Contacts of the helix formed by residues 14 - 24 (chain C) in PDB entry 1TU8
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 ALA 14 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5C LEU* 4.3 10.5 - - + -
7C TYR* 3.3 40.6 - - + -
11C ARG 3.3 0.4 + - - -
12C GLY 3.3 1.2 - - - -
13C LEU* 1.3 78.7 - - - +
15C GLU* 1.3 64.4 + - - +
16C PRO 3.4 0.7 - - - -
17C ILE* 3.0 24.1 + - - +
18C ARG* 3.0 25.8 + - - +
51C PRO* 4.4 6.1 - - + -
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Residues in contact with GLU 15 (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* 3.1 29.1 + - + +
12C GLY 4.0 1.3 - - - +
13C LEU 3.4 0.4 - - - -
14C ALA* 1.3 76.7 - - - +
16C PRO* 1.3 63.5 - - + +
18C ARG* 2.8 33.2 + - - +
19C LEU* 2.9 35.9 + - + +
32C ARG* 5.0 1.6 + - - -
156C GLU* 3.3 37.5 - - - +
191C TYR* 2.6 28.6 + - - -
195C ARG* 2.9 23.5 + - - +
200C VAL* 5.7 0.4 - - - +
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Residues in contact with PRO 16 (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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12C GLY 4.1 4.3 - - - +
13C LEU* 3.6 14.6 - - - +
14C ALA 3.5 4.3 - - - -
15C GLU* 1.3 92.9 - - + +
17C ILE* 1.3 56.6 + - + +
19C LEU* 3.4 12.5 + - + +
20C PHE* 3.0 28.1 + - - +
67C LEU* 4.3 14.6 - - + +
152C TYR* 3.7 7.6 - - - +
153C ALA* 3.9 35.2 - - + +
156C GLU* 4.3 12.1 - - + -
157C GLU* 6.1 0.4 - - - +
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Residues in contact with ILE 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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5C LEU* 3.9 26.0 - - + -
13C LEU 4.3 9.0 - - - +
14C ALA* 3.0 9.7 + - - +
16C PRO* 1.3 75.2 - - + +
18C ARG* 1.3 64.0 + - - +
20C PHE* 3.3 6.9 + - - +
21C LEU* 3.1 35.7 + - + +
51C PRO* 4.4 7.4 - - + -
53C LEU* 5.4 0.4 - - + -
63C SER* 3.8 33.9 - - - +
66C ILE* 3.7 30.3 - - + -
67C LEU* 4.3 15.5 - - + -
70C LEU* 4.0 14.1 - - + -
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Residues in contact with ARG 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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5C LEU* 3.6 17.9 + - + +
7C TYR* 3.8 16.6 - - - +
8C PHE 3.3 24.2 + - - -
10C ILE 2.8 20.2 + - - -
11C ARG 3.4 10.1 + - - -
14C ALA* 3.0 19.3 + - - +
15C GLU* 2.8 35.4 + - - +
17C ILE* 1.3 75.2 - - - +
19C LEU* 1.3 58.4 + - - +
21C LEU* 3.3 2.5 + - - +
22C VAL* 2.9 35.8 + - - +
28C PHE* 4.1 18.8 - - + -
30C ASP* 2.9 29.5 + - - -
31C ASP 6.0 0.2 - - - -
32C ARG* 3.3 22.4 - - - +
191C TYR* 3.6 20.0 - - + +
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Residues in contact with LEU 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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15C GLU* 2.9 25.3 + - + +
16C PRO* 3.7 4.0 - - + +
18C ARG* 1.3 73.8 - - - +
20C PHE* 1.3 66.1 + - - +
22C VAL* 4.5 1.8 - - - -
23C ASP* 3.0 28.2 + - - +
152C TYR* 3.8 25.1 - - + +
155C PHE* 4.0 21.1 - - + -
156C GLU* 3.8 35.2 - - + +
188C LEU* 3.7 18.8 - - + +
191C TYR* 3.6 31.4 - - + -
192C CYS* 4.9 1.3 - - - -
195C ARG* 4.2 7.2 - - - +
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Residues in contact with PHE 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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16C PRO 3.0 14.3 + - - +
17C ILE 3.3 9.2 + - - +
19C LEU* 1.3 77.1 - - - +
21C LEU* 1.3 69.1 + - - +
23C ASP* 3.9 0.5 - - - -
24C GLN* 3.0 29.4 + - + +
26C ILE* 3.9 20.6 - - + -
67C LEU* 3.8 21.5 - - + -
70C LEU* 3.6 45.5 - - + -
71C ALA* 3.9 7.9 - - - -
74C TYR* 4.2 9.4 - + + -
76C LEU* 3.8 26.5 - - + -
149C TYR* 3.9 15.7 - - + -
152C TYR* 3.8 28.9 - + + -
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Residues in contact with LEU 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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3C TYR* 5.2 4.3 - - + -
5C LEU* 4.8 2.2 - - + -
17C ILE* 3.1 35.1 + - + +
18C ARG* 4.6 0.2 - - - -
20C PHE* 1.3 82.1 - - + +
22C VAL* 1.3 61.3 + - - +
24C GLN 3.4 0.5 + - - -
25C ASP 3.1 3.6 + - - -
26C ILE* 2.9 65.8 + - + +
28C PHE* 3.6 48.5 - - + -
53C LEU* 4.9 8.7 - - + -
70C LEU* 3.9 27.8 - - + -
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Residues in contact with VAL 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 ARG 2.9 21.3 + - - +
19C LEU* 4.0 4.7 - - - +
21C LEU* 1.3 76.3 - - - +
23C ASP* 1.3 61.8 + - - +
25C ASP* 3.1 14.3 + - - +
26C ILE 5.2 1.1 - - - -
28C PHE* 4.1 16.8 - - + -
187C LYS* 3.7 38.5 - - + +
188C LEU* 4.5 3.1 - - + -
191C TYR* 3.8 37.7 - - + -
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Residues in contact with ASP 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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19C LEU 3.0 19.3 + - - +
22C VAL* 1.3 78.3 - - - +
24C GLN* 1.3 62.3 + - - +
25C ASP 3.2 1.1 + - - -
152C TYR* 2.6 34.5 + - + +
185C ARG* 3.0 43.9 + - - +
186C PRO* 5.8 0.3 - - - +
187C LYS* 4.0 29.5 + - - +
188C LEU* 3.6 19.4 - - + +
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Residues in contact with GLN 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 PHE* 3.0 30.3 + - + +
23C ASP* 1.3 83.0 + - - +
25C ASP* 1.3 69.2 + - - +
26C ILE* 3.3 22.7 + - + +
74C TYR* 5.4 6.3 - - + +
76C LEU* 3.7 34.5 - - + +
147C ILE* 4.3 8.9 - - - +
152C TYR* 2.9 25.3 + - - +
185C ARG* 4.6 3.4 - - - +
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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
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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