Contacts of the helix formed by residues 31 - 46 (chain C) in PDB entry 3ESF
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 LYS 31 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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27C PHE* 2.9 41.9 + - + +
30C ASP* 1.3 88.0 - - + +
32C HIS* 1.3 58.6 + - + +
35C GLY* 2.9 27.4 + - - -
173D ASN* 3.4 46.1 - - + +
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Residues in contact with HIS 32 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27C PHE 3.3 11.2 + - - -
28C HIS* 3.3 14.9 + - + +
31C LYS* 1.3 74.4 - - - +
33C HIS* 1.3 66.7 + - - +
35C GLY* 3.6 0.9 - - - -
36C TYR* 3.0 38.4 + - + -
76C HIS* 5.0 0.4 - - - +
165C HIS* 3.3 51.9 + + + +
164D GLU* 3.8 10.5 + - - -
167D TYR* 5.9 1.3 - - - -
168D TYR* 2.7 31.9 + + - -
173D ASN* 3.5 26.9 - - + +
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Residues in contact with HIS 33 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5C ILE* 3.4 26.9 - - + +
6C PRO 5.4 0.4 - - - -
28C HIS* 2.8 16.5 + - - +
29C TYR* 3.4 20.9 - + + +
32C HIS* 1.3 70.8 - - - +
34C MET* 1.3 63.4 + - - +
36C TYR* 3.2 20.6 + + - +
37C VAL* 3.5 8.1 + - - +
72C GLN 4.6 0.2 - - - -
73C ILE* 3.4 21.4 + - + -
76C HIS* 3.5 31.5 - + + +
77C ASN* 2.9 32.5 + - - -
80C TRP* 3.0 26.4 + + - +
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Residues in contact with MET 34 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4C SER* 5.9 0.4 - - - -
5C ILE* 3.6 31.0 - - + -
29C TYR* 2.9 25.5 + - + +
30C ASP* 3.4 22.4 - - - +
33C HIS* 1.3 70.2 - - - +
35C GLY* 1.3 60.6 + - - +
37C VAL* 3.2 24.7 + - + +
38C THR* 2.9 42.6 + - - +
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Residues in contact with GLY 35 (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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30C ASP 4.4 0.4 + - - -
31C LYS 2.9 24.9 + - - -
32C HIS 3.6 2.0 - - - -
33C HIS 3.2 0.2 - - - -
34C MET* 1.3 76.7 - - - +
36C TYR* 1.3 61.1 + - - +
38C THR* 3.4 8.2 + - - -
39C LYS* 3.1 30.1 + - - +
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Residues in contact with TYR 36 (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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32C HIS* 3.0 32.0 + - + +
33C HIS* 3.2 12.4 + - - +
35C GLY* 1.3 75.3 - - - +
37C VAL* 1.3 53.0 - - - +
39C LYS* 3.2 5.2 + - + +
40C LEU* 2.8 35.9 + - - +
69C LEU* 3.9 30.0 - - + +
72C GLN* 3.3 51.5 + - + +
73C ILE* 3.7 17.9 - - + -
76C HIS* 3.7 18.6 - + - -
163C TRP* 4.1 16.6 - - - -
165C HIS* 4.2 7.8 - - - -
121D PHE* 4.0 15.5 - + - -
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Residues in contact with VAL 37 (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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3C PHE* 3.5 32.3 - - + +
4C SER* 4.1 4.9 - - - -
5C ILE* 3.4 32.1 - - + -
33C HIS 3.7 11.9 - - - +
34C MET* 3.4 31.2 - - + +
36C TYR* 1.3 77.9 - - - +
38C THR* 1.3 53.2 + - - +
40C LEU* 3.2 2.6 + - - +
41C ASN* 2.8 41.5 + - - +
73C ILE* 3.7 15.9 - - + +
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Residues in contact with THR 38 (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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34C MET* 2.9 27.7 + - - +
35C GLY* 3.6 8.7 - - - -
