Contacts of the helix formed by residues 23 - 33 (chain A) in PDB entry 2L28
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 LEU 23 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21A TRP* 5.0 4.5 - - + +
22A HIS* 1.3 82.3 - - - +
24A PRO* 1.3 63.4 - - + +
25A ASP* 6.0 1.1 - - + -
26A ASP* 3.9 32.5 - - + +
27A LEU* 2.8 38.4 + - - +
122A PHE* 4.2 23.1 - - + -
151A LEU* 4.8 15.0 - - + -
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Residues in contact with PRO 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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22A HIS 4.0 2.4 - - - +
23A LEU* 1.3 90.1 - - + +
25A ASP* 1.3 72.0 + - + +
27A LEU* 3.9 7.3 - - + +
28A HIS* 3.2 22.9 + - - +
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Residues in contact with ASP 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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23A LEU* 4.4 1.8 - - + +
24A PRO* 1.3 81.3 - - + +
26A ASP* 1.3 74.1 + - - +
27A LEU 3.2 1.0 + - - -
28A HIS* 3.5 13.5 + - - +
29A TYR* 3.7 11.4 + - - +
146A ASP* 6.2 0.2 - - - -
151A LEU* 4.7 24.0 - - + +
153A HIS* 3.9 21.1 + - - -
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Residues in contact with ASP 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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6A ALA* 4.9 8.6 - - + +
23A LEU* 3.9 24.3 + - + +
24A PRO 3.5 0.2 - - - -
25A ASP* 1.3 85.7 - - - +
27A LEU* 1.3 59.8 - - - +
28A HIS 3.5 0.2 - - - -
29A TYR* 4.0 5.6 + - - +
30A PHE* 3.5 18.9 + - - +
118A LEU* 3.3 28.8 - - - +
122A PHE* 2.9 37.0 - - + -
151A LEU* 4.9 5.2 - - - +
153A HIS* 5.4 0.5 - - - -
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Residues in contact with LEU 27 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A HIS* 4.9 26.5 - - + +
23A LEU 2.8 23.5 + - - +
24A PRO* 3.9 7.0 - - + +
25A ASP 3.2 0.4 - - - -
26A ASP* 1.3 76.9 - - - +
28A HIS* 1.3 65.0 + - - +
29A TYR 3.2 2.0 - - - -
30A PHE* 3.2 29.1 + - + +
31A ARG* 3.1 31.0 + - + +
50A PRO* 5.5 14.8 - - + -
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Residues in contact with HIS 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 PRO 3.2 15.5 + - - +
25A ASP* 3.8 8.5 - - - +
26A ASP 3.5 0.4 - - - -
27A LEU* 1.3 80.2 - - - +
29A TYR* 1.3 56.7 + - - +
31A ARG* 3.3 33.2 + - - +
32A ALA* 2.8 45.1 + - + +
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Residues in contact with TYR 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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4A LEU* 6.1 0.2 - - + -
5A TRP 4.8 2.9 - - - -
6A ALA* 5.1 6.3 - - + -
25A ASP 3.7 8.7 + - - +
26A ASP* 4.3 8.1 - - - +
27A LEU 3.2 0.4 - - - -
28A HIS* 1.3 75.6 + - - +
30A PHE* 1.3 67.9 + - - +
31A ARG 3.1 1.8 - - - -
32A ALA* 4.4 4.9 - - + -
33A GLN* 2.7 76.5 + - + +
114A LEU* 4.6 4.2 - - - +
115A VAL 5.2 2.6 + - - -
116A THR* 3.1 39.1 - - + +
155A TYR* 3.3 41.5 - + - +
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Residues in contact with PHE 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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4A LEU* 3.0 34.7 - - + +
5A TRP* 5.3 7.0 - - + +
6A ALA 6.1 0.4 - - - -
22A HIS* 6.3 0.7 - + - -
26A ASP 3.5 14.0 + - - +
27A LEU* 3.2 26.2 + - + +
29A TYR* 1.3 80.6 - - - +
31A ARG* 1.3 62.3 + - + +
34A THR* 5.1 1.9 - - - +
39A MET* 5.5 1.0 - - - +
45A THR* 5.1 7.0 - - + -
49A PHE* 4.2 31.6 - + - -
97A ALA* 4.0 33.6 - - + +
98A GLY* 5.6 0.9 - - - -
103A PHE* 5.7 1.3 - + - -
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Residues in contact with ARG 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 LEU* 3.1 29.0 - - + +
28A HIS* 3.3 31.3 + - - +
30A PHE* 1.3 81.8 - - + +
32A ALA* 1.3 64.8 + - - +
33A GLN 2.7 16.5 + - - -
34A THR* 3.2 4.7 + - - +
35A VAL* 2.7 32.7 + - + +
39A MET* 5.5 5.3 - - - +
49A PHE* 6.0 4.3 - - + -
54A LEU* 5.9 3.1 - - + -
57A ARG* 3.2 46.1 - - - +
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Residues in contact with ALA 32 (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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28A HIS* 2.8 40.7 + - + +
29A TYR* 4.4 5.6 - - + +
31A ARG* 1.3 79.1 - - - +
33A GLN* 1.3 63.9 + - - +
35A VAL* 3.3 23.1 + - + +
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Residues in contact with GLN 33 (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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4A LEU* 3.2 46.8 - - + +
5A TRP 4.3 3.2 - - - +
29A TYR* 2.7 78.9 + - + +
30A PHE 4.1 0.4 - - - +
31A ARG 2.7 5.3 + - - -
32A ALA* 1.3 76.1 - - - +
34A THR* 1.3 58.3 + - - +
95A VAL* 5.7 0.4 - - - +
114A LEU* 3.5 31.2 + - - +
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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