Contacts of the helix formed by residues 44 - 52 (chain J) in PDB entry 2GLJ
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 CYS 44 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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39J LYS 4.6 3.6 - - - -
40J THR* 3.2 32.1 - - - +
41J GLU 4.4 0.4 - - - -
42J ARG* 2.1 48.3 + - - +
43J GLU* 1.3 67.8 - - - +
45J VAL* 1.3 64.3 + - - +
46J THR* 2.8 4.0 - - - -
47J GLU* 2.9 40.2 + - - +
48J LEU 3.3 9.4 + - - -
82J GLY 5.4 0.2 - - - -
148J HIS* 5.9 4.0 - - - -
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Residues in contact with VAL 45 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36J SER* 5.1 8.7 - - - +
40J THR* 3.5 22.1 - - + +
42J ARG 5.1 0.4 - - - -
43J GLU* 3.0 18.1 - - - +
44J CYS* 1.3 80.1 - - - +
46J THR* 1.3 53.3 + - - +
48J LEU* 5.0 0.7 - - + -
49J ILE* 2.7 66.6 + - + +
106J ILE* 4.1 31.9 - - + -
267J ARG* 4.1 30.7 - - + +
270J ALA* 5.9 1.8 - - + -
271J TYR* 6.4 0.2 - - + -
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Residues in contact with THR 46 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43J GLU 4.0 2.7 + - - -
44J CYS* 2.8 1.0 - - - +
45J VAL* 1.3 79.1 - - - +
47J GLU* 1.3 58.1 + - + +
49J ILE* 3.5 2.6 - - - -
50J LYS* 2.5 65.1 + - + +
79J ASN* 3.5 23.1 - - - +
82J GLY* 3.2 28.2 + - - +
83J LYS 4.0 4.5 - - - -
84J GLY 4.0 9.1 - - - +
85J LEU* 4.2 7.5 - - + +
106J ILE* 4.0 17.7 - - - +
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Residues in contact with GLU 47 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42J ARG* 4.9 4.4 + - - -
44J CYS* 2.9 33.7 + - + +
46J THR* 1.3 79.3 - - + +
48J LEU* 1.3 53.8 + - - +
50J LYS* 3.5 6.0 - - - +
51J THR* 2.7 39.6 + - - +
82J GLY 6.0 0.7 - - - +
160J ASN* 5.6 1.6 - - - +
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Residues in contact with LEU 48 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36J SER* 5.7 7.6 - - - +
39J LYS* 4.9 17.5 - - + +
40J THR* 3.9 32.3 - - + +
44J CYS 3.3 2.4 + - - -
45J VAL* 4.2 1.3 - - + +
47J GLU* 1.3 78.4 - - - +
49J ILE* 1.3 64.5 + - + +
51J THR* 3.5 13.1 + - + +
52J ALA* 3.2 20.3 + - + +
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Residues in contact with ILE 49 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36J SER* 5.8 2.2 - - - +
45J VAL* 2.7 47.0 + - + +
46J THR 3.7 0.7 - - - +
48J LEU* 1.3 73.4 - - + +
50J LYS* 1.3 66.8 + - - +
52J ALA* 3.0 26.2 + - - +
53J GLU* 4.0 2.6 - - + +
85J LEU* 3.4 24.9 - - + -
106J ILE* 5.7 0.2 - - + -
270J ALA* 4.8 4.7 - - + +
271J TYR* 5.4 9.6 - - + -
274J PHE* 3.2 45.9 - - + -
291J LEU* 4.0 21.1 - - + -
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Residues in contact with LYS 50 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46J THR* 2.5 39.1 + - + +
47J GLU* 3.5 5.6 - - - +
49J ILE* 1.3 71.8 - - - +
51J THR* 1.3 58.6 + - - +
52J ALA 2.5 16.2 - - - +
53J GLU* 4.6 4.3 - - - +
54J LYS* 4.6 2.8 + - - +
77J TYR* 3.4 58.6 - - + +
79J ASN* 3.3 31.2 - - + +
85J LEU* 3.4 27.2 - - - +
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Residues in contact with THR 51 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47J GLU* 2.7 16.8 + - - +
48J LEU* 3.6 19.1 - - + +
50J LYS* 1.3 71.4 - - - +
52J ALA* 1.3 69.2 + - - +
54J LYS* 3.3 23.0 - - - +
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Residues in contact with ALA 52 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48J LEU* 3.2 11.8 + - + +
49J ILE* 3.0 13.1 + - - +
50J LYS 2.5 20.4 - - - +
51J THR* 1.3 77.9 - - - +
53J GLU* 1.3 67.4 + - - +
54J LYS* 2.8 7.9 - - - +
274J PHE* 4.0 18.4 - - + -
278J LEU* 4.9 2.5 - - + -
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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