Contacts of the helix formed by residues 35 - 53 (chain C) in PDB entry 5EWL
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 35 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33C LEU* 4.6 0.3 - - - +
34C SER* 1.3 85.7 - - - +
36C LYS* 1.4 59.1 + - - +
37C LYS* 3.5 14.0 + - - +
38C HIS* 2.8 56.0 + - + +
39C GLU* 3.1 15.9 + - - +
66C THR* 3.6 7.3 - - - +
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Residues in contact with LYS 36 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35C THR* 1.4 72.5 - - - +
37C LYS* 1.4 62.4 + - + +
38C HIS 3.4 0.2 - - - -
39C GLU* 3.5 23.1 - - + +
40C GLN* 3.1 43.1 + - - +
43C ARG* 4.0 3.3 + - - +
66C THR* 4.0 3.7 - - + +
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Residues in contact with LYS 37 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35C THR* 3.1 13.2 - - - +
36C LYS* 1.4 81.2 - - - +
38C HIS* 1.3 61.4 + - + +
39C GLU 3.3 0.2 - - - -
40C GLN* 3.2 30.3 - - - +
41C ILE* 2.9 35.3 + - + +
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Residues in contact with HIS 38 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33C LEU* 3.6 12.5 - - + +
34C SER* 3.7 4.2 - - - -
35C THR* 2.8 44.2 + - + +
37C LYS* 1.3 73.6 - - + +
39C GLU* 1.4 55.5 + - - +
41C ILE* 3.0 23.7 + - + +
42C PHE 2.8 30.1 + - - -
298C GLU* 3.5 49.0 + - + +
299C SER* 4.1 8.5 + - - -
302C ILE* 3.6 17.3 - - + +
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Residues in contact with GLU 39 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33C LEU* 3.9 12.3 - - + +
35C THR 3.1 14.1 + - - +
36C LYS* 3.5 27.2 - - + +
38C HIS* 1.4 74.6 - - - +
40C GLN* 1.4 59.7 + - - +
42C PHE* 3.2 5.2 + - - +
43C ARG* 3.0 36.3 + - - +
64C SER* 2.7 49.0 + - - +
65C VAL* 3.3 15.7 + - - +
66C THR* 3.6 19.7 + - + +
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Residues in contact with GLN 40 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36C LYS* 3.1 37.0 + - - +
37C LYS* 3.2 37.1 - - - +
38C HIS 3.2 0.2 - - - -
39C GLU* 1.4 75.1 - - - +
41C ILE* 1.4 59.5 + - + +
43C ARG* 3.3 45.9 + - - +
44C GLU* 3.3 12.6 + - - +
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Residues in contact with ILE 41 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37C LYS* 2.9 23.1 + - + +
38C HIS* 3.4 21.3 - - + +
40C GLN* 1.4 76.4 - - + +
42C PHE* 1.4 55.1 + - - +
44C GLU* 3.4 7.7 + - - +
45C ALA* 3.0 27.7 + - + +
299C SER* 3.6 40.8 - - - +
302C ILE* 3.8 21.1 - - + -
303C SER* 5.0 4.3 - - - +
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Residues in contact with PHE 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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29C ILE* 3.4 39.0 - - + -
30C GLY 3.7 1.1 - - - -
31C ALA* 3.5 22.0 - - + -
33C LEU* 3.7 13.5 - - + -
38C HIS 2.8 15.4 + - - +
39C GLU 3.4 7.4 - - - +
41C ILE* 1.4 69.3 - - - +
43C ARG* 1.4 60.9 + - + +
45C ALA* 3.2 2.9 + - - +
46C VAL* 2.9 40.6 + - + +
62C ALA* 3.6 23.3 - - + -
63C THR 3.2 22.4 - - - -
64C SER* 3.8 18.6 - - - -
91C LEU* 3.9 10.5 - - + -
302C ILE* 3.7 11.9 - - + +
306C VAL* 3.8 23.6 - - + -
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Residues in contact with ARG 43 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36C LYS* 4.0 8.1 + - - +
39C GLU* 3.0 18.2 + - - +
40C GLN* 3.3 63.7 + - - +
42C PHE* 1.4 76.1 - - + +
44C GLU* 1.4 56.3 + - - +
46C VAL* 3.6 4.3 + - - +
47C ASN* 3.2 24.1 + - - +
62C ALA* 4.1 21.5 - - + +
64C SER* 5.7 1.7 + - - +
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Residues in contact with GLU 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 GLN 3.3 9.1 + - - +
41C ILE* 3.7 9.6 - - - +
42C PHE 3.2 0.6 - - - -
43C ARG* 1.4 74.8 - - - +
45C ALA* 1.4 56.5 + - - +
