Contacts of the helix formed by residues 10 - 24 (chain C) in PDB entry 2PWZ
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 GLY 10 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7C GLY 3.4 9.9 + - - -
8C ALA 3.3 1.6 - - - -
9C ALA* 1.3 83.4 - - - +
11C GLY* 1.3 60.1 + - - -
12C ILE 3.4 2.7 - - - -
13C GLY 3.8 1.6 - - - -
14C GLN* 3.0 28.4 + - - +
34C ASP* 3.8 4.7 + - - -
76C SER 6.1 0.2 - - - -
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Residues in contact with GLY 11 (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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10C GLY* 1.3 72.3 - - - +
12C ILE* 1.3 60.6 + - - +
14C GLN* 4.4 2.8 - - - +
15C ALA* 3.5 20.6 + - - +
224C THR* 3.7 25.4 - - - -
225C LEU* 4.9 3.1 - - - +
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Residues in contact with ILE 12 (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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10C GLY* 3.4 0.6 - - - -
11C GLY* 1.3 72.6 - - - +
13C GLY* 1.3 60.2 + - - +
15C ALA* 3.5 1.7 + - - +
16C LEU* 3.0 30.7 + - + +
76C SER* 3.8 30.3 - - - +
117C ILE* 4.3 15.9 - - + -
222C SER* 5.9 1.6 - - - +
223C ALA 3.7 22.4 - - - +
224C THR* 3.7 16.4 - - + +
227C MET* 3.8 29.8 - - + +
228C GLY* 4.0 10.8 - - - +
231C ALA* 5.3 0.2 - - + -
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Residues in contact with GLY 13 (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 VAL* 4.3 6.2 - - - +
7C GLY 3.5 23.0 + - - -
8C ALA* 3.3 12.0 - - - +
10C GLY 3.3 5.8 + - - -
12C ILE* 1.3 79.0 - - - +
14C GLN* 1.3 56.8 + - - +
16C LEU* 3.5 5.3 + - - +
17C ALA* 2.9 30.3 + - - +
76C SER* 3.9 9.1 + - - -
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Residues in contact with GLN 14 (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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217A LYS* 4.9 6.2 + - - +
224A THR* 4.4 6.8 + - - -
225A LEU* 3.8 36.5 - - + +
8C ALA 3.3 15.9 - - - +
9C ALA* 2.9 24.0 + - - +
10C GLY 3.0 15.4 + - - +
11C GLY* 4.4 3.6 - - - +
13C GLY* 1.3 74.4 - - - +
15C ALA* 1.3 57.9 + - - +
17C ALA* 3.3 5.0 + - - +
18C LEU* 2.9 31.8 + - - +
38C VAL* 5.1 4.0 - - - +
42C VAL* 4.0 23.8 - - + +
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Residues in contact with ALA 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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18A LEU* 3.9 23.5 - - + +
225A LEU* 5.3 0.8 - - - +
11C GLY 3.5 16.9 + - - +
12C ILE 3.7 4.0 - - - +
14C GLN* 1.3 76.3 - - - +
16C LEU* 1.3 58.9 + - - +
18C LEU* 3.4 6.4 + - - +
19C LEU* 3.0 35.5 + - - +
224C THR 4.0 14.1 - - - +
225C LEU* 4.1 13.2 - - + -
228C GLY* 4.0 7.2 - - - -
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Residues in contact with LEU 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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5C VAL* 3.8 28.7 - - + -
12C ILE* 3.0 20.3 + - + +
13C GLY 3.6 2.9 - - - +
15C ALA* 1.3 77.6 - - - +
17C ALA* 1.3 56.7 + - - +
19C LEU* 3.2 2.6 + - - +
20C LEU* 2.8 52.0 + - + +
74C LEU* 4.2 10.5 - - + +
76C SER* 4.7 4.7 - - - +
117C ILE* 4.2 25.1 - - + -
228C GLY* 3.8 13.0 - - - +
231C ALA* 3.9 7.2 - - + +
232C ALA* 3.6 31.6 - - - +
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Residues in contact with ALA 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 VAL* 5.1 2.2 - - + -
8C ALA 5.2 0.7 - - - +
13C GLY 2.9 19.1 + - - +
14C GLN* 3.8 5.4 - - - +
16C LEU* 1.3 77.2 - - - +
18C LEU* 1.3 56.9 + - - +
20C LEU* 4.4 2.2 - - - -
21C LYS* 2.9 30.8 + - - +
30C LEU* 3.6 11.6 - - - +
