Contacts of the helix formed by residues 44 - 52 (chain g) in PDB entry 3J7Y
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 GLU 44 (chain g).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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273M TRP* 3.5 20.1 + - + -
282M ILE* 3.2 25.5 - - + +
284M LYS* 3.1 31.0 + - - +
42g VAL* 3.6 10.8 + - + -
43g ASP* 1.3 76.8 - - - +
45g TYR* 1.3 59.0 + - - +
46g GLN* 3.2 7.7 + - - -
47g PHE* 3.6 37.7 + - + +
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Residues in contact with TYR 45 (chain g).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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275M VAL* 4.0 8.1 - - + -
276M ASN 3.7 18.8 - - - -
277M MET* 3.1 36.2 + - - +
280M LYS* 3.6 40.0 - - + +
281M LYS* 4.0 15.0 - - - -
282M ILE* 3.9 7.4 - - + +
43g ASP* 3.4 20.6 + - - +
44g GLU* 1.3 73.4 - - - +
46g GLN* 1.3 57.8 + - - +
47g PHE 3.2 2.7 - - - -
48g VAL* 3.2 28.1 + - + +
49g GLU* 2.9 55.8 + - + +
52g LEU* 5.1 5.5 - - + +
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Residues in contact with GLN 46 (chain g).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44g GLU 3.2 2.4 - - - +
45g TYR* 1.3 76.9 - - - +
47g PHE* 1.3 78.9 - - + +
49g GLU* 3.2 19.1 + - - +
50g ARG* 3.1 34.3 + - + +
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Residues in contact with PHE 47 (chain g).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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268M GLY* 3.5 38.4 - - - +
269M LEU* 3.4 21.5 - - + -
44g GLU* 3.6 32.9 + - + +
45g TYR 3.2 0.4 - - - -
46g GLN* 1.3 90.7 - - + +
48g VAL* 1.3 65.0 + - - +
50g ARG* 3.1 42.8 + - - +
51g LEU* 3.5 9.5 + - - +
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Residues in contact with VAL 48 (chain g).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194M PHE* 4.3 11.0 - - + -
269M LEU* 3.7 24.2 - - + -
275M VAL* 3.6 27.4 - - + -
277M MET* 4.2 9.0 - - - -
282M ILE* 3.7 16.6 - - + -
45g TYR* 3.2 40.5 + - + +
47g PHE* 1.3 78.0 - - - +
49g GLU* 1.3 57.8 + - - +
51g LEU* 2.9 32.5 + - - +
52g LEU* 3.6 9.7 + - + +
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Residues in contact with GLU 49 (chain g).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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291F SER* 5.1 4.0 - - - -
280M LYS* 3.7 20.8 + - - +
45g TYR* 2.9 39.5 + - + +
46g GLN* 3.2 19.3 + - - +
48g VAL* 1.3 77.4 - - - +
50g ARG* 1.3 61.5 + - - +
51g LEU 3.4 0.3 + - - -
52g LEU* 3.4 30.2 + - + +
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Residues in contact with ARG 50 (chain g).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114M GLN* 3.9 39.7 + - - +
115M PRO* 5.5 3.0 - - - +
120M GLN* 4.1 19.8 + - - +
123M ASN* 4.9 1.4 + - - -
267M PHE* 5.2 13.1 - - - +
46g GLN* 3.1 28.8 + - + +
47g PHE* 3.1 36.7 + - - +
49g GLU* 1.3 76.6 - - - +
51g LEU* 1.3 62.7 + - + +
52g LEU 3.3 6.8 + - - +
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Residues in contact with LEU 51 (chain g).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119M THR* 4.3 25.7 - - + +
120M GLN* 5.3 5.8 - - - +
123M ASN* 2.8 27.7 + - - +
190M PRO* 4.1 19.0 - - + +
194M PHE* 4.1 16.4 - - + -
266M PHE* 3.3 45.8 - - + -
267M PHE* 5.8 2.7 - - + +
269M LEU* 4.7 7.9 - - + -
47g PHE 3.8 12.1 - - - +
48g VAL* 2.9 21.0 + - - +
50g ARG* 1.3 75.9 - - + +
52g LEU* 1.3 55.7 + - + +
53g PRO* 3.5 2.8 - - - +
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Residues in contact with LEU 52 (chain g).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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289F PRO* 5.7 0.9 - - + -
290F TYR* 3.9 19.7 - - - +
291F SER* 3.6 26.0 + - - +
123M ASN* 3.4 2.5 + - - -
191M VAL* 3.3 28.9 - - + -
194M PHE* 5.6 0.9 - - + -
277M MET* 3.9 22.4 - - + -
280M LYS* 6.4 0.4 - - - +
45g TYR* 5.1 7.2 - - + +
48g VAL* 3.8 17.5 - - + +
49g GLU* 3.8 26.3 - - + +
50g ARG 3.3 7.8 - - - +
51g LEU* 1.3 78.2 - - + +
53g PRO* 1.4 69.5 - - + +
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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