Contacts of the helix formed by residues 29 - 44 (chain B) in PDB entry 1R23
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 ALA 29 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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50A ARG* 4.6 0.9 - - - +
27B ALA 3.6 2.3 + - - -
28B ILE* 1.3 77.0 - - - +
30B PRO* 1.3 73.3 - - + +
31B GLU* 3.4 28.9 - - - +
32B VAL* 3.1 13.9 + - + +
33B ALA* 3.0 18.0 + - - +
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Residues in contact with PRO 30 (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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46A PRO* 5.2 1.6 - - - +
50A ARG* 3.9 26.7 - - - +
28B ILE 3.5 1.1 - - - +
29B ALA* 1.3 88.3 - - + +
31B GLU* 1.3 63.0 + - + +
33B ALA* 3.5 9.2 + - + +
34B GLN* 3.0 26.0 + - - +
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Residues in contact with GLU 31 (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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29B ALA* 3.4 24.3 - - - +
30B PRO* 1.3 80.4 - - - +
32B VAL* 1.3 74.1 + - + +
34B GLN* 3.6 8.2 - - - +
35B SER* 2.9 34.4 + - - +
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Residues in contact with VAL 32 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115A LEU* 4.3 25.1 - - + -
118A LEU* 5.1 5.6 - - + +
28B ILE* 4.1 20.4 - - + -
29B ALA* 3.1 21.5 + - + +
31B GLU* 1.3 93.8 - - + +
33B ALA* 1.3 60.4 + - - +
35B SER* 3.3 7.5 + - - +
36B LEU* 2.9 29.6 + - + +
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Residues in contact with ALA 33 (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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46A PRO* 3.6 29.6 - - + +
49A LEU* 3.6 6.9 - - + +
50A ARG* 3.7 12.8 - - + -
28B ILE* 3.6 24.9 - - + +
29B ALA 3.0 8.8 + - - +
30B PRO* 3.7 9.6 - - + +
31B GLU 3.3 0.2 - - - -
32B VAL* 1.3 79.2 - - - +
34B GLN* 1.3 55.7 + - - +
36B LEU* 4.4 2.5 - - - -
37B ALA* 2.9 29.1 + - - +
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Residues in contact with GLN 34 (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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46A PRO* 3.1 28.2 - - + +
30B PRO 3.0 17.5 + - - +
31B GLU* 3.6 9.0 - - - +
32B VAL 3.2 0.4 - - - -
33B ALA* 1.3 74.1 - - - +
35B SER* 1.3 61.1 + - - +
37B ALA* 3.3 2.6 + - - +
38B GLU* 3.0 68.8 + - + +
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Residues in contact with SER 35 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118A LEU* 4.1 14.1 - - - +
31B GLU* 2.9 18.6 + - - +
32B VAL* 3.3 6.7 + - - -
34B GLN* 1.3 76.3 - - - +
36B LEU* 1.3 58.7 + - - +
38B GLU* 3.3 14.5 + - - +
39B PHE* 3.0 26.7 + - - +
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Residues in contact with LEU 36 (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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49A LEU* 3.6 22.9 - - + -
111A TYR* 3.6 34.3 - - + +
114A ALA* 3.6 29.4 - - + -
115A LEU* 3.9 16.6 - - + +
118A LEU* 3.6 24.1 - - + +
28B ILE* 4.5 8.5 - - + -
32B VAL* 2.9 17.9 + - + +
33B ALA* 3.7 1.8 - - - +
35B SER* 1.3 76.0 - - - +
37B ALA* 1.3 57.0 - - - +
39B PHE* 3.1 5.5 + - + +
40B PHE* 3.0 44.1 + - + -
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Residues in contact with ALA 37 (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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44A ALA* 3.2 19.9 - - - +
45A ASP 3.7 7.4 - - - +
46A PRO* 3.7 32.8 - - + -
49A LEU* 3.4 8.2 - - + +
33B ALA 2.9 18.8 + - - +
