Contacts of the helix formed by residues 44 - 52 (chain P) 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 P).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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39P LYS 4.5 2.9 - - - -
40P THR* 3.1 32.2 - - - +
41P GLU 4.4 0.7 - - - -
42P ARG* 2.1 48.5 + - - +
43P GLU* 1.3 67.0 - - - +
45P VAL* 1.3 66.5 + - - +
46P THR* 2.8 3.6 - - - +
47P GLU* 2.8 38.6 + - - +
48P LEU 3.3 9.2 + - - -
148P HIS* 5.9 4.0 - - - -
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Residues in contact with VAL 45 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36P SER* 5.0 8.5 - - - +
40P THR* 3.4 22.6 - - + +
42P ARG 5.1 0.2 - - - -
43P GLU* 3.0 17.7 - - - +
44P CYS* 1.3 80.7 - - - +
46P THR* 1.3 53.9 + - - +
48P LEU* 3.5 1.2 + - + +
49P ILE* 2.7 65.2 + - + +
106P ILE* 4.1 25.8 - - + -
267P ARG* 4.1 35.0 - - + +
270P ALA* 5.9 1.6 - - + -
271P TYR* 6.4 0.7 - - + -
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Residues in contact with THR 46 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43P GLU 4.0 3.0 + - - -
44P CYS* 2.8 1.3 - - - -
45P VAL* 1.3 77.9 - - - +
47P GLU* 1.3 57.3 + - + +
49P ILE* 4.6 2.5 - - - -
50P LYS* 2.5 66.1 + - + +
79P ASN* 3.5 22.7 - - - +
82P GLY* 3.2 26.8 + - - +
83P LYS 4.0 4.9 - - - -
84P GLY 4.0 9.3 - - - +
85P LEU* 4.2 7.3 - - + +
106P ILE* 4.0 17.7 - - - +
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Residues in contact with GLU 47 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42P ARG* 4.9 4.8 + - - -
44P CYS* 2.8 33.7 + - + +
46P THR* 1.3 80.9 - - + +
48P LEU* 1.3 54.6 + - - +
50P LYS* 2.9 5.2 + - - +
51P THR* 2.7 40.1 + - - +
82P GLY 6.0 0.7 - - - +
160P ASN* 5.7 1.4 - - - +
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Residues in contact with LEU 48 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36P SER* 5.7 7.0 - - - +
39P LYS* 4.9 18.4 - - + +
40P THR* 3.9 32.8 - - + +
44P CYS 3.3 2.6 + - - -
45P VAL* 4.1 0.9 - - + +
47P GLU* 1.3 78.9 - - - +
49P ILE* 1.3 62.7 + - + +
51P THR* 3.5 13.5 + - + -
52P ALA* 3.2 20.1 + - + +
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Residues in contact with ILE 49 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36P SER* 5.7 1.8 - - - +
45P VAL* 2.7 47.2 + - + +
46P THR* 3.8 0.9 - - - +
48P LEU* 1.3 74.9 - - + +
50P LYS* 1.3 67.1 + - - +
52P ALA* 2.9 25.7 + - - +
53P GLU* 4.0 1.9 - - - +
85P LEU* 3.4 24.7 - - + -
87P MET* 4.8 0.9 - - - -
270P ALA* 4.9 4.7 - - + +
271P TYR* 5.4 10.8 - - + -
274P PHE* 3.2 47.3 - - + -
291P LEU* 4.0 20.2 - - + -
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Residues in contact with LYS 50 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46P THR* 2.5 38.0 + - + +
47P GLU* 3.5 4.7 - - - +
49P ILE* 1.3 71.3 - - - +
51P THR* 1.3 58.4 + - - +
52P ALA 2.5 16.0 - - - +
53P GLU* 4.6 3.9 - - - +
54P LYS* 4.6 2.6 + - - +
77P TYR* 3.4 60.3 - - + +
79P ASN* 3.3 30.7 - - + +
85P LEU* 3.3 27.7 - - - +
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Residues in contact with THR 51 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47P GLU* 2.7 15.8 + - - +
48P LEU* 3.6 18.8 - - + +
49P ILE 3.1 0.2 - - - -
50P LYS* 1.3 71.9 - - - +
52P ALA* 1.3 68.3 + - - +
54P LYS* 3.2 23.5 - - - +
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Residues in contact with ALA 52 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48P LEU* 3.2 11.6 + - + +
49P ILE* 2.9 12.3 + - - +
50P LYS 2.5 20.3 - - - +
51P THR* 1.3 78.0 - - - +
53P GLU* 1.3 68.5 + - - +
54P LYS* 2.8 7.9 - - - +
274P PHE* 4.0 19.1 - - + -
278P LEU* 4.9 2.7 - - + -
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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