Contacts of the helix formed by residues 44 - 52 (chain L) 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 L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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39L LYS 4.5 3.8 - - - -
40L THR* 3.1 32.6 - - - +
41L GLU 4.5 0.4 - - - -
42L ARG* 2.1 47.7 + - - +
43L GLU* 1.3 67.0 - - - +
45L VAL* 1.3 65.8 + - - +
46L THR* 2.8 3.4 - - - +
47L GLU* 2.9 39.1 + - - +
48L LEU 3.3 9.4 + - - -
82L GLY 5.4 0.7 - - - -
148L HIS* 5.9 4.3 - - - -
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Residues in contact with VAL 45 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36L SER* 5.1 8.7 - - - +
40L THR* 3.4 22.6 - - + +
42L ARG 5.0 0.2 - - - -
43L GLU* 3.0 17.9 - - - +
44L CYS* 1.3 80.2 - - - +
46L THR* 1.3 53.0 + - - +
48L LEU* 3.5 0.8 + - + -
49L ILE* 2.7 66.6 + - + +
106L ILE* 4.1 31.0 - - + -
267L ARG* 4.1 31.0 - - + +
270L ALA* 5.9 1.8 - - + -
271L TYR* 6.4 0.2 - - + -
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Residues in contact with THR 46 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43L GLU 4.0 3.1 + - - -
44L CYS* 2.8 0.6 - - - -
45L VAL* 1.3 78.5 - - - +
47L GLU* 1.3 56.4 + - + +
49L ILE* 4.6 2.7 - - - -
50L LYS* 2.5 67.0 + - + +
79L ASN* 3.5 22.2 - - - +
82L GLY* 3.1 28.5 + - - +
83L LYS 4.0 4.3 - - - -
84L GLY 4.0 9.3 - - - +
85L LEU* 4.3 6.9 - - + +
106L ILE* 4.0 17.3 - - - +
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Residues in contact with GLU 47 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42L ARG* 4.9 4.7 + - - +
44L CYS* 2.9 33.7 + - + +
46L THR* 1.3 79.4 - - + +
48L LEU* 1.3 54.4 + - - +
50L LYS* 3.5 5.4 - - - +
51L THR* 2.8 39.5 + - - +
82L GLY 6.0 0.7 - - - +
160L ASN* 5.7 1.4 - - - +
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Residues in contact with LEU 48 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36L SER* 5.8 7.2 - - - +
39L LYS* 4.9 19.5 - - + +
40L THR* 3.9 31.9 - - + +
44L CYS 3.3 3.0 + - - -
45L VAL* 4.2 0.9 - - - +
47L GLU* 1.3 77.8 - - - +
49L ILE* 1.3 64.3 + - + +
51L THR* 3.5 12.9 + - + +
52L ALA* 3.2 19.9 + - + +
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Residues in contact with ILE 49 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36L SER* 5.8 2.0 - - - +
45L VAL* 2.7 48.8 + - + +
46L THR 3.8 0.9 - - - +
48L LEU* 1.3 75.5 - - + +
50L LYS* 1.3 60.4 + - - +
51L THR 3.1 0.2 - - - -
52L ALA* 2.9 31.3 + - - +
53L GLU* 4.0 2.3 - - + +
85L LEU* 3.4 24.9 - - + -
106L ILE* 5.7 0.2 - - + -
270L ALA* 4.9 4.9 - - + +
271L TYR* 5.4 9.6 - - + -
274L PHE* 3.2 47.5 - - + -
291L LEU* 4.0 20.4 - - + -
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Residues in contact with LYS 50 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46L THR* 2.5 38.4 + - + +
47L GLU* 3.6 5.2 - - - +
49L ILE* 1.3 71.9 - - - +
51L THR* 1.3 58.5 + - - +
52L ALA 2.5 15.5 - - - +
53L GLU* 4.6 4.9 - - - +
54L LYS* 4.6 2.9 + - - +
77L TYR* 3.4 59.8 - - + +
79L ASN* 3.3 30.7 - - + +
85L LEU* 3.4 27.6 - - - +
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Residues in contact with THR 51 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47L GLU* 2.8 19.5 + - - +
48L LEU* 3.6 15.1 - - + +
49L ILE 3.1 0.2 - - - -
50L LYS* 1.3 71.2 - - - +
52L ALA* 1.3 67.6 + - - +
54L LYS* 3.3 23.2 - - - +
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Residues in contact with ALA 52 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48L LEU* 3.2 12.7 + - + +
49L ILE* 2.9 13.2 + - - +
50L LYS 2.5 20.1 - - - +
51L THR* 1.3 78.2 - - - +
53L GLU* 1.3 67.6 + - - +
54L LYS* 2.8 7.6 - - - +
274L PHE* 4.0 18.6 - - + -
278L 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