Contacts of the helix formed by residues 44 - 52 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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39C LYS 4.5 3.4 - - - -
40C THR* 3.1 39.9 - - - +
41C GLU 4.4 0.4 - - - -
42C ARG* 2.1 48.3 + - - +
43C GLU* 1.3 66.2 - - - +
45C VAL* 1.3 67.0 + - - +
46C THR* 2.8 4.0 - - - +
47C GLU* 2.8 39.0 + - - +
48C LEU 3.3 9.2 + - - -
82C GLY 5.4 0.2 - - - -
148C HIS* 6.0 3.8 - - - -
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Residues in contact with VAL 45 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36C SER* 5.1 8.7 - - - +
40C THR* 3.5 21.5 - - + +
42C ARG 5.1 0.7 - - - -
43C GLU* 3.0 17.9 - - - +
44C CYS* 1.3 79.8 - - - +
46C THR* 1.3 53.7 + - - +
48C LEU* 3.8 0.8 - - + -
49C ILE* 2.7 66.5 + - + +
106C ILE* 4.1 30.3 - - + -
267C ARG* 4.1 30.5 - - + +
270C ALA* 5.9 1.6 - - + -
271C TYR* 6.4 0.4 - - + -
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Residues in contact with THR 46 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43C GLU 4.0 3.1 + - - -
44C CYS* 2.8 1.1 - - - -
45C VAL* 1.3 78.0 - - - +
47C GLU* 1.3 57.2 + - + +
49C ILE* 3.7 2.9 - - - +
50C LYS* 2.5 66.1 + - + +
79C ASN* 3.5 22.0 - - - +
82C GLY* 3.1 28.5 + - - +
83C LYS 4.0 4.5 - - - -
84C GLY 4.1 9.0 - - - +
85C LEU* 4.3 7.3 - - + +
106C ILE* 4.0 16.9 - - - +
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Residues in contact with GLU 47 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42C ARG* 4.9 4.6 + - - -
44C CYS* 2.8 34.7 + - + +
46C THR* 1.3 79.5 - - + +
48C LEU* 1.3 54.6 + - - +
50C LYS* 3.5 5.3 - - - +
51C THR* 2.7 40.5 + - - +
82C GLY* 6.0 0.7 - - - +
160C ASN* 5.7 1.6 - - - +
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Residues in contact with LEU 48 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36C SER* 5.7 7.6 - - - +
39C LYS* 4.9 17.9 - - + +
40C THR* 3.9 33.0 - - + +
44C CYS 3.3 2.6 + - - -
45C VAL* 4.2 1.6 - - + +
47C GLU* 1.3 78.4 - - - +
49C ILE* 1.3 63.3 + - + +
51C THR* 3.5 12.7 + - + +
52C ALA* 3.2 20.4 + - + +
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Residues in contact with ILE 49 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36C SER* 5.8 1.8 - - - +
45C VAL* 2.7 48.0 + - + +
46C THR 3.7 0.9 - - - +
48C LEU* 1.3 74.3 - - + +
50C LYS* 1.3 65.8 + - - +
52C ALA* 3.0 25.8 + - - +
53C GLU* 3.9 2.4 - - + +
85C LEU* 3.4 24.0 - - + -
106C ILE* 5.7 0.2 - - + -
270C ALA 4.9 4.9 - - - +
271C TYR* 5.4 9.4 - - + -
274C PHE* 3.2 46.9 - - + -
291C LEU* 4.0 21.1 - - + -
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Residues in contact with LYS 50 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46C THR* 2.5 39.3 + - + +
47C GLU* 3.5 5.4 - - - +
49C ILE* 1.3 71.5 - - - +
51C THR* 1.3 59.7 + - - +
52C ALA 2.5 15.3 - - - +
53C GLU* 4.6 5.5 - - - +
54C LYS* 4.7 2.3 + - - +
77C TYR* 3.4 59.1 - - + +
79C ASN* 3.3 30.5 - - + +
85C LEU* 3.3 27.3 - - - +
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Residues in contact with THR 51 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47C GLU* 2.7 19.8 + - - +
48C LEU* 3.6 15.0 - - + +
50C LYS* 1.3 71.9 - - - +
52C ALA* 1.3 68.3 + - - +
54C LYS* 3.3 23.4 - - - +
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Residues in contact with ALA 52 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48C LEU* 3.2 12.0 + - + +
49C ILE* 3.0 12.0 + - - +
50C LYS 2.5 21.0 - - - +
51C THR* 1.3 77.3 - - - +
53C GLU* 1.3 67.5 + - - +
54C LYS* 2.8 7.6 - - - +
274C PHE* 4.0 18.6 - - + -
278C 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