Contacts of the helix formed by residues 37 - 51 (chain B) in PDB entry 3LEE
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 SER 37 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38B SER* 1.3 63.9 + - - +
39B SER* 3.8 9.2 + - - -
40B LEU* 3.0 29.9 + - - +
41B LYS* 3.1 18.4 + - - +
131B GLU* 4.2 4.2 + - - -
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Residues in contact with SER 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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37B SER* 1.3 71.9 - - - +
39B SER* 1.3 57.4 + - - +
41B LYS* 3.1 14.3 + - - +
42B THR* 2.9 41.0 + - - +
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Residues in contact with SER 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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37B SER* 3.2 5.0 + - - -
38B SER* 1.3 80.5 + - - +
40B LEU* 1.3 57.5 + - - +
42B THR* 3.4 16.3 + - - -
43B CYS* 3.4 18.5 - - - -
127B THR* 3.4 13.6 - - - +
130B LEU* 4.0 23.2 - - - +
131B GLU* 2.6 32.6 + - - +
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Residues in contact with LEU 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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37B SER* 3.0 19.1 + - - +
39B SER* 1.3 79.8 + - - +
41B LYS* 1.3 63.4 + - - +
42B THR 3.3 0.4 - - - -
43B CYS* 3.4 6.4 - - + +
44B TYR* 3.2 55.9 + - + -
67B ASN* 3.3 30.1 - - + +
131B GLU* 3.3 29.6 - - + +
368C THR* 4.4 14.6 - - - +
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Residues in contact with LYS 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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37B SER 3.1 13.8 + - - +
38B SER* 3.1 18.3 + - - +
40B LEU* 1.3 78.3 - - - +
42B THR* 1.3 59.3 + - + +
44B TYR* 3.4 3.8 + - - +
45B LYS* 3.0 26.2 + - - +
361C GLN* 4.1 23.4 + - - +
364C SER* 3.8 27.0 + - - -
365C THR* 4.0 23.3 - - + +
367C ARG* 6.1 0.2 - - - -
368C THR* 3.5 32.8 - - + +
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Residues in contact with THR 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 SER* 2.9 23.0 + - - +
39B SER* 3.4 9.6 + - - -
41B LYS* 1.3 76.0 - - + +
43B CYS* 1.3 65.7 + - - +
45B LYS* 3.4 14.4 - - - +
46B TYR* 3.0 38.5 + - - -
124B ASP* 4.5 3.9 + - - -
127B THR* 3.5 15.2 - - - +
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Residues in contact with CYS 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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39B SER 3.4 16.5 + - - -
40B LEU* 3.4 13.2 + - + +
41B LYS 3.2 0.2 - - - -
42B THR* 1.3 76.4 + - - +
44B TYR* 1.3 56.5 + - + +
45B LYS 2.9 3.8 - - - -
46B TYR* 2.6 34.7 + - - +
47B LEU 2.8 9.5 + - - -
70B CYS* 4.6 8.7 - - - -
71B ILE* 5.0 7.6 - - + -
74B LEU* 3.6 14.8 - - + +
127B THR* 4.3 12.3 - - - -
128B ILE* 4.4 20.0 - - - -
131B GLU* 4.3 20.0 - - - -
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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
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40B LEU* 3.2 47.2 + - + +
41B LYS 3.9 6.3 - - - +
43B CYS* 1.3 78.0 - - + +
45B LYS* 1.3 60.7 + - - +
47B LEU* 3.5 25.4 - - + +
48B ASN* 3.2 28.8 + - - +
58B ILE* 5.1 0.7 - - + -
59B GLN* 4.0 21.8 - - + +
66B ARG* 3.2 42.4 + - + +
