Contacts of the helix formed by residues 245 - 257 (chain T) in PDB entry 3EXG
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 ASP 245 (chain T).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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196T GLY 3.3 21.9 - - - +
197T LYS* 3.4 12.4 - - - +
198T ALA* 2.7 37.2 + - + +
238T MET* 5.4 5.5 + - - +
240T THR* 4.8 2.2 + - - -
243T PRO 3.8 0.8 + - - -
244T MET* 1.3 70.3 - - - +
246T MET* 1.3 60.0 + - - +
247T GLU* 3.4 10.7 + - - +
248T THR* 2.9 36.1 + - - -
249T ILE* 3.5 19.1 + - - +
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Residues in contact with MET 246 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244T MET* 3.1 17.9 + - + +
245T ASP* 1.3 72.5 - - - +
247T GLU* 1.3 66.5 + - + +
249T ILE* 3.1 28.3 + - + +
250T GLU* 3.0 49.8 + - + +
275T ILE* 4.0 11.4 - - + +
278T ARG* 3.5 48.9 - - + +
279T ILE* 3.5 48.2 - - + +
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Residues in contact with GLU 247 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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245T ASP* 3.3 8.9 - - - +
246T MET* 1.3 79.8 - - + +
248T THR* 1.3 57.7 + - - +
250T GLU* 3.2 13.8 + - - +
251T ALA* 2.9 32.6 + - - +
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Residues in contact with THR 248 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197T LYS* 4.6 7.6 + - - +
198T ALA* 4.5 18.0 + - + +
200T ILE* 4.4 21.9 - - + +
236T ILE* 4.1 16.8 - - + +
245T ASP* 2.9 31.0 + - - -
246T MET 3.4 0.2 - - - -
247T GLU* 1.3 77.5 - - - +
249T ILE* 1.3 57.1 + - - +
251T ALA* 3.7 6.4 - - - +
252T SER* 3.0 26.9 + - - -
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Residues in contact with ILE 249 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198T ALA* 5.6 0.7 - - + -
208T THR* 4.7 2.5 - - + -
210T VAL* 3.7 44.6 - - + -
236T ILE* 4.1 15.9 - - + -
238T MET* 4.9 7.4 - - + -
244T MET* 5.6 2.2 - - - -
245T ASP 3.5 19.3 - - - +
246T MET* 3.1 31.6 + - + +
248T THR* 1.3 76.3 - - - +
250T GLU* 1.3 61.3 + - - +
252T SER* 3.7 1.4 + - - -
253T VAL* 2.9 29.6 + - + +
259T LEU* 4.4 15.3 - - + -
275T ILE* 4.3 14.1 - - + -
279T ILE* 5.1 0.4 - - + -
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Residues in contact with GLU 250 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246T MET* 3.0 41.4 + - + +
247T GLU* 3.2 14.8 + - - +
249T ILE* 1.3 73.4 - - - +
251T ALA* 1.3 58.8 + - - +
253T VAL* 2.8 4.8 + - - +
254T MET* 2.6 47.2 + - + +
278T ARG* 3.9 13.5 + - - +
279T ILE* 4.5 1.2 - - - +
282T GLY* 4.2 1.4 - - - -
283T PRO* 3.5 34.0 - - + +
284T ALA* 3.6 23.9 - - + +
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Residues in contact with ALA 251 (chain T).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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247T GLU 2.9 17.5 + - - +
248T THR* 3.7 8.7 - - + +
250T GLU* 1.3 76.8 - - - +
252T SER* 1.3 62.6 + - - +
254T MET* 3.3 29.4 + - + +
255T LYS* 3.6 8.3 + - - +
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Residues in contact with SER 252 (chain T).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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200T ILE* 5.7 0.4 - - - -
208T THR* 2.3 31.5 + - - +
234T GLU* 2.9 34.1 + - - +
236T ILE* 4.0 13.0 - - - -
248T THR* 3.0 18.9 + - - -
249T ILE 3.8 3.4 - - - -
251T ALA* 1.3 76.1 - - - +
253T VAL* 1.3 63.4 + - - +
255T LYS* 2.8 19.0 + - - +
256T THR* 2.9 12.5 + - - +
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Residues in contact with VAL 253 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208T THR* 4.1 11.2 - - - +
249T ILE 2.9 20.3 + - - +
250T GLU* 2.8 13.1 + - - +
252T SER* 1.3 70.9 - - - +
254T MET* 1.3 56.7 + - - +
255T LYS 2.9 1.7 + - - -
256T THR* 3.3 5.2 - - - -
257T ASN* 2.9 31.0 + - - -
258T HIS 4.2 3.6 - - - +
259T LEU* 4.1 33.2 - - + -
279T ILE* 4.7 4.9 - - + -
284T ALA* 3.9 20.9 - - + +
287T PHE* 4.1 5.9 - - + +
288T LEU* 3.7 25.4 - - + -
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Residues in contact with MET 254 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250T GLU* 2.6 22.0 + - + +
251T ALA* 3.5 33.2 - - + +
252T SER 3.1 0.4 - - - -
253T VAL* 1.3 70.9 - - - +
255T LYS* 1.3 58.5 + - - +
257T ASN* 4.8 3.0 + - - -
283T PRO* 5.1 10.1 - - + +
284T ALA* 4.5 9.9 - - - -
287T PHE* 3.7 60.6 - - + -
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Residues in contact with LYS 255 (chain T).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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203T GLN* 3.7 13.7 + - - -
204T GLY 3.1 18.3 + - - +
205T THR* 3.6 26.7 - - + +
234T GLU* 2.5 37.3 + - - -
251T ALA 3.6 6.5 + - - +
252T SER* 2.8 9.2 + - - +
254T MET* 1.3 81.7 - - - +
256T THR* 1.3 60.4 + - + +
257T ASN* 3.7 7.2 - - - +
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Residues in contact with THR 256 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204T GLY 4.0 7.2 - - - +
205T THR* 3.3 34.8 - - - +
206T HIS* 3.3 8.3 - - - +
207T ILE* 3.5 29.8 - - - +
208T THR* 2.9 22.5 + - - +
234T GLU* 4.5 0.7 - - + -
252T SER* 2.9 13.4 + - - +
253T VAL* 3.3 5.7 - - - -
255T LYS* 1.3 79.1 - - + +
257T ASN* 1.3 63.3 + - - +
258T HIS* 2.8 31.3 + - - -
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Residues in contact with ASN 257 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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253T VAL* 2.9 12.2 + - - -
254T MET 4.8 5.9 + - - -
255T LYS 4.2 6.9 - - - +
256T THR* 1.3 79.9 + - - +
258T HIS* 1.3 68.7 + - + +
287T PHE* 2.7 42.6 + - - +
288T LEU* 3.6 7.2 - - - +
289T ASP* 3.0 47.3 + - - +
290T ALA 4.3 0.5 + - - -
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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