Contacts of the helix formed by residues 35 - 49 (chain B) in PDB entry 5FDK
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 LEU 35 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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34B THR* 1.3 84.7 - - + +
36B GLU* 1.3 57.7 + - - +
37B ASP 3.1 1.6 - - - -
38B ASP* 2.9 13.4 + - + +
39B LEU* 2.8 45.4 + - + +
102B ALA* 3.8 31.0 - - + +
103B LYS 3.8 24.7 - - - +
104B GLU* 4.7 5.8 - - + -
137B ILE* 4.2 13.2 - - + +
139B SER* 3.8 24.9 - - - +
144B VAL* 4.5 11.2 - - + -
187B ILE* 4.6 12.1 - - + -
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Residues in contact with GLU 36 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34B THR* 2.3 35.3 + - - -
35B LEU* 1.3 75.9 + - - +
37B ASP* 1.3 73.1 + - - +
39B LEU* 3.8 2.2 - - - +
40B ASN* 2.9 32.9 + - - +
56B LYS* 5.2 8.0 - - + +
89B TYR* 3.7 23.0 + - - +
102B ALA* 6.1 0.4 - - - -
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Residues in contact with ASP 37 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34B THR* 4.0 7.0 - - - +
35B LEU 3.1 0.8 - - - -
36B GLU* 1.3 90.2 - - - +
38B ASP* 1.3 69.4 + - - +
40B ASN* 2.8 42.3 + - - +
41B GLU* 2.9 16.7 + - - +
186B ARG* 3.1 27.9 + - - -
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Residues in contact with ASP 38 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34B THR* 3.5 17.2 + - - +
35B LEU* 2.9 18.2 + - + +
37B ASP* 1.3 78.3 - - - +
39B LEU* 1.3 48.8 + - - +
41B GLU* 3.9 2.3 - - - +
42B THR* 2.1 38.4 + - - -
186B ARG* 2.5 49.8 + - - +
187B ILE* 3.6 29.0 - - + +
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Residues in contact with LEU 39 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35B LEU* 2.8 36.7 + - + +
36B GLU* 3.8 0.9 - - - +
38B ASP* 1.3 72.2 - - - +
40B ASN* 1.3 61.0 + - - +
42B THR* 3.7 1.9 - - - -
43B ASN* 2.8 32.1 + - - +
89B TYR* 3.6 32.7 - - + +
100B PHE* 6.3 2.2 - - + -
101B GLU 5.8 0.2 - - - -
102B ALA* 3.6 30.5 - - + -
137B ILE* 4.6 15.5 - - + -
187B ILE* 4.5 15.3 - - + -
189B TYR* 4.0 30.4 + - + -
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Residues in contact with ASN 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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36B GLU* 2.9 22.5 + - - +
37B ASP* 2.8 28.5 + - - +
39B LEU* 1.3 73.0 - - - +
41B GLU* 1.3 96.4 + - - +
43B ASN* 4.0 3.9 - - - +
44B LYS* 2.9 36.0 + - - +
89B TYR* 5.1 4.7 - - + -
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Residues in contact with GLU 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 ASP* 2.9 22.9 + - - +
38B ASP 3.9 3.8 - - - +
40B ASN* 1.3 97.0 + - - +
42B THR* 1.3 56.9 + - - +
44B LYS* 3.8 28.1 + - - +
45B TYR* 2.9 27.5 + - - +
186B ARG* 3.6 31.9 + - + +
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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 ASP 2.1 31.7 + - - -
39B LEU* 3.7 6.5 - - - -
40B ASN 3.2 0.2 - - - -
41B GLU* 1.3 74.5 - - - +
43B ASN* 1.3 67.4 + - - +
45B TYR* 2.9 9.1 + - - +
46B TYR* 2.9 45.7 + - + +
185B PRO* 3.9 8.5 - - + -
186B ARG 4.0 7.1 + - - +
187B ILE* 3.1 48.9 + - - +
189B TYR* 4.3 4.0 - - + -
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Residues in contact with ASN 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 LEU 2.8 22.3 + - - +
40B ASN* 4.0 4.3 - - - +
42B THR* 1.3 73.1 - - - +
44B LYS* 1.3 57.8 + - - +
46B TYR* 2.9 31.5 + - - +
47B LEU* 2.9 13.5 + - - +
52B ALA 4.2 1.7 - - - +
54B ILE* 3.4 40.4 + - + +
55B HIS* 5.8 0.4 - - + -
89B TYR* 5.7 4.3 - - + -
189B TYR* 4.0 7.6 - - - +
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Residues in contact with LYS 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 ASN* 2.9 16.5 + - - +
41B GLU* 4.0 32.6 + - - +
43B ASN* 1.3 73.3 - - - +
45B TYR* 1.3 60.0 + - - +
47B LEU* 3.7 14.1 - - + +
48B THR* 2.9 40.2 + - - +
54B ILE 5.1 0.2 + - - -
55B HIS* 6.0 5.1 - - + +
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Residues in contact with TYR 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 GLU 2.9 16.6 + - - +
42B THR* 2.9 12.5 + - - +
44B LYS* 1.3 73.9 - - - +
46B TYR* 1.3 71.5 + + - +
47B LEU 3.0 0.2 + - - -
48B THR* 3.1 8.6 + - + -
49B ASN* 2.9 40.9 + - + +
184B ALA 3.9 20.6 - - - +
185B PRO* 4.4 12.8 - - + -
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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* 2.9 47.3 + - + +
43B ASN* 2.9 15.3 + - - +
45B TYR* 1.3 74.8 - + - +
47B LEU* 1.3 57.3 + - - +
49B ASN* 3.6 0.8 - - - -
50B GLN 2.9 6.9 + - - -
51B ILE* 2.7 48.9 + - + -
52B ALA* 3.1 24.0 + - + +
54B ILE* 5.7 0.7 - - + -
185B PRO* 4.0 11.1 - - + +
187B ILE 3.4 2.8 + - - -
188B ASP* 2.7 42.4 + - - -
189B TYR* 3.6 14.6 + + - -
190B ILE* 3.4 40.6 - - + +
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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 ASN 2.9 11.9 + - - +
44B LYS* 3.7 15.7 - - + +
46B TYR* 1.3 73.6 - - - +
48B THR* 1.3 68.0 + - - +
49B ASN 3.0 9.4 + - - -
50B GLN* 3.1 13.7 + - - +
52B ALA 3.2 13.0 + - - +
53B VAL* 4.5 15.0 - - + -
54B ILE 5.3 0.9 - - - +
55B HIS* 3.8 33.0 - - + +
123D HIS* 5.2 0.9 - - + -
126D GLN* 4.1 34.1 - - + +
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Residues in contact with THR 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 LYS* 2.9 33.1 + - + +
45B TYR* 3.6 6.7 - - - +
47B LEU* 1.3 82.8 - - - +
49B ASN* 1.3 76.1 + - - +
50B GLN 3.7 0.2 - - - -
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Residues in contact with ASN 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 TYR* 2.9 26.2 + - + +
46B TYR* 4.2 2.2 - - - +
48B THR* 1.3 101.9 - - - +
50B GLN* 1.3 67.6 + - - +
51B ILE* 3.2 6.2 + - + +
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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