Contacts of the helix formed by residues 35 - 49 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33C MET* 2.7 14.5 + - - +
34C THR* 1.3 74.5 - - - +
36C GLU* 1.3 65.2 + - - +
37C ASP 3.7 0.4 - - - -
38C ASP* 4.0 21.7 + - + -
39C LEU* 3.3 37.8 + - + +
89C TYR* 4.5 1.7 + - - -
102C ALA* 4.6 9.1 - - + +
103C LYS 3.5 15.0 - - - +
104C GLU* 3.4 30.5 - - + +
137C ILE* 4.4 12.3 - - + +
138C ILE 4.9 0.4 - - - -
139C SER* 3.6 25.6 - - - +
187C ILE* 5.4 7.9 - - + -
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Residues in contact with GLU 36 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34C THR* 3.0 25.9 + - + -
35C LEU* 1.3 81.1 - - - +
37C ASP* 1.3 63.7 + - - +
39C LEU* 4.1 1.0 - - - +
40C ASN* 3.0 32.1 + - - +
89C TYR* 4.3 7.4 + - - -
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Residues in contact with ASP 37 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33C MET 5.7 1.8 - - - +
34C THR* 4.6 3.0 - - - +
35C LEU* 4.6 0.6 - - - +
36C GLU* 1.3 77.5 - - - +
38C ASP* 1.3 68.0 + - - +
39C LEU 2.9 1.6 + - - -
40C ASN* 3.0 18.3 + - - +
41C GLU* 3.0 39.1 + - - +
186C ARG* 4.8 8.7 + - - -
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Residues in contact with ASP 38 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33C MET* 3.4 30.5 - - - +
35C LEU* 4.0 20.8 - - + -
36C GLU 3.4 0.2 - - - -
37C ASP* 1.3 79.7 - - - +
39C LEU* 1.3 57.4 + - - +
41C GLU* 4.2 3.7 - - - +
42C THR* 3.0 26.0 + - - -
186C ARG* 3.9 40.7 + - + +
187C ILE* 4.7 5.8 - - + +
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Residues in contact with LEU 39 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35C LEU* 3.3 26.7 + - + +
37C ASP 3.1 0.4 - - - -
38C ASP* 1.3 75.1 - - - +
40C ASN* 1.3 56.1 + - - +
41C GLU 2.9 4.3 - - - -
42C THR* 2.8 20.0 + - - -
43C ASN* 2.4 28.0 + - - +
89C TYR* 4.0 18.2 - - + +
100C PHE* 4.3 10.8 - - + -
102C ALA* 3.5 31.6 - - + -
137C ILE* 4.4 15.9 - - + -
187C ILE* 4.4 11.7 - - + -
189C TYR* 3.4 37.2 - - + -
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Residues in contact with ASN 40 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36C GLU* 3.0 26.9 + - - +
37C ASP* 3.0 30.6 + - - +
39C LEU* 1.3 76.1 - - - +
41C GLU* 1.3 55.3 + - - +
43C ASN* 3.4 17.5 - - + +
44C LYS* 4.0 15.8 + - - +
56C LYS* 5.6 5.8 - - + +
89C TYR* 4.9 11.7 + - + +
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Residues in contact with GLU 41 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37C ASP* 3.0 26.4 + - - +
38C ASP 4.2 3.1 - - - +
39C LEU 2.9 0.2 - - - -
40C ASN* 1.3 76.3 - - - +
42C THR* 1.3 68.1 + - - +
43C ASN 3.1 0.9 - - - -
44C LYS* 3.0 40.2 + - - +
45C TYR* 3.1 13.6 + - - +
184C ALA 4.8 8.3 - - - +
186C ARG* 4.1 32.2 + - - +
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Residues in contact with THR 42 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38C ASP 3.0 15.9 + - - -
39C LEU* 2.8 14.2 + - - -
41C GLU* 1.3 80.4 - - - +
43C ASN* 1.3 56.2 + - - +
45C TYR* 3.6 3.9 + - - +
46C TYR* 3.1 54.3 + - + -
185C PRO* 3.8 13.5 - - + -
186C ARG* 2.8 35.8 + - - +
187C ILE* 3.4 12.8 + - - +
189C TYR* 4.3 8.3 - - + -
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Residues in contact with ASN 43 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39C LEU* 2.4 42.4 + - - +
40C ASN* 3.4 13.6 - - + +
42C THR* 1.3 74.7 - - - +
44C LYS* 1.3 64.5 + - - +
46C TYR* 3.3 8.2 + - - +
47C LEU* 2.9 23.8 + - - +
52C ALA 4.7 1.0 - - - +
54C ILE* 3.3 42.3 + - + +
55C HIS* 5.8 1.7 - - - -
89C TYR* 4.3 12.0 - - - -
189C TYR* 2.6 28.2 + - - -
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Residues in contact with LYS 44 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40C ASN 4.0 11.0 + - - +
41C GLU* 3.0 39.8 + - - +
43C ASN* 1.3 72.7 - - - +
45C TYR* 1.3 68.7 + - - +
47C LEU* 2.8 20.6 + - + +
48C THR* 2.9 29.7 + - + +
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Residues in contact with TYR 45 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41C GLU* 3.1 12.6 + - - +
42C THR 3.7 8.5 - - - +
44C LYS* 1.3 77.6 - - - +
46C TYR* 1.3 83.2 + + - +
48C THR* 2.8 24.8 + - - -
49C ASN* 3.1 34.7 + - + +
51C ILE* 5.5 3.1 - - + -
184C ALA* 3.4 50.6 - - + +
185C PRO* 4.3 12.7 - - + +
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Residues in contact with TYR 46 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42C THR* 3.1 39.6 + - + -
43C ASN* 3.3 11.2 - - - +
44C LYS 3.1 0.2 - - - -
45C TYR* 1.3 90.8 - + - +
47C LEU* 1.3 62.3 + - - +
49C ASN 3.6 0.5 + - - -
50C GLN 3.2 1.0 + - - -
51C ILE* 3.0 43.9 + - + +
52C ALA 3.5 17.7 + - - +
54C ILE* 5.9 4.3 - - + +
185C PRO* 4.3 13.7 - - + -
188C ASP* 3.7 11.4 - - - -
189C TYR* 3.8 29.2 - + - -
190C ILE* 3.3 47.1 - - + -
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Residues in contact with LEU 47 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126A GLN* 4.4 28.7 - - - +
43C ASN 2.9 12.2 + - - +
44C LYS* 2.8 15.3 + - + +
46C TYR* 1.3 72.5 - - - +
48C THR* 1.3 58.9 + - + +
50C GLN* 2.6 44.9 + - - +
52C ALA 3.8 7.0 - - - +
53C VAL* 4.0 32.1 - - + -
54C ILE 5.9 1.1 - - - +
55C HIS* 3.7 28.5 - - + +
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Residues in contact with THR 48 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44C LYS* 2.9 37.3 + - + +
45C TYR* 2.8 16.3 + - - -
47C LEU* 1.3 75.1 - - + +
49C ASN* 1.3 71.5 + - - +
50C GLN* 3.6 6.8 + - - +
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Residues in contact with ASN 49 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45C TYR* 3.1 47.8 + - + +
46C TYR 4.3 1.6 - - - +
48C THR* 1.3 89.7 + - - +
50C GLN* 1.3 68.1 + - - +
51C ILE* 3.0 9.7 + - + +
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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