Contacts of the helix formed by residues 44 - 64 (chain C) in PDB entry 3H90
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 VAL 44 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40C LEU 5.5 0.7 - - - +
41C ALA* 3.1 12.5 + - - +
43C LEU* 1.3 96.1 - - + +
45C ASP* 1.3 56.1 + - - +
46C SER 3.1 1.6 - - - -
47C LEU* 3.4 13.9 - - + -
48C VAL* 2.7 43.8 + - + +
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Residues in contact with ASP 45 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41C ALA 3.8 3.5 + - - +
42C ALA* 4.4 17.6 - - + +
44C VAL* 1.3 78.6 - - - +
46C SER* 1.3 56.7 + - - +
48C VAL* 3.5 10.6 - - - +
49C ASP* 2.9 26.4 + - - +
153C HIS* 3.8 9.4 - - - -
157C ASP* 3.9 8.1 - - - +
291C ZN 2.9 22.8 - - - -
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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
----------------------------------------------------------
24C LEU* 3.2 31.6 - - - +
27C LYS* 4.3 20.1 + - - +
28C ILE* 3.7 19.1 + - - +
31C TRP* 6.0 0.2 - - - +
42C ALA 3.6 18.3 + - - -
43C LEU* 3.6 9.8 + - - -
44C VAL 3.1 1.4 - - - +
45C ASP* 1.3 76.3 - - - +
47C LEU* 1.3 61.4 + - - +
49C ASP* 3.8 11.9 - - - -
50C ILE* 3.6 12.8 + - - +
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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
----------------------------------------------------------
28C ILE* 4.1 20.6 - - + -
43C LEU* 3.4 21.1 + - + +
44C VAL* 2.9 19.8 + - + +
46C SER* 1.3 76.2 - - - +
48C VAL* 1.3 66.0 + - - +
49C ASP 3.3 0.2 - - - -
50C ILE* 3.5 15.5 + - + +
51C GLY* 3.5 14.2 + - - -
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Residues in contact with VAL 48 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44C VAL* 2.7 32.5 + - + +
45C ASP* 3.5 11.7 - - - +
47C LEU* 1.3 72.3 - - - +
49C ASP* 1.3 62.1 + - - +
51C GLY* 3.1 3.5 + - - -
52C ALA* 2.8 36.9 + - + +
153C HIS* 6.4 0.9 - - + -
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Residues in contact with ASP 49 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24C LEU* 3.7 26.7 - - + +
45C ASP* 2.9 16.2 + - - +
46C SER* 3.8 5.5 - - - +
47C LEU 3.3 0.4 - - - -
48C VAL* 1.3 79.0 - - - +
50C ILE* 1.3 63.5 + - - +
52C ALA* 4.5 4.9 - - - +
53C SER* 2.6 33.2 + - - -
153C HIS* 2.8 25.5 + - - -
154C TYR* 3.3 18.0 - - - +
157C ASP* 3.1 5.9 - - - +
291C ZN 2.4 26.3 - - - -
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Residues in contact with ILE 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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22C LEU* 4.3 2.7 - - - +
24C LEU* 3.7 19.7 - - + +
25C LEU* 3.8 40.6 - - + -
28C ILE* 3.7 37.9 - - + -
46C SER 3.6 8.4 + - - +
47C LEU* 3.5 18.0 + - + +
48C VAL 3.3 0.4 - - - -
49C ASP* 1.3 76.5 - - - +
51C GLY* 1.3 59.9 + - - +
54C LEU* 2.8 46.1 + - + +
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Residues in contact with GLY 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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47C LEU 3.5 5.9 + - - -
48C VAL* 3.1 5.4 + - - -
50C ILE* 1.3 79.7 - - - +
52C ALA* 1.3 64.3 + - - +
54C LEU* 3.0 9.6 + - - +
55C THR* 2.8 29.1 + - - -
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Residues in contact with ALA 52 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48C VAL* 2.8 30.6 + - + +
49C ASP* 4.0 4.7 - - - +
51C GLY* 1.3 70.6 - - - +
53C SER* 1.3 59.6 + - - +
55C THR* 3.1 9.9 - - - -
56C ASN* 2.9 24.0 + - - +
86C GLN* 5.6 6.4 - - + +
150C ASP* 6.0 0.4 - - - +
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Residues in contact with SER 53 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18C ALA* 4.1 3.5 - - - +
21C SER* 2.6 21.7 + - - -
22C LEU* 3.7 10.4 - - - +
49C ASP* 2.6 26.5 + - - -
52C ALA* 1.3 72.6 - - - +
54C LEU* 1.3 58.7 + - - +
56C ASN* 3.6 9.9 + - - +
57C LEU* 3.1 19.9 + - - +
86C GLN* 5.6 0.2 - - - -
150C ASP* 3.2 26.4 + - - +
153C HIS* 6.0 0.7 - - - -
154C TYR* 2.7 18.4 + - - -
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Residues in contact with LEU 54 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22C LEU* 3.7 28.9 - - + +
50C ILE* 2.8 33.6 + - + +
51C GLY* 3.4 6.5 - - - +
53C SER* 1.3 76.0 - - - +
55C THR* 1.3 65.3 + - - +
57C LEU* 3.1 24.9 + - + +
58C LEU* 3.1 25.3 + - + +
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Residues in contact with THR 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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51C GLY 2.8 16.7 + - - -
