Contacts of the helix formed by residues 351 - 360 (chain S) 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 S).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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344S ILE 4.3 7.4 - - - -
345S LEU 3.5 14.4 - - - -
346S THR* 2.8 28.2 + - - -
348S PRO* 3.0 10.5 + - - -
349S HIS 3.2 0.2 - - - -
350S ALA* 1.3 80.2 - - - +
352S LEU* 1.3 55.5 + - - +
353S THR* 3.2 6.1 + - - -
354S GLU* 2.8 35.1 + - - +
355S GLN* 2.7 31.7 + - - +
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Residues in contact with LEU 352 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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344S ILE* 4.9 4.9 + - + +
345S LEU* 3.7 23.4 + - + -
350S ALA 5.2 0.2 - - - +
351S SER* 1.3 70.8 - - - +
353S THR* 1.3 67.8 + - - +
355S GLN* 3.7 20.8 - - + +
356S TYR* 2.9 38.9 + - + +
396S LEU* 3.5 35.4 - - + -
397S HIS* 3.6 30.7 - - + +
400S MET* 3.8 24.7 - - + -
51X LYS* 6.3 2.2 - - - -
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Residues in contact with THR 353 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345S LEU* 2.7 36.8 + - + +
346S THR* 3.6 20.8 - - + +
351S SER* 3.2 8.3 + - - -
352S LEU* 1.3 76.3 - - - +
354S GLU* 1.3 69.9 + - - +
357S LYS* 3.0 31.3 + - - +
369S PHE* 3.2 46.2 - - + -
374S VAL* 5.2 4.7 - - + -
400S MET* 4.7 3.1 - - + +
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Residues in contact with GLU 354 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346S THR* 4.6 5.0 - - - +
348S PRO 4.8 1.8 - - - +
349S HIS* 6.0 0.2 - - - -
350S ALA* 4.6 7.0 - - - +
351S SER* 2.8 37.4 + - - +
353S THR* 1.3 88.4 + - - +
355S GLN* 1.3 64.1 + - - +
357S LYS* 3.0 19.6 + - - +
358S ALA* 3.0 26.0 + - - +
44X LEU* 4.9 14.7 - - + +
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Residues in contact with GLN 355 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350S ALA* 2.6 34.9 + - - +
351S SER 2.7 11.9 + - - +
352S LEU* 3.2 25.8 + - + +
354S GLU* 1.3 73.9 - - - +
356S TYR* 1.3 62.5 + - + +
358S ALA* 4.2 3.0 - - - +
359S LEU* 3.0 36.9 + - + +
397S HIS* 5.9 0.6 + - - -
40X LEU* 5.5 0.6 - - - +
44X LEU* 5.4 9.2 - - + -
47X GLU 3.5 12.4 + - - +
48X VAL* 2.8 48.5 - - + +
51X LYS* 5.6 0.9 + - - -
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Residues in contact with TYR 356 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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352S LEU* 2.9 29.3 + - + +
353S THR 4.2 1.8 - - - +
355S GLN* 1.3 78.8 - - + +
357S LYS* 1.3 65.0 + - - +
359S LEU* 3.9 13.9 - - + -
360S MET* 3.1 28.4 + - + +
367S ILE* 3.0 15.1 - - - +
369S PHE* 4.7 2.9 - - + -
397S HIS* 6.4 0.2 - - - -
400S MET* 4.1 25.1 - - + -
401S GLU* 2.8 28.5 + - - -
404S MET* 3.5 50.5 - - + -
408S SER* 5.7 3.4 - - - -
33X ASN* 5.2 14.7 + - - -
51X LYS* 3.0 34.3 + - - +
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Residues in contact with LYS 357 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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353S THR 3.0 19.0 + - - +
354S GLU* 3.2 23.6 - - - +
356S TYR* 1.3 79.7 - - - +
358S ALA* 1.3 56.8 + - - +
360S MET* 3.4 1.9 + - - -
361S ALA* 3.1 26.4 + - + +
365S VAL 4.9 0.7 - - - +
366S ASN* 4.4 15.2 + - - +
367S ILE* 3.2 42.5 + - + +
368S ALA* 5.2 1.4 - - - +
369S PHE* 5.6 2.6 - - + +
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Residues in contact with ALA 358 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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354S GLU 3.0 14.0 + - - +
355S GLN* 4.2 3.6 - - - +
357S LYS* 1.3 75.0 - - - +
359S LEU* 1.3 60.3 + - - +
360S MET 3.0 5.6 + - - -
361S ALA* 3.2 14.2 + - - +
362S THR* 3.1 21.5 + - - -
40X LEU* 3.6 28.4 - - + +
44X LEU* 4.3 17.5 - - + -
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Residues in contact with LEU 359 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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355S GLN* 3.0 28.3 + - + +
356S TYR* 4.3 17.5 - - + +
357S LYS 3.4 0.2 - - - -
358S ALA* 1.3 75.5 - - - +
360S MET* 1.3 78.7 + - + +
361S ALA 3.5 0.4 - - - -
362S THR 4.4 2.2 + - - -
33X ASN* 4.7 16.8 - - + +
36X ARG* 3.3 49.2 - - + +
37X ARG* 3.4 23.1 - - + +
40X LEU* 3.6 13.7 - - + -
48X VAL* 3.4 26.7 - - + -
51X LYS* 5.3 5.8 - - - +
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Residues in contact with MET 360 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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356S TYR* 3.1 34.6 + - + +
357S LYS 3.7 0.4 - - - -
358S ALA 3.0 0.6 - - - -
359S LEU* 1.3 103.5 - - + +
361S ALA* 1.3 57.4 + - - +
362S THR 3.4 0.9 - - - -
363S GLU* 3.7 13.9 - - + +
365S VAL* 2.8 31.2 + - + +
367S ILE* 3.5 23.6 - - + -
404S MET* 5.0 2.5 - - + -
407S ILE* 4.2 21.1 - - + -
408S SER* 4.1 32.5 - - - +
411S ALA* 4.5 12.6 - - + -
32X ARG* 6.2 1.1 - - + -
33X ASN* 4.0 19.7 - - - +
36X ARG* 4.6 7.6 - - + -
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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