67B ASN* 2.4 23.5 + - - -
70B CYS* 3.8 24.0 - - + -
71B ILE* 6.2 0.9 - - + -
367C ARG* 4.2 19.0 - - + -
368C THR* 3.9 15.7 - - + -
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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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41B LYS 3.0 14.1 + - - +
42B THR* 3.4 17.7 - - - +
43B CYS 2.8 0.6 + - - -
44B TYR* 1.3 76.0 - - - +
46B TYR* 1.3 77.9 + - - +
48B ASN* 3.5 1.9 + - - +
49B GLN* 3.0 43.2 + - + +
346C TYR* 3.6 34.8 + - + +
364C SER* 5.3 5.4 - - - +
367C ARG* 4.3 12.3 + - - +
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Residues in contact with TYR 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 THR* 3.0 29.1 - - - -
43B CYS* 2.6 15.4 + - - +
45B LYS* 1.3 81.7 - - - +
47B LEU* 1.3 63.9 + - - +
49B GLN* 3.0 25.6 + - - +
50B THR* 2.8 35.4 + - + +
74B LEU* 4.0 16.4 - - + -
120B GLN* 3.3 36.0 + - + +
121B VAL* 5.1 9.2 - - + -
124B ASP* 2.7 49.3 + - + +
127B THR* 5.0 3.4 - - + -
128B ILE* 4.9 11.4 - - + -
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Residues in contact with LEU 47 (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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43B CYS 2.8 10.3 + - - +
44B TYR* 3.5 41.3 - - + +
45B LYS 3.2 0.4 - - - -
46B TYR* 1.3 77.0 - - - +
48B ASN* 1.3 57.8 + - - +
50B THR* 3.3 0.5 + - - -
51B SER* 2.9 37.9 + - - -
55B ALA* 4.2 14.6 - - - +
58B ILE* 4.0 26.0 - - + -
59B GLN* 4.2 16.8 - - + -
70B CYS* 4.0 21.8 - - - +
73B TYR* 3.7 27.4 - - + -
74B LEU* 3.9 8.9 - - + +
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Residues in contact with ASN 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 3.2 15.4 + - - +
45B LYS 4.2 1.8 - - - +
47B LEU* 1.3 77.2 - - - +
49B GLN* 1.3 64.5 + - - +
50B THR 3.2 0.8 + - - -
51B SER 4.0 8.6 + - - +
55B ALA* 2.7 36.4 - - - +
59B GLN* 3.0 32.5 - - - +
339C TYR 4.7 2.2 + - - -
343C GLU* 3.0 54.0 + - - +
367C ARG* 3.2 16.0 + - - +
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Residues in contact with GLN 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* 3.0 33.7 + - + +
46B TYR* 3.0 32.6 + - - +
48B ASN* 1.3 79.3 - - - +
50B THR* 1.3 65.4 + - + +
117B LYS 5.4 2.9 - - - +
118B ASP* 4.7 10.0 - - - +
120B GLN* 4.0 20.5 - - - +
121B VAL 5.6 0.2 + - - -
343C GLU* 5.0 3.4 - - - -
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Residues in contact with THR 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 TYR* 2.8 26.7 + - + +
47B LEU 3.3 1.0 + - - -
49B GLN* 1.3 93.5 - - + +
51B SER* 1.3 53.0 + - - +
52B ARG 4.0 2.9 + - - -
73B TYR* 2.5 38.9 + - - -
74B LEU* 3.8 5.1 - - + +
77B ARG* 4.1 17.9 + - + -
118B ASP* 3.7 39.0 - - + +
121B VAL* 5.3 5.8 - - + +
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Residues in contact with SER 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 LEU* 2.9 22.2 + - - +
48B ASN 4.0 6.8 + - - +
49B GLN 3.7 1.8 - - - -
50B THR* 1.3 75.8 - - - +
52B ARG* 1.3 65.5 + - - +
53B SER 4.1 0.2 + - - -
54B PHE* 3.3 18.4 + - - +
55B ALA* 3.2 33.2 + - - +
58B ILE* 4.8 0.3 - - - +
73B TYR* 3.1 26.2 - - - -
77B ARG* 5.5 0.4 - - - +
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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