Contacts of the helix formed by residues 16 - 29 (chain C) in PDB entry 3U7U
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 16 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14C LEU* 3.3 4.7 - - + +
15C SER* 1.4 74.1 - - - +
17C LEU* 1.3 57.9 + - - +
18C GLU* 3.1 21.6 + - - +
19C GLN* 3.1 34.3 + - + +
20C GLN* 2.8 27.5 + - - +
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Residues in contact with LEU 17 (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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13C SER* 5.9 0.2 - - - +
14C LEU 4.2 9.6 - - - +
15C SER 3.2 13.6 + - - +
16C ASP* 1.3 70.6 + - - +
18C GLU* 1.4 60.0 + - - +
20C GLN* 3.5 5.9 + - + +
21C TYR* 3.1 25.8 + - - +
42C SER* 3.8 32.0 - - - +
43C ILE* 6.0 0.7 - - - +
44C GLU* 3.5 42.5 - - + +
68C GLN* 6.0 1.3 - - - +
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Residues in contact with GLU 18 (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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16C ASP* 3.1 12.5 + - - +
17C LEU* 1.4 74.3 - - - +
19C GLN* 1.4 56.4 + - - +
21C TYR* 3.2 6.1 + - - +
22C ARG* 2.8 60.9 + - - +
44C GLU* 5.1 0.2 - - - -
47C ARG* 3.4 42.2 + - - +
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Residues in contact with GLN 19 (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 LEU* 3.4 18.5 - - + +
16C ASP* 3.1 37.8 + - + +
18C GLU* 1.4 78.9 - - - +
20C GLN* 1.3 57.4 + - - +
22C ARG* 3.6 35.2 + - - +
23C ALA* 3.0 29.5 + - - +
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Residues in contact with GLN 20 (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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9C ASN* 5.9 1.4 + - - +
12C SER 4.9 0.6 + - - -
13C SER* 3.4 25.0 - - - +
14C LEU* 3.1 33.0 + - + +
16C ASP 2.8 12.8 + - - +
17C LEU* 3.5 13.9 - - + +
19C GLN* 1.3 76.1 - - - +
21C TYR* 1.4 62.5 + - - +
23C ALA* 3.3 7.5 + - - +
24C LEU* 3.1 22.6 + - - +
39C GLU 5.9 0.6 + - - -
41C THR* 2.8 38.4 + - - +
42C SER* 4.0 13.0 - - - +
43C ILE* 4.7 5.7 - - + +
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Residues in contact with TYR 21 (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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17C LEU 3.1 14.4 + - - +
18C GLU* 3.2 13.9 + - - +
20C GLN* 1.4 72.8 - - - +
22C ARG* 1.3 73.2 - - + +
24C LEU* 3.1 10.2 + - + +
25C ARG* 2.7 51.7 + - - +
43C ILE* 4.5 17.7 - - + +
44C GLU* 5.2 0.2 - - - +
47C ARG* 3.6 55.2 - - + +
48C ASP* 2.6 40.4 + - - +
49C LEU* 4.0 10.1 - - + -
51C PHE* 4.2 5.8 - + - -
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Residues in contact with ARG 22 (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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18C GLU* 2.8 49.3 + - - +
19C GLN* 3.6 31.3 + - - +
21C TYR* 1.3 79.4 - - + +
23C ALA* 1.4 56.1 + - - +
25C ARG* 3.5 9.1 + - + +
26C LYS* 2.9 27.6 + - - +
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Residues in contact with ALA 23 (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 LEU* 4.2 13.7 - - + -
19C GLN 3.0 20.5 + - - +
20C GLN* 3.4 9.2 - - - +
21C TYR 3.2 0.2 - - - -
22C ARG* 1.4 72.9 - - - +
24C LEU* 1.4 59.2 + - - +
26C LYS* 3.1 11.0 + - + +
27C TYR* 2.9 48.0 + - + -
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Residues in contact with LEU 24 (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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20C GLN* 3.1 14.9 + - - +
21C TYR* 3.1 11.0 + - + +
23C ALA* 1.4 73.7 - - - +
25C ARG* 1.3 62.3 + - - +
27C TYR* 3.3 1.1 + - - -
28C TYR* 3.1 48.2 + - + +
39C GLU 3.3 26.2 - - - +
40C ILE* 3.9 23.8 - - + -
43C ILE* 3.8 22.7 - - + -
49C LEU* 3.8 19.7 - - + -
51C PHE* 3.7 24.6 - - + -
52C LEU* 5.0 3.6 - - + -
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Residues in contact with ARG 25 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21C TYR* 2.7 49.7 + - + +
22C ARG* 3.6 12.3 - - - +
24C LEU* 1.3 78.4 - - - +
26C LYS* 1.3 62.1 + - - +
29C GLU* 3.1 61.8 + - - +
48C ASP* 3.5 21.2 + - - +
50C SER* 4.8 2.0 + - - -
51C PHE* 3.3 43.9 - - + +
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Residues in contact with LYS 26 (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 ARG 2.9 15.1 + - - +
23C ALA* 3.1 12.9 + - + +
25C ARG* 1.3 77.2 - - - +
27C TYR* 1.3 93.1 + - + +
28C TYR 3.6 0.2 + - - -
29C GLU* 4.4 5.6 + - - +
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Residues in contact with TYR 27 (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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4C CYS* 3.8 23.4 - - - +
5C ALA* 6.4 0.7 - - + -
6C GLY* 4.5 18.7 + - - -
7C THR* 3.8 31.5 - - + +
23C ALA* 2.9 35.0 + - + +
24C LEU* 3.9 3.4 - - - +
26C LYS* 1.3 111.6 + - + +
28C TYR* 1.3 75.4 + - + +
29C GLU 5.3 0.4 - - - +
31C CYS* 4.8 0.2 - - - +
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Residues in contact with TYR 28 (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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4C CYS* 4.3 2.2 - - - -
6C GLY* 3.7 16.4 - - - -
7C THR* 3.1 23.7 + - + -
24C LEU* 3.1 38.9 + - + +
27C TYR* 1.3 89.4 - - + +
29C GLU* 1.3 66.3 + - - +
30C ASN 3.6 0.7 + - - -
31C CYS* 3.5 20.1 + - + +
34C VAL* 3.8 21.3 - - + -
37C ASN 2.5 29.4 + - - -
38C LEU* 3.8 25.1 - - + -
39C GLU 3.2 23.4 + - - -
51C PHE* 4.3 6.7 - - + +
52C LEU* 4.5 15.0 - - + +
54C SER* 3.7 6.8 + - - -
55C VAL* 4.6 5.4 - - + +
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Residues in contact with GLU 29 (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 ARG* 3.1 57.7 + - - +
26C LYS* 4.4 5.0 + - - +
27C TYR 3.9 1.1 - - - +
28C TYR* 1.3 76.8 - - - +
30C ASN* 1.4 82.6 + - - +
31C CYS* 3.2 6.3 + - - +
51C PHE* 3.8 27.0 - - + +
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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