46C VAL 3.2 1.6 - - - -
47C ASN* 2.8 13.2 + - - +
48C GLN* 2.8 58.6 + - - +
51C LYS* 5.8 1.9 - - - +
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Residues in contact with ALA 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 ILE* 3.0 17.9 + - + +
42C PHE 3.6 3.8 - - - +
44C GLU* 1.4 76.3 + - - +
46C VAL* 1.4 61.7 + - - +
48C GLN* 3.3 8.6 + - - +
49C ALA* 3.2 17.8 + - - +
52C ARG* 4.0 3.3 + - - +
302C ILE* 4.2 10.1 - - + -
303C SER* 4.3 15.3 - - - +
306C VAL* 3.5 32.4 - - + +
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Residues in contact with VAL 46 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29C ILE* 5.0 9.2 - - + -
42C PHE* 2.9 39.1 + - + +
43C ARG 3.7 5.2 - - - +
45C ALA* 1.4 75.3 - - - +
47C ASN* 1.3 59.3 + - - +
49C ALA* 3.3 14.2 - - - +
50C ASN* 2.8 21.9 + - - +
60C LEU* 4.0 23.5 - - + +
61C GLN* 4.1 1.6 - - - -
62C ALA* 3.6 39.7 - - + +
306C VAL* 3.8 15.7 - - + -
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Residues in contact with ASN 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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43C ARG 3.2 13.0 + - - +
44C GLU* 2.8 18.9 + - - +
46C VAL* 1.3 73.8 - - - +
48C GLN* 1.4 52.3 + - - +
49C ALA 3.1 2.0 - - - -
50C ASN* 2.9 20.2 + - - +
51C LYS* 2.8 49.0 + - - +
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Residues in contact with GLN 48 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44C GLU* 2.8 37.2 + - - +
45C ALA* 3.3 11.6 + - - +
47C ASN* 1.4 71.8 - - - +
49C ALA* 1.4 55.0 + - - +
51C LYS* 3.3 38.8 - - + +
52C ARG* 3.0 52.7 + - - +
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Residues in contact with ALA 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 ALA 3.2 11.7 + - - +
46C VAL* 3.3 14.4 - - - +
48C GLN* 1.4 71.4 - - - +
50C ASN* 1.3 59.0 + - - +
52C ARG* 3.2 18.8 + - - +
53C HIS* 2.9 36.8 + - - +
60C LEU* 4.0 10.5 - - + -
306C VAL* 4.5 2.9 - - + -
310C ALA* 3.6 30.3 - - + -
314C HIS* 5.8 0.2 - - - -
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Residues in contact with ASN 50 (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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46C VAL* 2.8 27.1 + - - +
47C ASN* 2.9 23.7 + - - +
49C ALA* 1.3 74.6 - - - +
51C LYS* 1.3 63.1 + - - +
53C HIS* 3.1 12.7 - - - +
55C THR* 2.8 39.5 + - + +
59C GLN* 3.5 14.9 - - - +
60C LEU* 3.0 45.5 + - - +
314C HIS* 5.6 3.1 - - - -
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Residues in contact with LYS 51 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44C GLU* 5.8 1.8 - - - +
47C ASN* 2.8 33.2 + - - +
48C GLN* 3.3 38.7 - - + +
50C ASN* 1.3 74.9 - - - +
52C ARG* 1.4 60.6 + - + +
53C HIS 3.9 3.3 - - - +
55C THR* 5.1 0.2 + - - -
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Residues in contact with ARG 52 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45C ALA* 4.0 7.5 + - - +
48C GLN* 3.0 29.0 + - - +
49C ALA* 3.2 31.4 + - - +
51C LYS* 1.4 74.2 - - - +
53C HIS* 1.3 85.8 + - + +
303C SER 5.5 0.8 + - - -
306C VAL* 5.2 0.2 - - - +
307C ALA* 3.8 38.0 + - - +
351C TYR* 4.5 18.7 + - - -
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Residues in contact with HIS 53 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49C ALA* 2.9 31.4 + - - +
50C ASN* 3.1 16.7 - - - +
51C LYS 3.9 3.3 - - - +
52C ARG* 1.3 105.9 + - + +
54C PHE* 1.4 64.3 + - - +
55C THR* 3.2 4.6 + - - -
307C ALA 4.8 0.2 + - - -
310C ALA* 3.9 11.4 - - + +
311C GLN* 3.9 25.5 + - + +
314C HIS* 3.3 42.8 + + + +
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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
------------------------------------------------------------
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