Contacts of the helix formed by residues 21 - 32 (chain A) in PDB entry 2DVL
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 VAL 21 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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17A VAL* 2.9 30.0 + - + +
19A ARG 3.6 0.2 - - - -
20A GLU* 1.3 88.8 - - + +
22A LEU* 1.3 70.4 + - + +
24A PRO* 3.4 2.6 - - - +
25A LEU* 3.3 34.8 + - + +
38A PRO* 4.8 1.1 - - + +
39A GLN* 4.0 31.0 - - + +
42A ALA* 4.1 15.9 - - + -
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Residues in contact with LEU 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* 3.1 15.7 + - + +
18A ALA* 3.3 13.2 - - - +
21A VAL* 1.3 86.1 - - + +
23A TYR* 1.3 64.2 + - - +
25A LEU* 3.8 0.5 - - - +
26A ALA* 2.9 25.8 + - - +
39A GLN* 4.0 23.2 - - + +
43A LEU* 4.4 18.4 - - + -
74A LEU* 3.7 41.1 - - + +
77A ALA* 3.8 9.4 - - + -
78A ASP* 4.2 6.1 - - + +
81A VAL* 3.7 35.7 - - + -
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Residues in contact with TYR 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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18A ALA 2.7 19.3 + - - +
19A ARG* 3.9 11.0 - - - +
22A LEU* 1.3 72.6 - - - +
24A PRO* 1.3 73.4 - - + +
26A ALA 3.4 0.2 + - - -
27A PRO* 3.3 4.9 - - - +
76A ALA 4.8 1.6 - - - -
77A ALA* 3.8 25.2 - - + +
253A ILE* 4.3 15.9 - - + +
341A ARG* 3.0 70.4 + - - -
345A TYR* 4.2 13.2 - - - -
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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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19A ARG 3.4 16.6 - - - +
20A GLU* 3.5 19.1 - - - +
21A VAL 3.4 13.7 - - - +
23A TYR* 1.3 99.9 - - + +
25A LEU* 1.3 66.0 + - + +
27A PRO* 3.6 8.8 - - - +
28A GLU* 5.2 3.1 + - - +
341A ARG* 4.6 5.5 + - - +
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Residues in contact with LEU 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 VAL* 3.3 27.1 + - + +
22A LEU 3.3 2.4 + - - +
24A PRO* 1.3 81.5 - - + +
26A ALA* 1.3 66.5 + - - +
27A PRO* 3.1 4.4 - - - -
28A GLU* 3.3 18.7 + - - +
29A TYR* 3.2 37.6 + - + +
38A PRO* 4.5 12.3 - - + -
39A GLN* 3.6 34.1 - - + +
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Residues in contact with ALA 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 LEU 2.9 17.4 + - - +
23A TYR 3.8 2.9 - - - +
25A LEU* 1.3 75.5 - - - +
27A PRO* 1.3 71.1 - - + +
29A TYR* 3.3 3.1 + - - +
30A ASP* 2.9 25.3 + - - +
77A ALA 3.5 17.5 - - - +
78A ASP* 3.5 26.3 + - - +
341A ARG* 4.3 4.5 - - - +
344A ARG* 4.0 11.8 + - - +
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Residues in contact with PRO 27 (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 TYR 3.3 11.7 - - - +
24A PRO 3.6 7.2 - - - +
25A LEU 3.4 4.0 - - - -
26A ALA* 1.3 94.4 - - + +
28A GLU* 1.3 56.1 + - - +
30A ASP* 3.7 5.8 - - + +
31A ARG* 3.1 28.3 + - - +
338A ARG* 6.1 0.5 - - - -
341A ARG* 3.2 36.1 - - + +
344A ARG* 5.5 0.4 - - - +
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Residues in contact with GLU 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 5.2 2.7 + - - +
25A LEU* 3.3 20.4 + - - +
27A PRO* 1.3 79.9 - - - +
29A TYR* 1.3 85.0 + - + +
31A ARG* 4.2 20.9 - - - +
32A LYS* 2.9 44.2 + - + +
34A GLU* 5.1 4.1 - - - +
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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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25A LEU* 3.2 34.4 + - + +
26A ALA* 4.0 4.0 - - - +
28A GLU* 1.3 95.6 - - + +
30A ASP* 1.3 61.5 + - - +
33A ALA* 3.0 22.3 + - - -
34A GLU* 3.0 67.1 + - + +
35A TYR 3.4 12.6 - - - -
36A PRO* 3.9 9.4 - - + -
38A PRO* 3.3 25.7 - - + +
39A GLN* 3.6 27.1 - - - +
78A ASP* 5.2 2.7 - - - +
199A ALA* 3.8 12.3 - - + +
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Residues in contact with ASP 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 ALA 2.9 17.1 + - - +
27A PRO* 3.7 5.8 - - + +
29A TYR* 1.3 76.5 - - - +
31A ARG* 1.3 65.6 + - - +
33A ALA* 3.3 2.9 + - - +
197A LEU 4.8 1.4 + - - -
198A HIS* 3.2 60.3 + - - +
199A ALA* 4.7 3.9 + - - +
338A ARG* 5.9 2.6 - - - +
343A GLU* 5.0 0.3 - - - +
344A ARG* 3.6 37.2 + - + +
347A ARG* 3.0 27.0 + - - -
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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 PRO 3.1 17.4 + - - +
28A GLU* 3.7 20.7 - - - +
30A ASP* 1.3 80.9 - - - +
32A LYS* 1.3 92.1 - - - +
33A ALA* 3.5 1.6 + - - +
338A ARG* 3.2 52.9 - - - +
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Residues in contact with LYS 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 GLU* 2.9 28.6 + - + +
31A ARG* 1.3 106.9 - - - +
33A ALA* 1.3 72.2 + - - +
34A GLU* 3.0 36.9 + - + +
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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