Contacts of the helix formed by residues 37 - 57 (chain C) in PDB entry 1CUN
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 ASP 37 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35C GLY 3.6 0.4 - - - -
36C ARG* 1.3 83.8 + - - +
38C LEU* 1.3 65.4 + - - +
39C THR* 3.8 7.2 + - - -
40C GLY* 3.0 21.8 + - - -
41C VAL* 3.0 23.7 + - - +
115C GLN* 3.5 16.1 - - - +
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Residues in contact with LEU 38 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B GLN* 3.9 9.6 - - - +
13B ARG* 3.6 36.6 - - - +
37C ASP* 1.3 75.1 - - - +
39C THR* 1.3 64.1 + - - +
41C VAL* 3.2 2.0 + - + +
42C GLN* 2.9 44.3 + - - +
112C LEU* 3.5 31.2 - - + +
115C GLN* 3.8 27.5 + - + +
116C GLN* 3.6 16.2 - - + +
119C ALA* 4.3 11.8 - - + +
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Residues in contact with THR 39 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37C ASP* 3.4 7.8 + - - -
38C LEU* 1.3 79.8 - - - +
40C GLY* 1.3 57.5 + - - +
42C GLN* 3.3 15.5 + - - +
43C ASN* 2.9 49.6 + - - +
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Residues in contact with GLY 40 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35C GLY* 4.4 13.0 - - - -
36C ARG 4.9 0.9 - - - -
37C ASP* 3.0 21.0 + - - -
39C THR* 1.3 77.8 - - - +
41C VAL* 1.3 59.9 + - - +
43C ASN* 3.4 8.2 + - - +
44C LEU* 3.1 27.2 + - - +
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Residues in contact with VAL 41 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34C TYR 3.8 11.9 - - - +
35C GLY* 4.3 1.3 - - - -
37C ASP 3.0 17.4 + - - +
38C LEU* 3.8 3.8 - - - +
40C GLY* 1.3 71.4 - - - +
42C GLN* 1.3 61.9 + - - +
44C LEU* 3.0 5.9 + - - +
45C ARG* 2.8 33.5 + - + +
108C LEU* 3.5 30.1 - - + +
111C SER* 3.6 16.4 - - - +
112C LEU* 3.5 21.3 - - + +
115C GLN* 3.4 29.2 - - + -
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Residues in contact with GLN 42 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B GLN* 3.8 21.4 + - - -
14B ASP* 5.4 0.6 + - - -
38C LEU* 2.9 41.9 + - - +
39C THR* 3.6 16.5 + - - +
41C VAL* 1.3 77.0 - - - +
43C ASN* 1.3 60.7 + - - +
45C ARG* 3.3 8.5 + - - +
46C LYS* 3.0 41.2 + - - +
112C LEU* 4.1 17.0 - - + +
116C GLN* 5.2 0.2 - - - +
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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
----------------------------------------------------------
39C THR* 2.9 37.4 + - - +
40C GLY* 3.7 7.7 - - - +
42C GLN* 1.3 75.5 - - - +
44C LEU* 1.3 64.1 + - + +
46C LYS* 2.8 30.1 + - - +
47C LYS* 3.2 22.9 + - - +
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Residues in contact with LEU 44 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33C ASP* 3.6 28.0 - - + +
34C TYR* 3.5 9.2 - - - +
35C GLY* 3.3 32.8 - - - +
40C GLY 3.1 18.0 + - - +
41C VAL* 3.0 7.6 + - - +
43C ASN* 1.3 77.3 - - + +
45C ARG* 1.3 58.3 + - - +
47C LYS* 3.5 20.0 + - + +
48C HIS* 2.8 27.4 + - - +
104C ARG* 3.9 15.4 + - - +
108C LEU* 3.9 15.6 - - + +
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Residues in contact with ARG 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 VAL* 2.8 20.2 + - + +
42C GLN* 3.7 7.0 - - - +
43C ASN 3.2 0.4 - - - -
44C LEU* 1.3 76.3 - - - +
46C LYS* 1.3 66.7 + - - +
48C HIS* 3.0 6.6 + - - +
49C LYS* 2.8 61.9 + - + +
105C GLY 5.2 0.4 + - - -
108C LEU* 4.1 29.1 - - + +
109C GLU* 2.6 36.6 + - - +
112C LEU* 3.8 34.9 - - - +
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Residues in contact with LYS 46 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42C GLN* 3.0 33.4 + - - +
43C ASN* 2.8 34.2 + - - +
45C ARG* 1.3 74.3 - - - +
47C LYS* 1.3 64.6 + - - +
49C LYS* 3.0 22.5 + - - +
50C ARG* 3.2 21.0 + - - +
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Residues in contact with LYS 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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28C LEU* 5.9 9.4 - - - +
43C ASN 3.2 14.1 + - - +
44C LEU* 3.6 20.3 - - + +
45C ARG 3.1 0.2 - - - -
46C LYS* 1.3 81.3 - - - +
48C HIS* 1.3 63.8 + - - +
50C ARG* 3.1 48.5 + - - +
51C LEU* 3.2 12.5 + - + +
104C ARG* 6.3 0.2 - - - +