52C ALA* 3.1 10.8 + - - -
54C LEU* 1.3 74.0 - - - +
56C ASN* 1.3 59.2 + - - +
58C LEU* 2.9 20.7 + - + +
59C VAL* 2.9 42.2 + - + +
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Residues in contact with ASN 56 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18C ALA* 5.2 4.2 - - - +
52C ALA 2.9 13.5 + - - +
53C SER* 3.6 13.4 + - - +
54C LEU 3.2 0.2 - - - -
55C THR* 1.3 75.1 - - - +
57C LEU* 1.3 55.8 + - - +
59C VAL* 3.3 6.0 + - - +
60C VAL* 3.0 46.5 + - - +
82C ALA* 3.9 17.3 - - - +
86C GLN* 3.4 23.8 + - - +
146C ALA* 3.9 8.9 + - - +
147C VAL* 5.0 2.4 - - - +
150C ASP* 3.2 37.8 + - - +
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Residues in contact with LEU 57 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15C ALA* 4.4 2.5 - - + +
18C ALA* 3.5 35.4 - - + +
19C MET* 4.2 16.8 - - + -
22C LEU* 3.7 26.5 - - + -
53C SER 3.1 12.2 + - - +
54C LEU* 3.1 20.7 + - + +
56C ASN* 1.3 74.2 - - - +
58C LEU* 1.3 62.8 + - + +
60C VAL* 3.3 8.4 - - + +
61C ARG* 3.0 63.6 + - - +
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Residues in contact with LEU 58 (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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54C LEU* 3.1 30.6 + - + +
55C THR* 2.9 18.5 + - + +
57C LEU* 1.3 78.3 - - + +
59C VAL* 1.3 59.4 + - + +
61C ARG* 3.2 14.2 + - - +
62C TYR* 2.9 27.4 + - - +
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Residues in contact with VAL 59 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55C THR* 2.9 33.7 + - + +
56C ASN* 3.3 8.7 + - - +
58C LEU* 1.3 76.4 - - + +
60C VAL* 1.3 58.5 + - + +
62C TYR* 3.3 9.9 + - + +
63C SER* 2.8 24.8 + - - -
78C ALA* 3.6 31.7 - - + +
79C GLU* 5.3 0.4 - - - -
81C LEU* 5.9 0.7 - - + -
82C ALA* 3.6 19.7 - - + -
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Residues in contact with VAL 60 (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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14C ILE* 3.7 29.2 - - + +
15C ALA* 4.5 7.6 - - + -
18C ALA* 4.5 13.9 - - + -
56C ASN* 3.0 31.8 + - - +
57C LEU* 3.3 17.0 - - + +
59C VAL* 1.3 73.3 - - + +
61C ARG* 1.3 66.0 + - + +
63C SER* 2.8 24.3 + - - -
64C LEU* 2.8 25.6 + - + +
79C GLU* 5.2 0.9 - - + +
146C ALA* 4.0 20.2 - - + -
147C VAL* 5.3 4.3 - - + -
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Residues in contact with ARG 61 (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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15C ALA* 5.2 7.9 - - - +
19C MET* 3.4 29.3 - - - +
57C LEU* 3.0 43.5 + - + +
58C LEU* 3.2 14.9 + - + +
60C VAL* 1.3 80.9 - - + +
62C TYR* 1.3 59.6 + - - +
64C LEU* 3.6 14.4 + - - +
65C GLN* 3.7 13.9 + - - +
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Residues in contact with TYR 62 (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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203A GLN* 4.6 1.0 + - - -
206A LEU* 4.2 24.1 - - + +
58C LEU 2.9 13.1 + - - +
59C VAL* 3.4 11.4 - - + +
60C VAL 3.1 0.2 - - - -
61C ARG* 1.3 72.8 - - - +
63C SER* 1.3 68.2 + - - +
64C LEU 3.2 0.5 + - - -
65C GLN* 3.1 48.6 + - - +
71C HIS* 3.0 34.5 + - - -
75C HIS* 3.2 35.2 - + + +
78C ALA* 4.0 14.8 - - + -
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Residues in contact with SER 63 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14C ILE* 5.4 0.2 - - - +
59C VAL 2.8 14.7 + - - -
60C VAL* 2.8 17.9 + - - -
62C TYR* 1.3 77.1 - - - +
64C LEU* 1.3 63.3 + - - +
65C GLN 3.5 2.4 + - - +
75C HIS* 3.5 28.6 + - - +
76C GLY* 3.8 9.5 + - - -
78C ALA* 3.8 13.7 - - - -
79C GLU* 3.4 31.1 + - - +
241C PRO* 5.4 1.7 - - - +
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Residues in contact with LEU 64 (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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11C ARG* 4.7 23.3 - - + +
12C ALA* 5.7 1.6 - - - +
14C ILE* 4.0 28.5 - - + -
15C ALA* 5.0 9.4 - - + -
60C VAL* 2.8 35.3 + - + +
61C ARG* 4.1 10.3 - - - +
62C TYR 3.1 0.8 - - - -
63C SER* 1.3 83.1 - - - +
65C GLN* 1.3 65.3 + - - +
66C PRO* 3.6 4.5 - - - +
79C GLU* 5.2 1.1 - - - +
241C PRO* 5.2 13.2 - - + -
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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
------------------------------------------------------------
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