU* 2.8 23.3 + - + +
256A LEU 3.9 6.1 - - - +
257A ALA 3.4 0.2 - - - -
258A LEU* 1.3 74.6 - - - +
260A GLN* 1.3 62.2 + - - +
261A ARG 3.7 1.6 + - - -
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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