Contacts of the helix formed by residues 20 - 32 (chain B) in PDB entry 2YXD
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 LYS 20 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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18B ILE* 3.2 6.4 + - - +
19B THR* 1.3 72.1 - - - +
21B GLU* 1.3 57.9 + - - +
22B GLU* 3.6 3.4 - - - +
23B ILE* 2.8 47.1 + - + +
24B ARG* 2.9 11.0 + - - -
158B ILE* 4.6 7.6 - - - -
160B TYR* 2.7 43.5 - - + +
173B LYS* 3.5 38.5 - - + +
174B ASN* 4.0 15.1 + - - +
176B ILE* 5.7 2.6 - - - +
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Residues in contact with GLU 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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29A GLY* 4.7 6.1 - - - +
30A LYS* 3.5 39.4 + - - +
152A ASP* 5.3 0.5 - - - +
180A LYS* 4.1 12.2 + - - -
5B ILE* 3.9 21.0 - - + +
6B PRO 4.4 6.1 - - - +
7B ASP* 4.2 19.1 - - - +
8B GLU* 5.8 1.7 + - - +
19B THR 3.3 4.6 + - - -
20B LYS* 1.3 68.9 - - - +
22B GLU* 1.3 65.7 + - + +
24B ARG* 3.4 25.7 + - - +
25B ALA* 3.1 27.1 + - + +
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Residues in contact with GLU 22 (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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26A VAL* 3.7 29.3 - - + +
30A LYS* 2.8 32.2 + - - -
154A VAL* 3.4 15.7 - - + +
156A VAL* 5.4 0.4 - - + -
20B LYS* 3.0 4.3 + - + +
21B GLU* 1.3 81.6 - - - +
23B ILE* 1.3 67.0 + - - +
25B ALA* 3.9 2.9 - - - +
26B VAL* 3.2 28.8 + - - +
158B ILE* 3.2 33.7 - - + -
160B TYR* 2.6 30.8 + - - +
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Residues in contact with ILE 23 (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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19B THR* 3.3 21.3 - - + -
20B LYS* 2.8 33.1 + - - +
22B GLU* 1.3 80.0 - - - +
24B ARG* 1.3 56.5 + - - +
26B VAL* 3.2 5.3 + - + +
27B SER* 2.9 32.3 + - - +
130B ASN* 3.6 19.7 - - - +
156B VAL* 3.4 35.2 - - + +
158B ILE* 3.6 10.5 - - + -
176B ILE* 3.7 35.0 - - + -
178B ILE* 4.2 6.5 - - + +
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Residues in contact with ARG 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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5B ILE* 3.5 12.8 - - + +
6B PRO 3.3 21.2 + - - -
7B ASP 3.8 6.3 + - - -
8B GLU* 4.9 3.2 + - - -
10B PHE* 4.1 15.4 - - - -
18B ILE* 4.4 3.0 - - - +
19B THR* 3.0 27.2 + - + +
20B LYS 2.9 5.1 + - - -
21B GLU* 3.4 29.9 - - - +
23B ILE* 1.3 73.9 - - - +
25B ALA* 1.3 57.0 + - - +
27B SER* 3.8 0.2 - - - -
28B ILE* 2.6 44.0 + - + +
48B GLY* 3.5 30.7 + - - -
49B MSE 3.5 32.5 - - + +
52B GLU* 2.7 35.7 + - - +
1002B SO4 4.0 1.6 - - - -
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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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25A ALA* 3.6 36.8 - - - +
26A VAL* 4.1 7.6 - - - +
29A GLY* 5.4 1.8 - - - -
5B ILE* 3.9 25.7 - - + +
21B GLU* 3.1 18.3 + - + +
22B GLU* 3.9 5.8 - - - +
24B ARG* 1.3 76.4 - - - +
26B VAL* 1.4 57.2 + - - +
28B ILE* 3.8 1.8 - - - +
29B GLY* 3.0 23.2 + - - -
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Residues in contact with VAL 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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22A GLU* 3.6 35.4 - - + +
25A ALA* 4.4 5.4 - - - -
