Contacts of the helix formed by residues 10 - 24 (chain G) 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 G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7G GLY 3.4 9.0 + - - -
8G ALA 3.4 1.6 - - - -
9G ALA* 1.3 81.7 - - - +
11G GLY* 1.3 65.5 + - - -
12G ILE 3.4 2.5 - - - -
13G GLY 3.9 1.6 - - - -
14G GLN* 3.0 23.2 + - - +
34G ASP* 3.8 3.8 + - - -
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Residues in contact with GLY 11 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10G GLY* 1.3 71.1 - - - +
12G ILE* 1.3 62.4 + - - +
14G GLN* 4.1 3.4 - - - +
15G ALA* 3.2 23.6 + - - +
224G THR* 3.7 24.5 - - - +
225G LEU* 5.1 2.3 - - - +
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Residues in contact with ILE 12 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10G GLY 3.4 0.6 - - - -
11G GLY* 1.3 74.0 - - - +
13G GLY* 1.3 59.1 + - - +
15G ALA* 3.2 3.8 + - - +
16G LEU* 2.9 33.2 + - + +
76G SER* 3.9 28.5 - - - +
117G ILE* 4.2 12.6 - - + -
223G ALA 3.9 8.5 - - - +
224G THR* 3.6 31.1 - - + +
227G MET* 3.8 32.5 - - + +
228G GLY* 3.9 8.8 - - - +
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Residues in contact with GLY 13 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5G VAL* 4.3 4.5 - - - +
7G GLY 3.6 21.4 + - - -
8G ALA* 3.4 13.3 - - - +
10G GLY 3.3 5.0 + - - -
11G GLY 3.3 0.8 - - - -
12G ILE* 1.3 78.7 - - - +
14G GLN* 1.3 56.4 + - - +
16G LEU* 3.8 5.3 - - - +
17G ALA* 2.9 30.5 + - - +
76G SER* 3.8 11.9 + - - -
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Residues in contact with GLN 14 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217E LYS* 5.5 2.9 + - - +
224E THR* 4.3 6.6 + - - -
225E LEU* 3.6 35.7 - - + +
8G ALA 3.2 16.2 - - - +
9G ALA* 3.1 20.4 + - - +
10G GLY 3.0 15.6 + - - +
11G GLY* 4.2 4.0 - - - +
13G GLY* 1.3 74.8 - - - +
15G ALA* 1.3 64.3 + - - +
17G ALA* 3.9 4.2 - - - +
18G LEU* 3.1 25.6 + - - +
38G VAL* 5.2 3.8 - - - +
42G VAL* 3.9 28.3 - - + +
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Residues in contact with ALA 15 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18E LEU* 3.8 23.4 - - + +
225E LEU* 5.7 0.9 - - - -
11G GLY 3.2 17.2 + - - +
12G ILE 3.7 3.4 - - - +
14G GLN* 1.3 75.9 - - - +
16G LEU* 1.3 56.4 + - - +
18G LEU* 3.6 5.1 + - - +
19G LEU* 3.2 35.1 + - - +
224G THR 4.0 11.2 - - - +
225G LEU* 3.8 20.2 - - + -
228G GLY* 4.0 7.4 - - - -
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Residues in contact with LEU 16 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5G VAL* 3.8 24.5 - - + -
12G ILE* 2.9 16.5 + - + +
13G GLY* 3.8 2.0 - - - +
15G ALA* 1.3 74.4 - - - +
17G ALA* 1.3 59.5 + - - +
19G LEU* 3.3 4.3 + - - +
20G LEU* 2.9 59.0 + - + +
74G LEU* 3.8 19.5 - - + -
76G SER* 4.3 7.2 - - - +
117G ILE* 4.0 26.2 - - + -
228G GLY* 3.9 14.3 - - - -
231G ALA* 3.9 4.5 - - + -
232G ALA* 3.8 28.3 - - - +
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Residues in contact with ALA 17 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5G VAL* 5.2 1.8 - - + +
8G ALA 5.2 0.9 - - - +
13G GLY 2.9 22.8 + - - +
14G GLN* 3.9 6.7 - - - +
16G LEU* 1.3 72.1 - - - +
18G LEU* 1.3 57.4 + - - +
20G LEU* 3.4 7.3 + - - -
21G LYS* 2.9 31.0 + - - +
30G LEU* 3.7 6.0 - - - +
32G LEU* 3.7 29.2 - - + -
42G VAL* 5.2 1.1 - - + -
