Contacts of the helix formed by residues 41 - 55 (chain B) in PDB entry 1D2G
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 THR 41 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39B SER 4.5 0.2 - - - -
40B ARG* 1.3 76.6 - - - +
42B ALA* 1.3 58.3 + - - +
43B GLU* 3.1 30.2 + - + +
44B TYR* 2.8 24.6 - - + +
45B LYS* 2.9 30.1 + - - +
191B ASN 4.9 1.4 + - - -
192B ILE* 3.1 29.3 + - - +
193B TYR 2.6 15.5 + - - -
194B TYR 4.4 1.0 + - - -
195B LYS* 4.5 11.2 + - - +
270B PHE* 4.4 0.2 - - + -
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Residues in contact with ALA 42 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40B ARG 3.9 2.0 + - - -
41B THR* 1.3 73.0 - - - +
43B GLU* 1.3 68.9 + - - +
45B LYS* 3.9 7.3 - - - +
46B ALA* 2.9 32.9 + - - +
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Residues in contact with GLU 43 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41B THR* 3.1 23.2 + - + +
42B ALA* 1.3 90.8 + - - +
44B TYR* 1.3 58.1 + - - +
46B ALA* 3.9 4.2 - - - +
47B TRP* 2.9 32.4 + - - +
192B ILE 4.8 0.9 - - - +
270B PHE* 3.9 19.8 - - + +
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Residues in contact with TYR 44 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40B ARG* 3.1 38.6 - - + -
41B THR* 2.8 24.6 - - + +
43B GLU* 1.3 76.3 - - - +
45B LYS* 1.3 56.1 + - - +
47B TRP* 3.2 11.7 + + - +
48B LEU* 2.9 58.4 + - + +
70B ASP* 2.7 37.5 + - - +
73B MET* 4.3 3.1 - - + +
136B LEU* 4.2 9.3 - - + +
192B ILE 4.0 2.0 - - - +
193B TYR* 3.4 42.8 - + - -
194B TYR* 3.9 3.6 - + - -
270B PHE* 3.5 19.2 - + + -
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Residues in contact with LYS 45 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40B ARG* 4.6 13.9 - - + +
41B THR 2.9 18.8 + - - +
42B ALA* 3.9 6.5 - - - +
44B TYR* 1.3 76.3 - - - +
46B ALA* 1.3 64.2 - - - +
48B LEU* 4.3 0.8 - - - +
49B LEU* 3.1 45.8 + - + +
73B MET* 4.3 27.4 - - - -
77B GLU* 3.2 26.3 + - - -
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Residues in contact with ALA 46 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42B ALA 2.9 20.1 + - - +
43B GLU* 3.9 4.0 - - - +
45B LYS* 1.3 77.3 - - - +
47B TRP* 1.3 64.0 + - - +
49B LEU* 4.3 2.1 - - - +
50B GLY* 3.1 21.8 + - - -
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Residues in contact with TRP 47 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43B GLU 2.9 18.8 + - - +
44B TYR* 3.6 13.0 - + - +
46B ALA* 1.3 78.9 - - - +
48B LEU* 1.3 97.0 + - + +
50B GLY* 3.3 0.9 + - - -
51B LEU* 3.1 44.9 + - + +
136B LEU* 4.7 6.1 - - + -
171B VAL* 3.3 29.2 - - + -
193B TYR* 5.0 1.6 - + - -
267B LEU* 3.1 35.5 - - + +
270B PHE* 3.5 43.5 - + + -
285B ILE* 3.8 13.2 - - + -
287B VAL* 5.3 2.0 - - + -
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Residues in contact with LEU 48 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44B TYR* 2.9 38.5 + - + +
45B LYS 4.3 1.6 - - - +
47B TRP* 1.3 105.7 - - + +
49B LEU* 1.3 63.2 + - - +
51B LEU* 3.3 9.3 + - + +
52B LEU* 3.1 34.3 + - + +
73B MET* 3.5 29.8 - - + -
74B LEU* 4.3 11.9 - - + -
134B ILE* 4.6 15.9 - - + -
136B LEU* 4.4 15.9 - - + -
171B VAL* 4.6 6.5 - - + -
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Residues in contact with LEU 49 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45B LYS* 3.1 47.5 + - + +
46B ALA* 4.3 2.9 - - - +
48B LEU* 1.3 76.9 - - - +
50B GLY* 1.3 58.7 + - - +
52B LEU* 3.8 3.3 - - + +
53B ARG* 2.9 57.9 + - - +
73B MET* 4.5 10.3 - - + -
74B LEU* 4.1 15.5 - - + -
77B GLU* 3.6 27.8 - - + +
79B PHE* 3.8 24.7 - - + -
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Residues in contact with GLY 50 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46B ALA 3.1 18.8 + - - -
47B TRP 3.8 1.1 - - - -
49B LEU* 1.3 75.4 - - - +
51B LEU* 1.3 58.7 + - - +
53B ARG* 4.1 3.5 - - - +
54B GLN* 2.8 37.0 + - - +
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Residues in contact with LEU 51 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47B TRP* 3.1 49.4 + - + +
48B LEU* 3.3 5.1 + - + +
50B GLY* 1.3 74.5 - - - +
52B LEU* 1.3 69.5 + - + +
54B GLN* 3.8 11.4 - - - +
55B HIS* 2.9 49.8 + - + +
169B LEU* 3.9 13.8 - - + +
171B VAL* 3.8 27.1 - - + -
287B VAL* 4.4 20.4 - - + -
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Residues in contact with LEU 52 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48B LEU* 3.1 34.7 + - + +
49B LEU* 3.8 4.0 - - - +
51B LEU* 1.3 87.9 - - + +
53B ARG* 1.3 56.4 + - - +
55B HIS 3.2 2.4 + - - -
56B GLY 3.1 7.6 + - - -
57B CYS* 3.0 42.4 + - + +
60B VAL* 4.9 4.5 - - + -
74B LEU* 3.9 32.8 - - + -
79B PHE* 3.9 22.9 - - + -
132B ALA* 4.0 24.0 - - + -
134B ILE* 5.3 4.7 - - + -
169B LEU* 4.4 8.7 - - + -
171B VAL* 5.0 3.8 - - + -
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Residues in contact with ARG 53 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49B LEU* 2.9 40.4 + - - +
50B GLY* 4.1 4.3 - - - +
52B LEU* 1.3 72.2 - - - +
54B GLN* 1.3 65.0 + - - +
55B HIS 3.0 1.8 - - - -
56B GLY* 3.1 14.3 + - - +
57B CYS 5.0 1.1 - - - +
77B GLU* 2.7 53.5 + - - +
79B PHE* 4.1 17.3 - - + -
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Residues in contact with GLN 54 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50B GLY 2.8 22.7 + - - +
51B LEU* 3.8 13.3 - - - +
53B ARG* 1.3 77.1 - - - +
55B HIS* 1.3 85.5 + - + +
56B GLY 3.4 0.4 + - - -
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Residues in contact with HIS 55 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51B LEU* 2.9 38.5 + - + +
52B LEU 3.2 2.0 + - - -
53B ARG 3.0 0.4 - - - -
54B GLN* 1.3 110.6 - - + +
56B GLY* 1.3 65.8 + - - +
57B CYS* 3.5 18.5 + - - -
165B ARG* 5.1 6.9 + - - -
169B LEU* 3.5 28.2 - - + +
287B VAL* 6.0 0.4 - - - +
289B LYS* 4.0 24.4 + - - +
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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