26A VAL* 3.8 18.6 - - + -
158A ILE* 5.2 2.7 - - + -
22B GLU 3.2 18.4 + - - +
23B ILE* 3.2 6.3 + - - +
25B ALA* 1.4 76.7 - - - +
27B SER* 1.3 57.0 + - - +
29B GLY* 3.2 2.8 + - - -
30B LYS* 2.9 43.0 + - + +
154B VAL* 4.7 5.2 - - + -
156B VAL* 4.9 11.4 - - + -
178B ILE* 3.8 21.5 - - + -
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Residues in contact with SER 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 ILE 2.9 20.6 + - - -
24B ARG 3.8 2.7 - - - -
26B VAL* 1.3 70.6 - - - +
28B ILE* 1.3 66.9 + - - +
30B LYS* 3.2 5.0 + - - +
31B LEU* 3.2 26.5 + - - +
49B MSE 4.1 15.3 - - - -
105B PHE* 4.2 9.9 - - - -
128B VAL* 4.3 2.6 - - - +
130B ASN* 3.1 34.9 + - - -
178B ILE* 3.9 13.0 - - - +
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Residues in contact with ILE 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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5B ILE* 4.1 8.5 - - + -
24B ARG 2.6 27.2 + - - +
25B ALA* 3.8 4.0 - - - +
27B SER* 1.3 69.8 - - - +
29B GLY* 1.3 65.5 + - - +
31B LEU* 3.1 20.5 + - + +
32B ASN* 3.7 4.2 + - - -
33B LEU* 4.2 11.5 + - + +
49B MSE 4.3 10.5 - - - -
52B GLU* 3.8 33.0 - - + +
53B ILE* 3.7 31.0 - - + -
56B ARG* 3.7 31.4 - - - +
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Residues in contact with GLY 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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4A MSE 4.9 3.9 - - - +
5A ILE* 4.8 22.7 - - - +
21A GLU* 4.5 7.3 - - - +
25A ALA* 5.1 4.9 - - - -
25B ALA 3.0 15.5 + - - -
26B VAL 3.6 4.0 - - - -
28B ILE* 1.3 79.0 - - - +
30B LYS* 1.3 57.5 + - - +
31B LEU 3.2 0.7 + - - -
32B ASN* 2.7 29.1 + - - -
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Residues in contact with LYS 30 (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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21A GLU* 3.4 27.3 + - + +
22A GLU* 2.8 28.8 + - - -
26B VAL* 2.9 31.6 + - - +
27B SER 3.2 4.9 + - - +
29B GLY* 1.3 74.7 - - - +
31B LEU* 1.3 57.0 + - - +
32B ASN* 3.3 4.3 + - - +
126B HIS* 3.0 22.7 - - - -
128B VAL* 3.4 17.3 - - + +
152B ASP* 2.9 30.7 + - - +
154B VAL* 4.4 13.0 - - - +
178B ILE* 4.1 17.7 - - + -
180B LYS* 3.0 28.8 - - + +
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Residues in contact with LEU 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 SER 3.2 16.4 + - - +
28B ILE* 3.1 15.9 + - + +
30B LYS* 1.3 75.0 - - - +
32B ASN* 1.3 70.1 + - - +
33B LEU* 3.3 17.3 - - + -
39B VAL* 5.2 2.0 - - + -
49B MSE 5.9 0.7 - - - -
53B ILE* 4.0 28.3 - - + -
103B LYS* 2.8 45.4 + - + +
104B ALA 3.8 18.4 - - - +
105B PHE* 4.2 17.0 - - + -
126B HIS* 3.7 4.9 + - - +
128B VAL* 3.4 27.4 - - + -
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Residues in contact with ASN 32 (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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4A MSE 5.3 10.7 - - + +
5A ILE 5.2 1.0 - - - +
6A PRO* 3.9 29.2 - - + +
21A GLU* 4.9 5.9 + - - -
28B ILE 3.7 2.6 + - - -
29B GLY 2.7 29.1 + - - -
30B LYS* 3.6 3.3 - - - +
31B LEU* 1.3 81.6 - - - +
33B LEU* 1.3 65.3 + - - +
34B ASN* 3.6 7.1 - - - +
37B ASP* 3.5 1.0 - - - +
103B LYS* 3.1 11.5 + - - +
126B HIS* 3.3 20.3 + - + +
180B LYS* 3.6 19.0 + - - +
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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