Contacts of the helix formed by residues 18 - 31 (chain A) in PDB entry 3B3T
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 18 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16A GLN 3.8 6.7 - - - +
17A VAL* 1.3 74.7 - - - +
19A ALA* 1.3 63.7 + - - +
20A SER* 3.0 22.9 + - - -
21A GLN* 3.0 38.6 + - + +
22A ILE* 3.2 15.1 + - - +
127A GLU* 2.8 15.5 + - - +
130A ARG* 3.9 3.7 + - - +
273A LYS* 5.2 0.4 - - - +
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Residues in contact with ALA 19 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A VAL 4.1 2.4 + - - -
18A ASP* 1.3 73.4 + - - +
20A SER* 1.3 56.6 + - - +
22A ILE* 3.2 14.6 + - - +
23A THR* 2.9 32.6 + - - +
268A THR 3.4 23.3 - - - +
269A GLY 3.9 14.1 - - - +
270A SER* 4.6 2.0 - - - +
273A LYS* 4.3 18.8 - - + +
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Residues in contact with SER 20 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A ASP* 3.0 15.4 + - - -
19A ALA* 1.3 75.9 - - - +
21A GLN* 1.3 61.1 + - - +
23A THR* 3.4 8.7 + - - -
24A GLY* 2.9 25.1 + - - -
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Residues in contact with GLN 21 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A ASP* 3.0 32.5 + - + +
20A SER* 1.3 77.1 - - - +
22A ILE* 1.3 63.2 + - - +
24A GLY* 3.2 3.3 + - - -
25A THR* 3.0 26.1 + - - -
127A GLU* 3.3 23.1 - - - +
130A ARG* 3.7 29.4 - - - +
134A GLU* 5.5 0.2 + - - -
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Residues in contact with ILE 22 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A VAL* 4.1 8.5 - - + -
18A ASP 3.6 13.5 - - - +
19A ALA* 3.2 13.4 + - - +
21A GLN* 1.3 78.0 - - - +
23A THR* 1.3 59.8 + - + +
25A THR* 3.1 3.0 + - - -
26A ILE* 3.0 37.0 + - + +
123A ALA* 3.5 27.5 - - + +
124A ALA 4.8 0.7 - - - +
127A GLU* 3.8 18.6 - - + -
269A GLY 4.8 2.0 - - - +
272A ALA* 3.8 23.6 - - + -
273A LYS* 3.8 22.2 - - - +
276A THR* 3.4 26.5 - - - +
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Residues in contact with THR 23 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19A ALA 2.9 14.9 + - - +
20A SER* 3.4 10.7 + - - -
22A ILE* 1.3 72.9 - - + +
24A GLY* 1.3 62.0 + - - +
26A ILE* 4.3 8.7 - - + +
27A SER* 2.9 31.8 + - - -
262A LEU* 3.8 22.2 - - + +
267A PRO 3.6 16.5 + - - +
268A THR 3.8 1.9 + - - -
269A GLY* 3.5 37.9 - - - +
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Residues in contact with GLY 24 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20A SER 2.9 16.4 + - - -
21A GLN* 3.2 5.6 + - - -
23A THR* 1.3 77.0 + - - +
25A THR* 1.3 59.9 + - - +
27A SER* 3.1 7.7 + - - -
28A SER* 3.0 28.0 + - - -
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Residues in contact with THR 25 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A GLN* 3.0 14.8 + - - +
22A ILE* 3.1 7.9 + - - -
24A GLY* 1.3 75.3 - - - +
26A ILE* 1.3 62.1 + - - +
28A SER* 3.3 5.9 + - - -
29A LEU* 2.9 38.4 + - + +
48A TRP* 4.3 19.9 - - + -
52A GLU* 5.0 4.2 + - - -
122A ILE* 5.0 0.4 - - + -
123A ALA* 3.7 27.0 + - + -
126A THR* 4.3 24.0 - - + +
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Residues in contact with ILE 26 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22A ILE* 3.0 31.8 + - + +
23A THR* 3.9 7.2 - - + +
25A THR* 1.3 75.1 - - - +
27A SER* 1.3 65.0 + - - +
29A LEU* 3.2 2.4 + - - +
30A GLU* 2.9 22.5 + - - +
115A ALA* 3.6 35.7 - - + +
119A ALA* 3.9 14.3 - - + +
120A SER* 3.9 17.5 - - - -
123A ALA* 3.6 12.6 - - + -
182A ASN* 3.8 25.1 - - - +
262A LEU* 4.0 20.4 - - + -
272A ALA* 5.0 0.2 - - + -
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Residues in contact with SER 27 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A THR 2.9 18.8 + - - -
24A GLY* 3.1 13.2 + - - -
26A ILE* 1.3 77.9 - - - +
28A SER* 1.3 63.2 + - - +
30A GLU* 3.5 18.5 - - - +
31A SER* 3.5 18.2 + - - -
262A LEU* 4.2 12.5 - - - +
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Residues in contact with SER 28 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A GLY 3.0 19.0 + - - -
25A THR 3.6 3.4 - - - -
26A ILE 3.2 0.2 - - - -
27A SER* 1.3 77.4 + - - +
29A LEU* 1.3 60.8 + - - +
31A SER* 2.7 26.4 + - - -
32A PHE* 3.9 8.6 + - - -
48A TRP* 3.6 31.1 - - - -
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Residues in contact with LEU 29 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25A THR* 2.9 29.9 + - + +
28A SER* 1.3 76.7 - - - +
30A GLU* 1.3 61.9 + - - +
31A SER 3.1 1.1 + - - -
32A PHE* 3.2 29.2 + - + +
35A ARG* 3.2 32.8 + - - +
45A ALA 4.9 1.6 - - - +
48A TRP* 3.7 28.0 - - + -
49A ILE* 4.1 16.8 - - + -
119A ALA* 3.8 33.0 - - + +
122A ILE* 3.8 28.7 - - + -
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Residues in contact with GLU 30 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26A ILE 2.9 12.7 + - - +
27A SER* 3.5 22.9 - - - +
29A LEU* 1.3 76.0 - - - +
31A SER* 1.3 60.6 + - - +
32A PHE 3.3 9.9 - - - +
35A ARG* 4.1 0.2 - - - +
113A PRO* 3.4 38.0 - - + +
115A ALA* 3.3 7.7 - - + +
119A ALA* 5.0 0.4 - - - +
261A THR* 3.2 17.7 - - - +
262A LEU* 2.8 43.0 + - - +
263A ALA 5.2 0.3 + - - -
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Residues in contact with SER 31 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27A SER 3.5 11.1 + - - -
28A SER* 2.7 21.9 + - - -
29A LEU 3.1 0.2 - - - -
30A GLU* 1.3 77.3 - - - +
32A PHE* 1.3 65.1 + - - +
33A THR* 3.4 3.8 + - - -
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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