Contacts of the helix formed by residues 44 - 52 (chain M) 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 M).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39M LYS 4.5 3.4 - - - -
40M THR* 3.1 43.2 - - - +
41M GLU 4.4 0.4 - - - -
42M ARG* 2.1 48.9 + - - +
43M GLU* 1.3 67.4 - - - +
45M VAL* 1.3 66.1 + - - +
46M THR* 2.8 3.4 - - - +
47M GLU* 2.9 39.1 + - - +
48M LEU 3.3 9.5 + - - -
82M GLY 5.4 0.2 - - - -
148M HIS* 5.9 4.0 - - - -
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Residues in contact with VAL 45 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36M SER* 5.0 10.1 - - - +
40M THR* 3.5 21.9 - - + +
42M ARG 5.1 0.4 - - - -
43M GLU* 3.0 18.1 - - - +
44M CYS* 1.3 80.5 - - - +
46M THR* 1.3 53.5 + - - +
48M LEU* 6.0 0.4 - - + -
49M ILE* 2.7 65.6 + - + +
106M ILE* 4.0 30.7 - - + -
267M ARG* 4.1 30.5 - - + +
270M ALA* 5.9 1.8 - - + -
271M TYR* 6.4 0.4 - - + -
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Residues in contact with THR 46 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43M GLU 4.0 3.0 + - - -
44M CYS* 4.5 0.7 - - - -
45M VAL* 1.3 78.3 - - - +
47M GLU* 1.3 58.2 + - + +
49M ILE* 4.5 3.4 - - - -
50M LYS* 2.5 65.3 + - + +
79M ASN* 3.4 22.7 - - - +
82M GLY* 3.2 28.1 + - - +
83M LYS 4.0 4.5 - - - -
84M GLY 4.1 8.7 - - - +
85M LEU* 4.2 7.5 - - + +
106M ILE* 4.0 17.5 - - - +
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Residues in contact with GLU 47 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42M ARG* 4.9 4.8 + - - -
44M CYS* 2.9 33.9 + - + +
46M THR* 1.3 79.0 - - + +
48M LEU* 1.3 54.8 + - - +
50M LYS* 3.5 4.9 - - - +
51M THR* 2.7 40.1 + - - +
82M GLY* 6.0 1.1 - - - +
160M ASN* 5.7 1.2 - - - +
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Residues in contact with LEU 48 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36M SER* 5.7 8.1 - - - +
39M LYS* 4.8 18.4 - - + +
40M THR* 3.9 32.3 - - + +
44M CYS 3.3 3.0 + - - -
45M VAL* 4.2 1.3 - - + +
47M GLU* 1.3 79.7 - - - +
49M ILE* 1.3 64.7 + - + +
51M THR* 3.4 12.4 + - + +
52M ALA* 3.1 20.6 + - + +
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Residues in contact with ILE 49 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45M VAL* 2.7 47.6 + - + +
46M THR 3.7 1.3 - - - +
48M LEU* 1.3 73.2 - - + +
50M LYS* 1.3 66.2 + - - +
52M ALA* 3.0 25.2 + - - +
53M GLU* 4.0 3.0 - - + +
85M LEU* 3.4 24.7 - - + -
270M ALA* 4.8 4.5 - - + +
271M TYR* 5.4 9.6 - - + -
274M PHE* 3.2 46.3 - - + -
291M LEU* 4.0 20.9 - - + -
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Residues in contact with LYS 50 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46M THR* 2.5 39.0 + - + +
47M GLU* 3.6 4.9 - - - +
49M ILE* 1.3 71.7 - - - +
51M THR* 1.3 60.4 + - - +
52M ALA 2.5 15.3 - - - +
53M GLU* 4.6 5.2 - - - +
54M LYS* 4.7 2.4 + - - +
77M TYR* 3.4 58.4 - - + +
79M ASN* 3.2 31.0 - - - +
85M LEU* 3.3 26.8 - - - +
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Residues in contact with THR 51 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47M GLU* 2.7 17.1 + - - +
48M LEU* 3.5 17.8 - - + +
50M LYS* 1.3 71.8 - - - +
52M ALA* 1.3 68.6 + - - +
54M LYS* 3.3 22.8 - - - +
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Residues in contact with ALA 52 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48M LEU* 3.1 11.8 + - + +
49M ILE* 3.0 12.5 + - - +
50M LYS 2.5 20.4 - - - +
51M THR* 1.3 78.7 - - - +
53M GLU* 1.3 68.7 + - - +
54M LYS* 2.8 8.3 - - - +
274M PHE* 4.0 18.6 - - + -
278M 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