32C LEU* 3.7 34.1 - - + -
42C VAL* 5.3 0.2 - - + -
46C LEU* 3.7 16.8 - - + +
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Residues in contact with LEU 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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15A ALA* 4.0 29.8 - - + +
18A LEU* 4.5 12.1 - - + -
19A LEU* 4.2 33.7 - - + -
225A LEU* 3.9 27.1 - - + +
229A GLN* 4.5 1.8 - - + -
14C GLN 2.9 18.1 + - - +
15C ALA* 3.6 4.5 - - - +
17C ALA* 1.3 75.1 - - - +
19C LEU* 1.3 63.4 + - + +
21C LYS* 3.4 1.2 + - - +
22C THR* 3.1 29.0 + - + +
46C LEU* 3.8 15.4 - - + +
49C ILE* 4.0 19.3 - - + -
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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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18A LEU* 4.1 17.9 - - + -
19A LEU* 4.1 25.4 - - + -
22A THR* 5.1 4.7 - - - +
15C ALA 3.0 20.5 + - - +
16C LEU 3.9 2.9 - - - +
18C LEU* 1.3 76.3 - - + +
20C LEU* 1.3 59.0 + - - +
22C THR* 3.4 4.0 + - - +
23C GLN* 2.9 55.0 + - - +
228C GLY 3.9 3.8 - - - +
229C GLN* 3.5 55.9 - - - +
232C ALA* 3.9 14.1 - - + -
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Residues in contact with LEU 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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3C VAL* 4.3 4.7 - - + -
5C VAL* 4.0 18.6 - - + -
16C LEU* 2.8 38.9 + - + +
19C LEU* 1.3 74.5 - - - +
21C LYS* 1.3 60.5 + - - +
23C GLN* 4.8 0.2 - - - -
24C LEU* 2.9 51.9 + - + +
30C LEU* 3.8 20.4 - - + -
53C VAL* 4.4 0.2 - - - +
74C LEU* 4.2 12.3 - - + -
232C ALA* 4.2 20.0 - - + +
235C GLY 5.3 2.0 - - - -
236C LEU* 4.0 32.5 - - + +
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Residues in contact with LYS 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 ALA 2.9 20.0 + - - +
18C LEU 3.8 5.2 - - - +
19C LEU 3.4 0.2 - - - -
20C LEU* 1.3 76.7 - - - +
22C THR* 1.3 55.5 + - + +
30C LEU* 3.7 8.7 - - + +
46C LEU* 2.9 44.2 - - + +
47C SER* 4.1 4.5 + - - +
49C ILE* 3.1 30.6 + - + -
51C THR* 2.8 48.4 + - - +
53C VAL* 2.9 46.7 + - + +
55C ILE* 4.0 16.8 - - + +
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Residues in contact with THR 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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19A LEU* 5.2 5.9 - - - +
23A GLN* 5.8 1.6 + - - -
229A GLN* 3.4 27.2 + - - +
18C LEU* 3.1 19.4 + - + +
19C LEU* 3.4 8.8 + - - +
21C LYS* 1.3 77.7 - - + +
23C GLN* 1.3 66.1 + - - +
24C LEU 4.8 2.3 - - - +
49C ILE* 3.8 33.0 - - + -
51C THR* 4.0 14.8 - - + +
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Residues in contact with GLN 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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22A THR* 5.8 2.4 + - - -
23A GLN* 6.0 1.6 - - - +
19C LEU* 2.9 45.2 + - - +
22C THR* 1.3 85.7 + - - +
24C LEU* 1.3 67.0 + - - +
25C PRO* 3.7 1.7 - - - +
229C GLN* 4.5 12.1 + - - +
232C ALA* 5.4 1.4 - - - +
236C LEU* 3.4 37.9 - - + +
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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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1C MET* 6.3 0.4 - - + -
3C VAL* 4.0 25.1 - - + -
20C LEU* 2.9 45.6 + - + +
21C LYS 4.6 0.4 + - - -
22C THR 4.8 1.7 - - - +
23C GLN* 1.3 81.9 + - - +
25C PRO* 1.4 77.5 - - + +
26C SER 3.8 0.5 + - - -
28C SER* 3.8 18.8 - - - +
29C GLU 4.5 1.8 - - - +
30C LEU* 4.3 15.5 - - + -
53C VAL* 3.8 27.9 - - + +
235C GLY 5.8 0.2 - - - -
236C LEU* 3.8 19.5 - - + +
239C VAL* 4.0 13.5 - - + -
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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