37C VAL* 1.3 76.0 - - - +
39C LYS* 1.3 60.9 + - + +
41C ASN* 3.5 8.1 + - - +
42C ALA* 3.1 26.8 + - + +
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Residues in contact with LYS 39 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35C GLY 3.1 21.9 + - - +
36C TYR* 3.7 4.7 - - + +
38C THR* 1.3 75.1 - - + +
40C LEU* 1.3 64.8 + - - +
42C ALA* 3.5 7.7 + - - +
43C ALA* 3.2 21.5 + - - +
69C LEU* 3.8 30.6 - - + +
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Residues in contact with LEU 40 (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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3C PHE* 3.6 40.6 - - + -
36C TYR 2.8 20.5 + - - +
37C VAL 3.6 4.3 - - - +
39C LYS* 1.3 70.7 - - - +
41C ASN* 1.3 60.2 + - - +
43C ALA* 3.1 5.6 + - + +
44C ALA* 2.8 28.7 + - - +
50C LEU* 4.4 10.8 - - + -
55C VAL* 4.7 1.6 - - + -
58C ILE* 4.3 10.1 - - + -
66C ILE* 4.1 27.1 - - + +
69C LEU* 3.6 19.0 - - + +
70C ALA* 4.4 9.0 - - + -
73C ILE* 3.5 25.1 - - + -
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Residues in contact with ASN 41 (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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1C MET* 4.5 5.0 - - + +
2C ALA* 3.0 29.9 + - - +
3C PHE* 3.1 35.8 + - - +
34C MET* 6.0 0.2 - - - +
37C VAL* 2.8 30.4 + - - +
38C THR* 3.7 7.6 - - - +
40C LEU* 1.3 73.4 - - - +
42C ALA* 1.3 57.2 + - - +
44C ALA* 3.6 4.8 - - - +
45C ASN* 2.9 29.1 + - - +
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Residues in contact with ALA 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 THR 3.1 15.0 + - - +
39C LYS* 3.8 10.1 - - - +
40C LEU 3.3 0.2 - - - -
41C ASN* 1.3 74.0 - - - +
43C ALA* 1.3 63.9 + - - +
45C ASN* 3.4 18.5 - - - +
46C SER* 3.8 7.6 + - - -
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Residues in contact with ALA 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 LYS 3.2 12.8 + - - +
40C LEU* 3.1 11.7 + - + +
42C ALA* 1.3 77.2 - - - +
44C ALA* 1.3 60.3 + - - +
46C SER* 3.7 8.3 + - - -
47C ASN* 3.7 17.5 + - - +
50C LEU* 4.0 17.0 - - + +
66C ILE* 4.2 18.6 - - + -
69C LEU* 5.1 1.8 - - + -
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Residues in contact with ALA 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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2C ALA* 3.8 17.9 - - + -
3C PHE* 4.0 7.4 - - + -
40C LEU 2.8 15.4 + - - +
41C ASN* 3.6 5.8 - - - +
42C ALA 3.3 0.2 - - - -
43C ALA* 1.3 73.2 - - - +
45C ASN* 1.3 63.3 + - - +
46C SER 3.2 2.7 - - - -
47C ASN 3.0 26.8 + - - +
48C PRO* 4.1 0.7 - - - +
50C LEU* 4.1 6.5 - - + +
51C ALA* 3.7 30.0 - - + +
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Residues in contact with ASN 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 ASN 2.9 13.8 + - - +
42C ALA* 3.4 17.5 - - - +
44C ALA* 1.3 76.3 - - - +
46C SER* 1.3 59.5 + - - +
47C ASN 3.8 0.2 + - - -
48C PRO* 5.4 1.9 - - - +
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Residues in contact with SER 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 ALA 3.8 11.8 + - - -
43C ALA* 3.7 5.4 + - - -
44C ALA 3.2 0.8 - - - -
45C ASN* 1.3 77.2 + - - +
47C ASN* 1.3 58.9 + - - +
48C PRO* 3.6 10.2 - - - +
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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