34B GLN* 3.5 7.6 - - - +
35B SER 3.3 0.2 - - - -
36B LEU* 1.3 77.4 - - - +
38B GLU* 1.3 56.6 + - - +
40B PHE 3.4 0.3 + - - -
41B ALA* 2.9 23.4 + - - +
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Residues in contact with GLU 38 (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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34B GLN* 3.0 41.7 + - - +
35B SER* 3.7 13.5 + - - +
36B LEU 3.3 0.2 - - - -
37B ALA* 1.3 73.0 - - - +
39B PHE* 1.3 65.4 + - - +
41B ALA* 3.2 8.7 + - - +
42B VAL* 3.1 29.0 + - + +
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Residues in contact with PHE 39 (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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114A ALA* 3.7 23.8 - - + -
117A HIS* 3.4 34.1 - + - -
118A LEU* 4.5 9.0 - - + -
35B SER 3.0 14.3 + - - +
36B LEU* 3.1 15.0 + - + +
38B GLU* 1.3 77.5 - - - +
40B PHE* 1.3 67.5 + + - +
42B VAL* 2.9 33.2 - - + +
43B LEU* 3.4 22.9 + - + +
86B LEU 5.4 4.5 - - - -
87B ARG* 6.0 3.4 - - - -
88B LEU* 3.6 21.1 - - + -
107B ILE* 3.9 6.5 - - + -
110B LEU* 3.7 30.1 - - + -
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Residues in contact with PHE 40 (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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40A PHE* 3.6 54.5 - + - +
43A LEU* 3.7 29.8 - - + -
44A ALA 3.9 5.6 - - - +
49A LEU* 3.8 13.2 - - + -
110A LEU* 4.1 22.9 - - + -
111A TYR* 4.7 3.6 - - - -
114A ALA* 3.5 27.6 - - + -
36B LEU* 3.0 45.2 + - + +
37B ALA 3.9 3.4 - - - +
39B PHE* 1.3 84.4 - + - +
41B ALA* 1.3 62.6 + - - +
43B LEU* 3.1 8.4 + - + +
44B ALA* 3.1 17.2 + - - +
110B LEU* 5.2 2.2 - - + -
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Residues in contact with ALA 41 (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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44A ALA* 3.7 14.8 - - + +
37B ALA 2.9 14.8 + - - +
38B GLU* 3.3 14.6 - - - +
40B PHE* 1.3 78.4 - - - +
42B VAL* 1.3 62.5 + - + +
44B ALA* 3.1 23.7 + - - +
45B ASP* 5.5 0.2 - - - +
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Residues in contact with VAL 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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38B GLU* 3.1 15.3 + - + +
39B PHE* 2.9 33.2 - - + +
41B ALA* 1.3 77.4 - - + +
43B LEU* 1.3 62.0 + - + +
44B ALA 3.3 0.6 + - - -
45B ASP* 3.9 2.9 - - - +
48B ARG* 2.9 46.3 + - - +
86B LEU* 4.1 28.7 - - + +
88B LEU* 4.0 21.6 - - + +
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Residues in contact with LEU 43 (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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40A PHE* 3.8 25.7 - - + -
39B PHE* 3.8 30.7 - - + +
40B PHE* 3.1 12.5 + - + +
41B ALA 3.1 0.8 - - - -
42B VAL* 1.3 80.5 - - + +
44B ALA* 1.3 53.0 + - - +
45B ASP* 2.7 17.9 + - - +
48B ARG* 5.5 2.5 - - + +
49B LEU* 3.4 32.7 - - + +
52B LEU* 3.6 30.1 - - + -
88B LEU* 4.1 18.4 - - + -
107B ILE* 5.8 1.3 - - + -
110B LEU* 3.6 30.7 - - + -
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Residues in contact with ALA 44 (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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37A ALA* 3.4 33.7 - - - +
40A PHE* 4.1 0.7 - - - -
41A ALA* 3.7 24.9 - - + +
40B PHE 3.1 7.2 + - - +
41B ALA* 3.1 18.4 + - - +
43B LEU* 1.3 73.7 - - - +
45B ASP* 1.3 57.3 - - - +
46B PRO* 4.2 2.8 - - - +
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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