Contacts of the helix formed by residues 18 - 31 (chain B) in PDB entry 3ASZ
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 18 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16B ALA* 3.3 4.6 - - - +
17B SER* 1.3 78.0 - - - +
19B LYS* 1.3 60.3 + - - +
20B THR* 3.2 4.0 - - - +
21B THR* 3.3 11.2 + - - -
22B LEU* 2.9 31.4 + - - +
131B VAL* 4.0 7.0 - - - -
141B ARG* 5.4 3.8 - - - -
187B GLY 3.7 4.6 - - - +
188B GLY* 4.4 13.9 - - - -
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Residues in contact with LYS 19 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11B ILE* 4.0 12.5 - - + +
12B ALA 4.1 4.9 - - - +
13B GLY 3.7 15.7 - - - +
14B GLY 3.9 7.2 - - - +
15B THR* 4.7 0.2 - - - +
16B ALA 5.1 1.7 - - - +
17B SER* 3.3 15.2 + - - +
18B GLY* 1.3 79.3 - - - +
20B THR* 1.3 71.6 + - - +
22B LEU* 4.5 0.7 - - - -
23B ALA* 3.0 31.0 + - - +
40B ASP* 3.8 4.4 + - - -
111B GLU* 2.7 28.8 + - - +
112B GLY 3.8 11.4 - - - +
113B ILE* 3.6 33.0 - - - +
131B VAL* 3.7 22.6 - - + +
212B C5P 3.7 20.4 + - - -
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Residues in contact with THR 20 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B GLY 3.2 0.6 - - - -
19B LYS* 1.3 101.0 + - - +
21B THR* 1.3 62.1 + - - +
23B ALA* 3.4 0.9 + - - +
24B GLN* 2.9 56.2 + - + +
111B GLU* 3.8 17.0 + - - +
145B ARG* 5.6 1.0 + - - -
212B C5P 4.8 5.7 + - - -
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Residues in contact with THR 21 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18B GLY* 3.3 13.6 + - - -
20B THR* 1.3 80.5 - - - +
22B LEU* 1.3 55.4 + - - +
24B GLN* 3.8 7.4 - - - +
25B ALA* 2.9 31.2 + - + +
28B ARG* 4.9 4.2 + - - +
187B GLY 4.5 0.2 - - - +
188B GLY* 3.8 32.5 - - - +
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Residues in contact with LEU 22 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B ILE* 4.6 8.3 - - + -
18B GLY 2.9 17.6 + - - +
19B LYS 4.0 3.6 - - - +
21B THR* 1.3 76.5 - - - +
23B ALA* 1.3 57.4 + - - +
25B ALA* 3.2 6.1 + - + +
26B LEU* 2.9 32.0 + - + +
129B VAL* 4.6 4.7 - - + -
131B VAL* 3.8 24.0 - - + -
184B VAL* 4.0 23.1 - - + -
187B GLY* 3.6 17.6 + - - +
190B ASN* 5.1 4.0 - - + +
194B LEU* 4.4 29.6 - - + +
197B LEU* 4.0 27.4 - - + -
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Residues in contact with ALA 23 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B ILE* 3.9 20.6 - - + +
19B LYS 3.0 19.8 + - - +
20B THR* 3.8 3.1 - - - +
22B LEU* 1.3 75.7 - - - +
24B GLN* 1.3 59.4 + - + +
26B LEU* 3.3 4.5 + - - +
27B ALA* 2.9 28.6 + - - +
36B LEU* 4.0 16.3 - - + +
109B ILE* 4.0 6.4 - - + +
111B GLU* 3.8 25.4 - - + +
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Residues in contact with GLN 24 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20B THR* 2.9 42.0 + - + +
21B THR* 3.9 5.3 - - - +
23B ALA* 1.3 72.2 - - - +
25B ALA* 1.3 61.6 + - - +
27B ALA* 3.2 3.8 + - - +
28B ARG* 2.9 42.5 + - - +
36B LEU* 3.9 21.8 - - + +
38B PRO* 6.3 0.8 - - - +
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Residues in contact with ALA 25 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21B THR* 2.9 21.5 + - + +
22B LEU* 3.2 6.7 + - + +
24B GLN* 1.3 76.1 - - - +
26B LEU* 1.3 56.8 + - - +
28B ARG* 3.4 26.3 + - - +
29B THR* 2.8 33.8 + - - -
194B LEU* 3.9 22.6 - - + +
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Residues in contact with LEU 26 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9B ILE* 4.0 21.3 - - + -
11B ILE* 4.2 16.8 - - + -
22B LEU* 2.9 17.7 + - + +
23B ALA 3.6 4.7 - - - +
25B ALA* 1.3 73.2 - - - +
27B ALA* 1.3 65.4 + - - +
29B THR* 3.3 3.0 + - - -
30B LEU* 3.2 35.9 + - + +
109B ILE* 3.6 23.1 - - + -
194B LEU* 3.7 12.7 - - + +
197B LEU* 4.0 20.6 - - + +
198B ALA* 3.7 39.7 - - + +
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Residues in contact with ALA 27 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23B ALA 2.9 17.3 + - - +
24B GLN* 3.2 9.6 + - - +
26B LEU* 1.3 77.1 - - - +
28B ARG* 1.3 58.6 + - + +
30B LEU 3.3 1.0 + - - -
31B GLY 3.0 25.1 + - - +
34B VAL* 3.1 32.7 - - + +
36B LEU* 4.3 21.5 - - + -
109B ILE* 4.3 1.1 - - + +
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Residues in contact with ARG 28 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21B THR* 4.9 4.9 + - - +
24B GLN* 2.9 23.3 + - + +
25B ALA* 3.4 32.7 + - - +
27B ALA* 1.3 77.4 - - + +
29B THR* 1.3 61.8 + - - +
31B GLY* 3.3 13.3 + - - +
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Residues in contact with THR 29 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25B ALA 2.8 22.3 + - - -
26B LEU* 3.6 8.7 - - - -
27B ALA 3.3 0.4 - - - -
28B ARG* 1.3 77.1 - - - +
30B LEU* 1.3 62.7 + - + +
31B GLY 3.7 0.2 + - - -
33B ARG* 4.9 3.5 + - - -
194B LEU* 4.2 14.9 - - + +
198B ALA* 3.8 28.3 - - + -
202B LEU* 6.0 2.7 - - + -
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Residues in contact with LEU 30 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B ILE* 5.7 0.2 - - + -
26B LEU* 3.2 30.5 + - + +
27B ALA 3.3 0.2 + - - -
29B THR* 1.3 81.0 - - + +
31B GLY* 1.3 64.5 + - - +
32B GLU 3.3 0.7 + - - -
33B ARG* 3.3 34.4 + - + +
34B VAL* 4.0 19.1 - - + +
107B VAL* 4.2 22.2 - - + -
109B ILE* 5.4 0.2 - - + -
198B ALA* 4.1 13.2 - - + +
201B ALA* 3.8 23.8 - - + -
202B LEU* 3.9 34.8 - - + -
205B LEU* 4.5 5.6 - - + -
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Residues in contact with GLY 31 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27B ALA 3.0 12.0 + - - +
28B ARG* 3.3 13.1 + - - -
29B THR 3.3 0.6 + - - -
30B LEU* 1.3 75.7 - - - +
32B GLU* 1.3 60.4 + - - -
34B VAL* 3.2 23.0 + - - +
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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