46G LEU* 3.6 21.3 - - + +
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Residues in contact with LEU 18 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15E ALA* 3.9 32.8 - - + +
18E LEU* 4.5 11.7 - - + -
19E LEU* 4.1 22.6 - - + +
225E LEU* 3.7 24.7 - - + +
229E GLN* 3.5 25.6 - - - +
14G GLN 3.1 17.5 + - - +
15G ALA* 3.8 4.0 - - - +
16G LEU 3.3 0.2 - - - -
17G ALA* 1.3 76.5 - - - +
19G LEU* 1.3 61.3 + - - +
21G LYS* 3.5 12.3 - - - +
22G THR* 3.6 10.0 + - - +
46G LEU* 3.7 26.1 - - + +
49G ILE* 3.9 4.9 - - + -
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Residues in contact with LEU 19 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18E LEU* 4.1 21.8 - - + -
19E LEU* 4.1 21.3 - - + -
22E THR* 5.0 4.5 - - - +
15G ALA 3.2 19.2 + - - +
16G LEU 3.8 3.1 - - - +
18G LEU* 1.3 73.1 - - + +
20G LEU* 1.3 61.3 + - - +
22G THR* 3.3 6.2 + - - +
23G GLN* 2.8 55.3 + - - +
228G GLY 3.9 0.7 - - - +
229G GLN* 3.5 50.3 - - + +
232G ALA* 3.8 19.3 - - + -
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Residues in contact with LEU 20 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3G VAL* 4.4 5.8 - - + -
5G VAL* 3.9 19.1 - - + -
16G LEU* 2.9 45.7 + - + +
17G ALA 3.8 3.4 - - - +
19G LEU* 1.3 71.3 - - - +
21G LYS* 1.3 66.8 + - - +
23G GLN 4.4 0.2 - - - +
24G LEU* 2.9 48.5 + - + +
30G LEU* 3.8 17.0 - - + -
53G VAL* 4.3 0.3 - - - +
74G LEU* 4.3 11.0 - - + -
232G ALA* 4.1 25.1 - - + +
235G GLY 5.4 1.1 - - - -
236G LEU* 4.1 25.4 - - + +
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Residues in contact with LYS 21 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17G ALA 2.9 17.3 + - - +
18G LEU 3.5 8.5 - - - +
20G LEU* 1.3 76.5 - - - +
22G THR* 1.3 56.1 + - + +
30G LEU* 3.7 6.8 - - + +
46G LEU* 3.3 44.9 - - + +
47G SER* 4.1 5.1 + - - +
49G ILE* 3.1 27.8 + - + -
51G THR* 2.6 42.2 + - - +
53G VAL* 2.8 43.8 + - + +
55G ILE* 3.9 23.6 - - + -
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Residues in contact with THR 22 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19E LEU* 5.6 3.1 - - - +
23E GLN* 6.0 0.5 + - - -
229E GLN* 3.5 32.4 + - - +
18G LEU 3.6 10.0 + - - +
19G LEU* 3.3 10.4 + - - +
20G LEU 3.2 0.4 - - - -
21G LYS* 1.3 79.3 - - + +
23G GLN* 1.3 73.3 + - - +
24G LEU 3.7 4.3 - - - +
49G ILE* 3.7 26.7 - - + -
51G THR* 4.0 18.5 - - + +
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Residues in contact with GLN 23 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22E THR* 5.8 2.4 + - - -
23E GLN* 5.3 7.7 - - - +
19G LEU* 2.8 44.8 + - - +
22G THR* 1.3 85.4 + - - +
24G LEU* 1.3 68.1 + - - +
25G PRO* 3.7 2.1 - - - +
229G GLN* 5.1 10.5 + - - +
232G ALA* 5.5 0.7 - - - +
236G LEU* 3.4 38.5 - - + +
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Residues in contact with LEU 24 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3G VAL* 4.1 13.7 - - + -
20G LEU* 2.9 45.8 + - + +
22G THR 3.7 4.0 - - - +
23G GLN* 1.3 81.4 - - - +
25G PRO* 1.4 74.5 - - + +
26G SER 3.5 1.2 + - - -
28G SER* 3.7 20.0 - - - +
29G GLU 4.2 11.7 - - - +
30G LEU* 4.4 5.4 - - + -
53G VAL* 3.8 27.9 - - + +
235G GLY 5.4 0.4 - - - +
236G LEU* 3.7 17.4 - - + +
239G VAL* 4.0 26.0 - - + -
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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