Contacts of the helix formed by residues 351 - 360 (chain U) 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 U).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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344U ILE 4.2 7.2 - - - -
345U LEU 3.5 14.6 - - - -
346U THR* 2.8 31.3 + - - -
348U PRO* 3.1 11.4 + - - -
349U HIS 3.2 0.6 - - - -
350U ALA* 1.3 80.6 - - - +
352U LEU* 1.3 56.1 + - - +
353U THR* 3.2 5.9 + - - -
354U GLU* 2.8 30.6 + - - +
355U GLN* 2.7 31.4 + - - +
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Residues in contact with LEU 352 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51T LYS* 6.3 2.5 - - - -
344U ILE* 4.9 4.2 + - + +
345U LEU* 3.7 24.0 + - + -
351U SER* 1.3 70.2 - - - +
353U THR* 1.3 67.4 + - - +
355U GLN* 3.1 20.9 + - + +
356U TYR* 2.9 37.4 + - + +
396U LEU* 3.5 34.8 - - + -
397U HIS* 3.6 31.4 - - + +
400U MET* 3.8 25.1 - - + -
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Residues in contact with THR 353 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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345U LEU* 2.7 37.4 + - + +
346U THR* 3.6 22.2 - - + +
351U SER* 3.2 7.6 + - - -
352U LEU* 1.3 76.3 - - - +
354U GLU* 1.3 69.3 + - - +
357U LYS* 3.0 30.9 + - - +
369U PHE* 3.2 45.8 - - + -
374U VAL* 5.2 4.0 - - + -
400U MET* 4.7 3.8 - - + +
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Residues in contact with GLU 354 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44T LEU* 5.5 11.1 - - + +
346U THR* 4.5 6.1 - - - +
348U PRO 4.8 1.8 - - - +
349U HIS* 6.1 0.2 - - - -
350U ALA* 4.6 6.7 - - - +
351U SER* 2.8 36.5 + - - +
353U THR* 1.3 87.6 + - - +
355U GLN* 1.3 62.7 + - - +
357U LYS* 3.0 20.2 + - - +
358U ALA* 3.0 26.7 + - - +
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Residues in contact with GLN 355 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44T LEU* 5.7 6.9 - - + +
47T GLU 3.9 12.0 + - - +
48T VAL* 3.0 46.4 - - + +
51T LYS* 5.4 3.0 + - - +
350U ALA* 2.6 35.6 + - + +
351U SER 2.7 13.3 + - - +
352U LEU* 3.6 25.7 - - + +
354U GLU* 1.3 73.5 - - - +
356U TYR* 1.3 60.8 + - + +
358U ALA* 4.1 3.2 - - - +
359U LEU* 3.0 37.7 + - + +
397U HIS* 5.8 0.4 + - - -
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Residues in contact with TYR 356 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33T ASN* 5.3 11.8 + - - -
51T LYS* 3.1 32.8 + - - +
352U LEU* 2.9 28.0 + - + +
353U THR 4.2 2.2 - - - +
355U GLN* 1.3 80.1 - - + +
357U LYS* 1.3 63.8 + - - +
358U ALA 3.4 0.2 - - - -
359U LEU* 3.9 13.7 - - + -
360U MET* 3.1 28.8 + - + +
367U ILE* 3.0 15.1 - - - +
369U PHE* 4.7 2.7 - - + -
397U HIS* 5.6 0.7 - - - -
400U MET* 4.0 24.2 - - + -
401U GLU* 2.8 29.6 + - - -
404U MET* 3.5 50.7 - - + -
408U SER* 5.7 4.3 - - - -
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Residues in contact with LYS 357 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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353U THR 3.0 19.6 + - - +
354U GLU* 3.0 23.1 + - - +
356U TYR* 1.3 79.2 - - - +
358U ALA* 1.3 56.9 + - - +
360U MET* 3.4 1.4 + - - -
361U ALA* 3.1 27.4 + - + +
365U VAL 4.9 0.5 - - - +
366U ASN* 4.5 15.0 + - - +
367U ILE* 3.2 41.8 + - + +
368U ALA* 5.2 1.4 - - - +
369U PHE* 5.6 2.8 - - + +
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Residues in contact with ALA 358 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40T LEU* 4.1 24.8 - - + +
44T LEU* 4.6 16.4 - - + -
354U GLU 3.0 13.6 + - - +
355U GLN* 4.2 3.4 - - - +
357U LYS* 1.3 75.6 - - - +
359U LEU* 1.3 59.8 + - - +
360U MET 3.1 6.3 + - - -
361U ALA* 3.3 12.8 + - - +
362U THR* 3.1 22.5 + - - -
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Residues in contact with LEU 359 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33T ASN* 4.8 16.4 - - + +
36T ARG* 3.4 53.8 - - + +
37T ARG* 3.7 15.3 - - + +
40T LEU* 3.8 13.7 - - + -
48T VAL* 3.7 25.6 - - + -
51T LYS* 5.2 8.3 - - - +
355U GLN* 3.0 30.0 + - + +
356U TYR* 4.3 17.0 - - + +
357U LYS 3.4 0.2 - - - -
358U ALA* 1.3 75.4 - - - +
360U MET* 1.3 78.6 + - + +
361U ALA 3.5 0.2 - - - -
362U THR 4.4 3.0 + - - -
363U GLU 4.9 0.5 + - - -
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Residues in contact with MET 360 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32T ARG* 6.3 1.6 - - + -
33T ASN* 4.2 17.9 - - - +
36T ARG* 4.9 4.3 - - + -
356U TYR* 3.1 30.3 + - + +
357U LYS 3.7 0.4 - - - -
358U ALA 3.1 0.6 - - - -
359U LEU* 1.3 104.6 - - + +
361U ALA* 1.3 59.0 + - - +
362U THR 3.4 1.1 - - - -
363U GLU* 3.7 16.7 - - + +
365U VAL* 2.8 31.8 + - + +
367U ILE* 3.5 23.6 - - + -
404U MET* 4.9 6.1 - - + -
407U ILE* 4.2 21.1 - - + -
408U SER* 4.1 33.9 - - - +
411U ALA* 4.5 11.2 - - + -
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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