Contacts of the helix formed by residues 351 - 360 (chain T) 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 T).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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344T ILE 4.2 7.4 - - - -
345T LEU 3.5 14.6 - - - -
346T THR* 2.8 23.5 + - - -
348T PRO* 3.0 18.6 + - - -
349T HIS 3.2 0.4 - - - -
350T ALA* 1.3 80.1 - - - +
352T LEU* 1.3 54.9 + - - +
353T THR* 3.2 6.1 + - - -
354T GLU* 2.8 30.8 + - - +
355T GLN* 2.7 32.1 + - - +
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Residues in contact with LEU 352 (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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51S LYS* 6.4 1.8 - - - -
344T ILE* 4.9 4.7 + - + +
345T LEU* 3.7 24.0 + - + -
351T SER* 1.3 71.0 - - - +
353T THR* 1.3 67.8 + - - +
355T GLN* 3.2 21.7 + - + +
356T TYR* 2.9 38.1 + - + +
396T LEU* 3.5 34.3 - - + -
397T HIS* 3.6 31.4 - - + +
400T MET* 3.8 24.7 - - + -
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Residues in contact with THR 353 (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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345T LEU* 2.7 36.7 + - + +
346T THR* 3.6 21.9 - - + +
351T SER* 3.2 8.3 + - - -
352T LEU* 1.3 76.0 - - - +
354T GLU* 1.3 69.7 + - - +
357T LYS* 3.0 31.0 + - - +
369T PHE* 3.2 47.2 - - + -
374T VAL* 5.2 4.3 - - + -
400T MET* 4.7 2.9 - - + +
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Residues in contact with GLU 354 (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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44S LEU* 5.2 11.8 - - + +
346T THR* 4.5 6.2 - - - +
348T PRO 4.8 1.8 - - - +
350T ALA* 4.6 7.0 - - - +
351T SER* 2.8 36.3 + - - +
353T THR* 1.3 87.2 + - - +
355T GLN* 1.3 64.3 + - - +
357T LYS* 3.0 21.4 + - - +
358T ALA* 2.9 26.3 + - - +
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Residues in contact with GLN 355 (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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40S LEU* 5.6 0.2 - - - +
44S LEU* 5.4 9.6 - - + -
47S GLU 3.7 12.0 + - - +
48S VAL* 3.0 47.0 - - + +
51S LYS* 5.7 0.9 + - - -
350T ALA* 2.6 36.3 + - - +
351T SER 2.7 12.5 + - - +
352T LEU* 3.7 24.9 - - + +
354T GLU* 1.3 73.3 - - - +
356T TYR* 1.3 62.4 + - + +
358T ALA* 3.7 3.5 + - - +
359T LEU* 2.9 37.7 + - + +
397T HIS* 5.8 0.6 + - - -
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Residues in contact with TYR 356 (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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33S ASN* 5.3 12.1 + - - -
51S LYS* 3.1 31.7 + - - +
352T LEU* 2.9 27.6 + - + +
353T THR 4.2 1.8 - - - +
355T GLN* 1.3 80.7 - - + +
357T LYS* 1.3 63.6 + - - +
359T LEU* 3.9 14.4 - - + -
360T MET* 3.1 28.5 + - + +
367T ILE* 3.0 15.5 - - - +
369T PHE* 4.7 2.9 - - + -
397T HIS* 5.6 0.7 - - - -
400T MET* 4.0 27.1 - - + -
401T GLU* 2.8 28.6 + - - -
404T MET* 3.5 50.5 - - + -
408T SER* 5.7 3.6 - - - -
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Residues in contact with LYS 357 (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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353T THR 3.0 18.6 + - - +
354T GLU* 3.0 23.5 + - - +
356T TYR* 1.3 79.6 - - - +
358T ALA* 1.3 58.0 + - + +
360T MET 3.7 1.4 - - - -
361T ALA* 3.2 26.2 + - - +
365T VAL 4.9 0.3 - - - +
366T ASN* 4.5 15.0 + - - +
367T ILE* 3.2 41.5 + - + +
368T ALA* 5.2 1.6 - - - +
369T PHE* 5.6 3.2 - - + +
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Residues in contact with ALA 358 (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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40S LEU* 3.9 25.3 - - + +
44S LEU* 4.3 18.4 - - + -
354T GLU 2.9 13.7 + - - +
355T GLN* 4.3 3.1 - - - +
357T LYS* 1.3 74.1 - - + +
359T LEU* 1.3 60.3 + - - +
360T MET 3.0 6.5 + - - -
361T ALA* 3.3 13.7 + - - +
362T THR* 3.1 21.3 + - - -
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Residues in contact with LEU 359 (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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33S ASN* 5.0 14.8 - - + +
36S ARG* 3.3 48.5 - - + +
37S ARG* 3.6 15.3 - - + +
40S LEU* 3.6 19.7 - - + -
48S VAL* 3.6 25.8 - - + -
51S LYS* 5.4 6.5 - - - +
355T GLN* 2.9 29.8 + - + +
356T TYR* 4.3 17.7 - - + +
358T ALA* 1.3 76.7 - - - +
360T MET* 1.3 78.7 + - + +
361T ALA 3.5 0.2 - - - -
362T THR* 4.4 3.3 + - - -
363T GLU* 4.9 0.7 + - - +
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Residues in contact with MET 360 (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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32S ARG* 6.4 0.7 - - + -
33S ASN* 4.3 17.3 - - - +
36S ARG* 4.9 6.7 - - + -
356T TYR* 3.1 31.0 + - + +
357T LYS 3.7 0.4 - - - -
358T ALA 3.0 0.6 - - - -
359T LEU* 1.3 105.5 - - + +
361T ALA* 1.3 58.9 + - - +
362T THR 3.4 1.3 - - - -
363T GLU* 3.7 15.4 - - + +
365T VAL* 2.8 31.3 + - + +
367T ILE* 3.5 20.2 - - + -
404T MET* 4.9 6.7 - - + -
407T ILE* 4.2 23.8 - - + -
408T SER* 4.1 32.3 - - - +
411T ALA* 4.5 11.4 - - + -
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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