Contacts of the helix formed by residues 351 - 360 (chain W) 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 W).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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344W ILE 4.2 7.4 - - - -
345W LEU 3.5 14.6 - - - -
346W THR* 2.7 31.1 + - - -
348W PRO* 3.0 11.1 + - - -
349W HIS 3.2 0.6 - - - -
350W ALA* 1.3 80.3 - - - +
352W LEU* 1.3 55.1 + - - +
353W THR* 3.2 6.2 + - - -
354W GLU* 2.8 30.5 + - - +
355W GLN* 2.7 31.5 + - - +
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Residues in contact with LEU 352 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51V LYS* 6.5 0.7 - - - -
344W ILE* 4.9 4.7 + - + +
345W LEU* 3.7 23.8 + - + -
351W SER* 1.3 69.7 - - - +
353W THR* 1.3 69.2 + - - +
355W GLN* 3.1 21.8 + - + +
356W TYR* 2.9 37.9 + - + +
396W LEU* 3.5 34.8 - - + -
397W HIS* 3.6 31.0 - - + +
400W MET* 3.8 25.6 - - + -
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Residues in contact with THR 353 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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345W LEU* 2.7 38.0 + - + +
346W THR* 3.6 21.8 - - + +
351W SER* 3.2 8.3 + - - -
352W LEU* 1.3 76.6 - - - +
354W GLU* 1.3 68.3 + - - +
356W TYR 3.5 0.2 + - - -
357W LYS* 3.0 30.9 + - - +
369W PHE* 3.3 45.3 - - + -
374W VAL* 5.2 4.0 - - + -
400W MET* 4.7 2.9 - - + +
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Residues in contact with GLU 354 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44V LEU* 5.2 12.1 - - + +
346W THR* 4.6 5.5 - - - +
348W PRO 4.8 2.0 - - - +
349W HIS* 6.1 0.2 - - - -
350W ALA* 4.6 6.7 - - - +
351W SER* 2.8 36.5 + - - +
353W THR* 1.3 87.1 + - - +
355W GLN* 1.3 63.4 + - - +
357W LYS* 3.0 20.5 + - - +
358W ALA* 3.0 26.0 + - - +
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Residues in contact with GLN 355 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44V LEU* 5.5 8.5 - - + -
47V GLU 3.1 11.8 + - - +
48V VAL* 3.0 43.3 - - + +
51V LYS* 5.7 1.2 + - - -
350W ALA* 2.6 36.3 + - + +
351W SER 2.7 13.2 + - - +
352W LEU* 3.1 26.1 + - + +
354W GLU* 1.3 72.9 - - - +
356W TYR* 1.3 62.2 - - + +
358W ALA* 3.7 3.6 + - - +
359W LEU* 3.0 37.4 + - + +
397W HIS* 5.8 0.4 + - - -
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Residues in contact with TYR 356 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33V ASN* 5.4 10.2 + - - -
51V LYS* 2.9 32.5 + - - +
352W LEU* 2.9 27.8 + - + +
353W THR 4.2 1.6 - - - +
355W GLN* 1.3 79.9 - - + +
357W LYS* 1.3 63.3 + - - +
359W LEU* 3.9 14.1 - - + -
360W MET* 3.1 28.2 + - + +
367W ILE* 3.0 15.5 - - - +
369W PHE* 4.7 3.8 - - + -
397W HIS* 6.4 0.7 - - - -
400W MET* 4.0 26.9 - - + -
401W GLU* 2.8 30.1 + - - -
404W MET* 3.5 48.0 - - + -
408W SER* 5.7 4.9 - - - -
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Residues in contact with LYS 357 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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353W THR 3.0 19.6 + - - +
354W GLU* 3.0 23.5 + - - +
356W TYR* 1.3 79.6 - - - +
358W ALA* 1.3 57.9 - - - +
360W MET 3.7 1.7 - - - -
361W ALA* 3.1 27.4 + - + +
365W VAL 4.9 0.2 - - - +
366W ASN* 4.5 15.4 + - - +
367W ILE* 3.2 41.6 + - + +
368W ALA* 5.2 1.4 - - - +
369W PHE* 5.6 3.0 - - + +
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Residues in contact with ALA 358 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40V LEU* 3.9 25.5 - - + +
44V LEU* 4.2 19.5 - - + -
354W GLU 3.0 13.6 + - - +
355W GLN* 4.3 2.2 - - - +
357W LYS* 1.3 75.3 - - - +
359W LEU* 1.3 59.1 + - - +
360W MET 3.0 5.6 + - - -
361W ALA* 3.3 12.7 + - - +
362W THR* 3.1 22.9 + - - -
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Residues in contact with LEU 359 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33V ASN* 5.0 14.8 - - + +
36V ARG* 3.5 46.0 - - + +
37V ARG* 3.6 16.2 - - + +
40V LEU* 3.5 18.8 - - + -
48V VAL* 3.4 28.0 - - + -
51V LYS* 5.2 8.1 - - - +
355W GLN* 3.0 28.5 + - + +
356W TYR* 3.7 16.8 + - + +
357W LYS 3.4 0.2 - - - -
358W ALA* 1.3 75.8 - - - +
360W MET* 1.3 80.4 + - + +
361W ALA 3.5 0.2 - - - -
362W THR* 4.4 3.4 + - - -
363W GLU* 4.8 0.5 + - - +
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Residues in contact with MET 360 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33V ASN* 4.1 18.4 - - - +
36V ARG* 4.9 7.2 - - + -
356W TYR* 3.1 34.9 + - + +
357W LYS 3.7 0.4 - - - -
358W ALA 3.0 0.4 - - - -
359W LEU* 1.3 105.5 - - + +
361W ALA* 1.3 57.6 + - - +
362W THR 3.4 1.1 - - - -
363W GLU* 3.7 14.0 - - + +
365W VAL* 2.8 32.2 + - + +
367W ILE* 3.5 22.7 - - + -
404W MET* 4.9 2.2 - - + -
407W ILE* 4.2 20.0 - - + -
408W SER* 4.1 32.8 - - - +
411W 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