Contacts of the helix formed by residues 351 - 360 (chain X) in PDB entry 1G3I
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 351 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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344X ILE 4.2 7.0 - - - -
345X LEU 3.5 14.4 - - - -
346X THR* 2.8 31.1 + - - -
348X PRO* 3.1 10.9 + - - -
349X HIS 3.2 0.2 - - - -
350X ALA* 1.3 81.7 - - - +
352X LEU* 1.3 54.5 + - - +
353X THR* 3.2 5.7 + - - -
354X GLU* 2.8 30.5 + - - +
355X GLN* 2.7 31.7 + - - +
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Residues in contact with LEU 352 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51W LYS* 6.2 2.5 - - - -
344X ILE* 4.9 4.2 + - + +
345X LEU* 3.7 23.4 + - + -
351X SER* 1.3 70.5 - - - +
353X THR* 1.3 66.6 + - - +
355X GLN* 3.7 21.4 - - + +
356X TYR* 2.9 37.8 + - + +
396X LEU* 3.5 34.5 - - + -
397X HIS* 3.6 32.1 - - + +
400X MET* 3.8 25.4 - - + -
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Residues in contact with THR 353 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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345X LEU* 2.7 37.8 + - + +
346X THR* 3.6 21.4 - - + +
351X SER* 3.2 8.0 + - - -
352X LEU* 1.3 76.2 - - - +
354X GLU* 1.3 68.4 + - - +
357X LYS* 3.0 30.9 + - - +
369X PHE* 3.2 47.2 - - + -
374X VAL* 5.2 4.0 - - + -
400X MET* 4.7 2.9 - - + +
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Residues in contact with GLU 354 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44W LEU* 5.0 14.0 - - + +
346X THR* 4.6 5.2 - - - +
348X PRO 4.8 1.8 - - - +
349X HIS* 6.0 0.2 - - - -
350X ALA* 4.6 7.4 - - - +
351X SER* 2.8 35.9 - - - +
353X THR* 1.3 87.6 + - - +
355X GLN* 1.3 63.1 + - - +
357X LYS* 3.0 21.2 + - - +
358X ALA* 3.0 26.6 + - - +
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Residues in contact with GLN 355 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40W LEU* 6.5 0.2 - - - -
44W LEU* 5.5 9.8 - - + +
47W GLU 3.5 12.4 + - - +
48W VAL* 2.8 49.6 - - + +
51W LYS* 5.6 2.5 + - - +
350X ALA* 2.5 35.3 + - - +
351X SER 2.7 13.6 + - - +
352X LEU* 3.2 25.2 + - + +
354X GLU* 1.3 71.3 - - - +
356X TYR* 1.3 63.1 + - + +
358X ALA* 3.7 3.0 + - - +
359X LEU* 3.0 36.6 + - + +
397X HIS* 5.9 0.2 + - - -
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Residues in contact with TYR 356 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33W ASN* 5.2 13.8 + - - -
51W LYS* 2.9 35.3 + - - +
352X LEU* 2.9 28.2 + - + +
353X THR 4.2 1.6 - - - +
355X GLN* 1.3 80.6 - - + +
357X LYS* 1.3 64.2 + - - +
359X LEU* 3.9 11.9 - - + -
360X MET* 3.1 28.8 + - + +
367X ILE* 3.0 15.7 - - - +
369X PHE* 4.7 2.9 - - + -
397X HIS* 6.4 0.2 - - - -
400X MET* 4.0 24.5 - - + -
401X GLU* 2.8 28.9 + - - -
404X MET* 3.5 52.3 - - + -
408X SER* 5.7 3.4 - - - -
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Residues in contact with LYS 357 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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353X THR 3.0 19.9 + - - +
354X GLU* 3.0 24.2 + - - +
356X TYR* 1.3 79.4 - - - +
358X ALA* 1.3 56.6 + - - +
360X MET 3.4 1.9 + - - -
361X ALA* 3.2 26.7 + - + +
365X VAL 4.9 0.3 - - - +
366X ASN* 4.5 14.7 + - - +
367X ILE* 3.2 42.9 + - + +
368X ALA* 5.2 1.6 - - - +
369X PHE* 5.6 2.6 - - + +
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Residues in contact with ALA 358 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40W LEU* 3.7 27.7 - - + +
44W LEU* 4.3 18.4 - - + -
354X GLU 3.0 13.9 + - - +
355X GLN* 4.2 3.4 - - - +
357X LYS* 1.3 74.5 - - + +
359X LEU* 1.3 58.1 + - - +
360X MET 3.0 6.3 + - - -
361X ALA* 3.3 13.6 + - - +
362X THR* 3.1 22.7 + - - -
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Residues in contact with LEU 359 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33W ASN* 4.8 17.5 - - + +
36W ARG* 3.3 49.3 - - + +
37W ARG* 3.4 22.0 - - + +
40W LEU* 3.6 13.2 - - + -
48W VAL* 3.5 26.5 - - + -
51W LYS* 5.3 6.7 - - - +
355X GLN* 3.0 28.9 + - + +
356X TYR* 4.3 17.0 - - + +
358X ALA* 1.3 76.3 - - - +
360X MET* 1.3 77.7 + - + +
361X ALA 3.5 0.4 - - - -
362X THR 4.4 2.3 + - - -
363X GLU 4.8 0.3 + - - -
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Residues in contact with MET 360 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32W ARG* 6.3 1.3 - - + -
33W ASN* 4.1 18.6 - - - +
36W ARG* 4.7 7.9 - - + -
356X TYR* 3.1 29.7 + - + +
357X LYS 3.7 0.7 - - - -
358X ALA 3.0 0.6 - - - -
359X LEU* 1.3 104.6 - - + +
361X ALA* 1.3 57.9 + - - +
362X THR 3.4 1.1 - - - -
363X GLU* 3.7 14.8 - - + +
365X VAL* 2.8 32.6 + - + +
367X ILE* 3.5 23.1 - - + -
404X MET* 4.9 6.5 - - + -
407X ILE* 4.2 20.9 - - + -
408X SER* 4.1 31.9 - - - +
411X ALA* 4.5 11.0 - - + -
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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