Contacts of the helix formed by residues 44 - 52 (chain R) 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 R).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39R LYS 4.5 3.1 - - - -
40R THR* 3.1 40.4 - - - +
41R GLU 4.4 0.7 - - - -
42R ARG* 2.1 47.5 + - - +
43R GLU* 1.3 67.2 - - - +
45R VAL* 1.3 66.0 + - - +
46R THR* 2.8 4.0 - - - +
47R GLU* 2.8 38.5 + - - +
48R LEU 3.3 8.5 + - - -
82R GLY 5.4 0.2 - - - -
148R HIS* 5.9 4.3 - - - -
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Residues in contact with VAL 45 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36R SER* 5.0 9.0 - - - +
40R THR* 3.5 22.6 - - + +
42R ARG 5.1 0.4 - - - -
43R GLU* 2.9 18.5 - - - +
44R CYS* 1.3 79.9 - - - +
46R THR* 1.3 52.9 + - - +
48R LEU* 3.5 0.6 + - + +
49R ILE* 2.7 65.7 + - + +
106R ILE* 4.1 30.5 - - + -
267R ARG* 4.1 30.3 - - + +
270R ALA* 5.9 1.8 - - + -
271R TYR* 6.5 0.2 - - + -
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Residues in contact with THR 46 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43R GLU 4.0 3.2 + - - -
44R CYS* 2.8 0.8 - - - -
45R VAL* 1.3 78.3 - - - +
47R GLU* 1.3 57.0 + - + +
49R ILE* 3.5 3.8 - - - -
50R LYS* 2.5 65.8 + - + +
79R ASN* 3.4 22.7 - - - +
82R GLY* 3.2 27.4 + - - +
83R LYS 4.0 0.2 - - - -
84R GLY 4.0 14.3 - - - +
85R LEU* 4.2 7.3 - - + +
106R ILE* 4.0 17.2 - - - +
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Residues in contact with GLU 47 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42R ARG* 4.9 4.2 + - - -
44R CYS* 2.8 34.7 + - + +
46R THR* 1.3 78.9 - - + +
48R LEU* 1.3 55.4 + - - +
50R LYS* 3.5 4.9 - - - +
51R THR* 2.7 40.0 + - - +
82R GLY 6.0 0.4 - - - +
160R ASN* 5.6 1.7 - - - +
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Residues in contact with LEU 48 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36R SER* 5.8 7.6 - - - +
39R LYS* 4.8 18.6 - - + +
40R THR* 3.9 31.6 - - + +
44R CYS 3.3 3.0 + - - -
45R VAL* 4.2 1.1 - - - +
47R GLU* 1.3 77.4 - - - +
49R ILE* 1.3 64.5 + - + +
51R THR* 3.5 13.1 + - + +
52R ALA* 3.2 19.3 + - + +
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Residues in contact with ILE 49 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36R SER* 5.8 1.6 - - - +
45R VAL* 2.7 48.4 + - + +
46R THR* 3.8 0.9 - - - +
48R LEU* 1.3 74.7 - - + +
50R LYS* 1.3 65.0 + - - +
52R ALA* 3.0 25.4 + - - +
53R GLU* 4.0 2.5 - - + +
85R LEU* 3.4 24.2 - - + -
106R ILE* 5.7 0.2 - - + -
270R ALA 4.8 4.3 - - - +
271R TYR* 5.4 10.5 - - + -
274R PHE* 3.2 46.7 - - + -
291R LEU* 4.0 21.1 - - + -
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Residues in contact with LYS 50 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46R THR* 2.5 37.6 + - + +
47R GLU* 3.5 4.7 - - - +
49R ILE* 1.3 72.3 - - - +
51R THR* 1.3 59.4 + - - +
52R ALA 2.5 15.5 - - - +
53R GLU* 4.6 4.5 - - - +
54R LYS* 4.7 2.6 + - - +
77R TYR* 3.4 58.3 - - + +
79R ASN* 3.3 30.3 - - - +
85R LEU* 3.3 27.2 - - - +
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Residues in contact with THR 51 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47R GLU* 2.7 16.2 + - - +
48R LEU* 3.6 17.6 - - + +
50R LYS* 1.3 72.8 - - - +
52R ALA* 1.3 69.0 + - - +
54R LYS* 3.2 23.7 - - - +
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Residues in contact with ALA 52 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48R LEU* 3.2 11.8 + - + +
49R ILE* 3.0 12.9 + - - +
50R LYS 2.5 20.1 - - - +
51R THR* 1.3 77.9 - - - +
53R GLU* 1.3 67.9 + - - +
54R LYS* 2.8 7.9 - - - +
274R PHE* 4.0 18.6 - - + -
278R 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