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Residues in contact with HIS 48 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29C VAL* 4.1 12.0 - - + +
44C LEU 2.8 18.6 + - - +
45C ARG* 3.0 6.0 + - - +
47C LYS* 1.3 77.4 - - - +
49C LYS* 1.3 58.2 + - + +
51C LEU* 3.2 14.7 + - + +
52C GLU* 3.0 64.0 + - + +
101C ALA* 3.0 33.7 + - + -
104C ARG* 4.0 23.4 + - + +
105C GLY* 3.4 22.4 - - - -
108C LEU* 3.8 13.9 - - + -
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Residues in contact with LYS 49 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45C ARG* 2.8 52.4 + - + +
46C LYS* 3.0 14.1 + - - +
48C HIS* 1.3 73.6 - - + +
50C ARG* 1.3 66.7 + - - +
52C GLU* 3.2 19.3 + - - +
53C ALA* 3.0 23.4 + - - +
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Residues in contact with ARG 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 LYS* 3.2 18.8 + - - +
47C LYS* 3.1 43.3 + - - +
49C LYS* 1.3 76.5 - - - +
51C LEU* 1.3 63.7 + - - +
53C ALA* 3.0 8.4 + - - +
54C GLU* 2.9 24.6 + - - +
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Residues in contact with LEU 51 (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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25C LYS* 5.0 13.5 - - + +
28C LEU* 4.7 26.2 - - + -
29C VAL* 4.6 19.3 - - + +
47C LYS* 3.2 9.5 + - + +
48C HIS* 3.2 19.0 + - + +
50C ARG* 1.3 80.1 - - - +
52C GLU* 1.3 59.6 + - - +
54C GLU* 3.3 18.4 - - - +
55C LEU* 3.1 49.7 + - + +
97C LEU* 5.9 1.1 - - + -
101C ALA* 4.4 13.7 - - + -
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Residues in contact with GLU 52 (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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48C HIS* 3.0 47.7 + - + +
49C LYS* 3.6 24.8 + - - +
50C ARG 3.1 0.4 - - - -
51C LEU* 1.3 78.9 - - + +
53C ALA* 1.3 64.7 + - - +
55C LEU* 3.5 9.3 + - + +
56C ALA* 3.2 19.4 + - - +
101C ALA* 4.6 6.6 - - + +
102C ALA* 5.1 5.5 - - - -
105C GLY* 4.7 4.3 - - - -
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Residues in contact with ALA 53 (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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49C LYS 3.0 13.0 + - - +
50C ARG* 3.6 9.6 - - - +
52C GLU* 1.3 76.7 - - - +
54C GLU* 1.3 57.7 + - - +
56C ALA* 3.1 10.4 + - - +
57C ALA* 2.9 28.6 + - - +
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Residues in contact with GLU 54 (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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21C TRP* 3.6 22.8 + - + -
25C LYS* 3.1 33.9 + - - -
50C ARG 2.9 11.7 + - - +
51C LEU* 3.3 21.7 - - - +
53C ALA* 1.3 72.8 - - - +
55C LEU* 1.3 69.2 + - + +
56C ALA 2.9 1.3 - - - -
57C ALA* 2.8 19.7 + - - +
58C HIS* 3.0 15.9 + - + +
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Residues in contact with LEU 55 (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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21C TRP* 3.5 26.7 - - + -
25C LYS* 4.5 7.9 - - + -
51C LEU* 3.1 37.0 + - + +
52C GLU* 3.9 9.0 - - + +
53C ALA 3.5 0.2 - - - -
54C GLU* 1.3 80.3 - - + +
56C ALA* 1.3 60.8 + - - +
58C HIS* 3.3 8.1 + - - +
59C GLU* 3.3 20.3 + - - +
94C TRP* 3.8 17.0 - - + -
97C LEU* 3.7 26.5 - - + -
98C LYS* 4.9 12.8 - - + -
101C ALA* 4.0 19.7 - - + -
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Residues in contact with ALA 56 (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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52C GLU 3.2 10.8 + - - +
53C ALA* 3.1 15.4 + - - +
54C GLU 2.9 0.8 - - - -
55C LEU* 1.3 76.2 - - - +
57C ALA* 1.3 55.4 + - - +
58C HIS 3.1 8.5 + - - -
59C GLU* 3.6 24.6 + - - +
60C PRO* 4.1 3.5 - - - +
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Residues in contact with ALA 57 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53C ALA 2.9 13.0 + - - +
54C GLU* 2.8 14.4 + - - +
56C ALA* 1.3 71.1 - - - +
58C HIS* 1.3 56.8 + - - +
59C GLU 3.6 0.4 - - - -
60C PRO* 4.2 8.4 - - - +
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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
------------------------------------------------------------
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