Contacts of the helix formed by residues 281 - 292 (chain E) in PDB entry 3TMP
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 281 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176E ASN* 5.8 0.8 - - - +
177E SEP 2.9 33.5 + - - +
180E GLU* 2.8 28.6 + - - +
225E LEU* 3.8 2.8 - - - +
269E TYR* 5.0 1.3 - - - +
280E GLY* 1.3 74.6 - - - +
282E HIS* 1.3 81.0 + - - +
283E ILE* 3.3 4.7 - - + +
284E GLU* 2.9 24.9 + - - +
285E MET* 3.1 20.5 + - - +
42F ARG* 5.4 1.2 - - - +
70F VAL* 6.1 1.6 - - - -
71F LEU 3.7 3.7 - - - +
73F LEU 3.0 28.9 + - - -
74F ARG* 3.4 12.6 - - - +
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Residues in contact with HIS 282 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281E ASN* 1.3 80.7 + - - +
283E ILE* 1.3 64.6 + - - +
285E MET* 3.2 8.7 + - - -
286E GLN* 3.0 19.7 + - + +
314E PHE* 3.3 40.4 - + - -
8F LEU* 3.6 36.3 - - + +
69F LEU 4.9 1.1 - - - -
70F VAL* 3.8 7.8 - - + +
71F LEU* 3.0 61.4 + - + +
73F LEU* 4.0 11.3 - - + +
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Residues in contact with ILE 283 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176E ASN* 4.3 9.6 - - - +
251E LEU* 3.7 25.1 - - + +
258E PHE* 4.5 8.0 - - + +
261E TYR* 3.6 38.6 - - + +
262E VAL* 3.9 15.9 - - + -
266E PHE* 5.7 0.4 - - + -
269E TYR* 3.6 24.2 - - + +
281E ASN* 3.3 2.8 - - + +
282E HIS* 1.3 78.7 - - - +
284E GLU* 1.3 72.7 + - - +
286E GLN* 3.5 2.1 + - - +
287E ALA* 3.1 21.8 + - - +
8F LEU* 3.7 21.8 - - + -
70F VAL* 4.4 7.9 - - + -
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Residues in contact with GLU 284 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225E LEU* 4.4 0.7 - - + -
226E PHE* 3.9 15.7 - - + -
247E CYS* 3.7 14.8 - - - -
248E MET* 3.6 28.9 - - + +
251E LEU* 4.1 3.1 - - + +
269E TYR* 2.3 38.4 + - - -
273E LYS* 3.0 20.8 + - + +
281E ASN* 2.9 35.5 + - - +
283E ILE* 1.3 78.6 - - - +
285E MET* 1.3 57.9 + - - +
287E ALA* 3.3 3.3 + - - +
288E MET* 2.8 40.6 + - + +
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Residues in contact with MET 285 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225E LEU* 3.7 22.2 - - + -
281E ASN 3.1 21.7 + - - +
282E HIS* 3.7 9.0 - - - +
284E GLU* 1.3 76.8 - - - +
286E GLN* 1.3 60.9 + - - +
288E MET* 3.4 9.0 + - + +
289E ALA* 3.1 24.1 + - - +
296E VAL* 4.1 16.9 - - + +
298E VAL* 3.2 33.4 - - + -
314E PHE* 3.9 23.8 - - + -
327E VAL* 3.9 17.9 - - + -
335E TYR* 3.7 27.6 - - + +
73F LEU* 4.3 4.7 - - - -
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Residues in contact with GLN 286 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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258E PHE* 3.9 10.5 - - + -
282E HIS* 3.0 18.4 + - + +
283E ILE 3.9 3.6 - - - +
285E MET* 1.3 75.1 - - - +
287E ALA* 1.3 63.4 + - - +
289E ALA* 3.3 4.6 + - - +
290E GLU* 2.9 53.9 + - - +
314E PHE* 3.4 24.8 - - - +
315E HIS 3.0 24.6 + - - -
316E GLY* 4.4 0.2 - - - -
8F LEU* 3.5 41.5 + - + +
9F THR* 3.7 16.7 + - - +
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Residues in contact with ALA 287 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247E CYS* 4.2 9.0 - - - +
250E TYR* 3.8 15.6 - - + -
251E LEU* 3.6 32.1 - - + -
258E PHE* 4.2 9.3 - - + -
283E ILE 3.1 17.9 + - - +
284E GLU 3.6 4.3 - - - +
286E GLN* 1.3 76.0 - - - +
288E MET* 1.3 56.4 + - - +
290E GLU* 3.4 3.3 + - - +
291E MET* 2.8 32.3 + - - +
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Residues in contact with MET 288 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225E LEU* 3.8 30.3 - - + -
226E PHE* 3.9 16.6 - - + -
229E VAL* 3.9 24.0 - - + -
243E VAL* 3.5 30.1 - - - -
247E CYS* 3.8 13.2 - - + -
284E GLU 2.8 28.0 + - - +
285E MET* 4.0 8.1 - - + +
286E GLN 3.3 0.2 - - - -
287E ALA* 1.3 70.0 - - - +
289E ALA* 1.3 60.9 + - - +
291E MET* 3.9 16.6 - - + -
292E TYR* 2.9 46.1 + - + +
296E VAL* 4.8 7.2 - - + -
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Residues in contact with ALA 289 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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285E MET 3.1 13.6 + - - +
286E GLN 3.3 9.2 + - - +
288E MET* 1.3 74.8 - - - +
290E GLU* 1.3 58.7 + - - +
293E ASN* 3.0 23.2 + - - -
294E ARG 3.1 30.0 + - - +
296E VAL* 4.0 11.0 - - + +
314E PHE* 3.4 28.7 - - + +
315E HIS* 4.0 6.3 - - - -
316E GLY 4.6 4.3 + - - -
325E ILE* 5.5 0.2 - - - -
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Residues in contact with GLU 290 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170C HIS* 2.7 36.4 + - - -
250E TYR* 2.7 35.8 + - + +
258E PHE* 3.5 14.1 - - - -
286E GLN* 2.9 35.4 + - - +
287E ALA 3.7 3.8 - - - +
289E ALA* 1.3 76.8 - - - +
291E MET* 1.3 61.6 + - - +
293E ASN* 3.3 21.8 + - - +
316E GLY* 3.6 26.3 - - - -
317E ILE 5.5 0.4 - - - -
8F LEU 4.5 0.2 - - - +
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Residues in contact with MET 291 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243E VAL 4.6 0.9 - - - +
246E HIS* 3.2 38.8 - - + +
247E CYS* 3.6 26.5 - - + +
250E TYR* 3.6 30.5 - - + -
287E ALA 2.8 16.5 + - - +
288E MET* 3.3 24.9 + - + -
290E GLU* 1.3 74.6 - - - +
292E TYR* 1.3 78.1 + - + +
293E ASN* 3.7 5.7 + - - -
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Residues in contact with TYR 292 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229E VAL* 3.8 21.3 - - + -
233E VAL* 3.9 27.8 - - + -
234E TYR* 4.1 14.6 + - - -
243E VAL* 3.3 34.5 + - + +
246E HIS* 4.6 8.1 + - - -
288E MET* 2.9 36.0 + - + +
291E MET* 1.3 95.4 - - + +
293E ASN* 1.3 71.1 + - - +
294E ARG* 3.2 24.8 + - - +
325E ILE* 3.8 19.5 - - + -
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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