Contacts of the helix formed by residues 24 - 36 (chain A) in PDB entry 2VDE
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 ASN 24 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23A GLU* 1.3 74.4 - - - +
25A LEU* 1.3 57.0 + - - +
26A MET* 3.7 6.2 - - - +
27A GLN* 2.4 50.3 + - - +
28A VAL* 2.8 34.5 + - - +
135A TYR* 3.4 9.9 - - - -
216A ALA* 3.7 17.9 - - + -
438A ASN* 2.7 39.3 + - - +
441A LEU* 4.6 1.3 - - + -
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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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24A ASN* 1.3 74.8 - - - +
26A MET* 1.3 63.0 + - - +
28A VAL* 3.4 1.6 + - - +
29A TYR* 3.2 19.9 + - - +
131A THR* 4.7 5.4 - - + -
132A ALA* 4.0 21.8 - - + +
135A TYR* 3.2 36.6 + - + -
136A PHE* 3.8 12.1 - - + -
434A LEU* 3.8 35.2 - - + +
437A LEU* 3.7 39.0 - - + -
438A ASN* 4.5 2.0 - - - +
441A LEU* 3.6 16.1 - - + +
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Residues in contact with MET 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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24A ASN* 3.7 1.3 - - - +
25A LEU* 1.3 82.5 - - - +
27A GLN* 1.3 64.0 + - + +
29A TYR* 3.3 13.3 + - - +
30A GLN* 3.3 39.8 + - + +
431A GLU* 3.4 19.1 - - + +
434A LEU* 3.5 15.1 + - + +
435A LEU* 3.2 46.9 - - + +
438A ASN* 3.5 32.7 + - - +
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Residues in contact with GLN 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 GLU* 2.4 47.9 - - + +
24A ASN* 2.4 33.6 + - - +
26A MET* 1.3 78.3 - - + +
28A VAL* 1.3 66.0 + - - +
30A GLN* 3.2 11.9 + - - +
31A GLN* 3.0 28.8 + - - +
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Residues in contact with VAL 28 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A GLU* 4.7 3.1 - - + -
24A ASN 2.8 23.9 + - - +
25A LEU 3.4 4.7 + - - +
27A GLN* 1.3 71.2 - - - +
29A TYR* 1.3 61.7 + - - +
31A GLN* 3.3 9.1 + - - +
32A ALA* 3.1 17.8 + - - +
131A THR* 4.0 17.3 - - + -
135A TYR* 4.1 10.1 - - + -
204A LEU* 4.1 16.4 - - + -
208A THR* 3.4 12.7 + - - +
212A TYR* 3.7 36.6 - - + +
215A LEU* 4.0 21.3 - - + -
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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 7.9 + - - +
26A MET* 3.5 7.6 - - - +
27A GLN 3.2 0.2 - - - -
28A VAL* 1.3 77.4 - - - +
30A GLN* 1.3 64.5 + - - +
32A ALA* 2.9 3.9 + - + +
33A ARG* 2.6 56.9 + - + +
39A LEU* 5.5 1.6 - - - +
124A GLN* 4.5 6.4 + - - +
127A LEU* 4.1 22.7 - - + +
128A ILE* 3.5 38.5 - - + +
131A THR* 4.2 23.7 - - + +
431A GLU* 3.6 34.1 - - + +
434A LEU* 3.4 31.6 - - + -
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Residues in contact with GLN 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 MET* 3.3 40.4 - - + +
27A GLN* 3.2 8.9 + - - +
29A TYR* 1.3 81.6 - - - +
31A GLN* 1.3 61.4 + - + +
32A ALA 3.7 0.2 + - - -
33A ARG* 3.1 23.3 + - - +
34A LEU* 3.4 27.0 + - - +
431A GLU* 3.1 29.2 + - - +
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Residues in contact with GLN 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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23A GLU* 3.0 26.2 + - - +
27A GLN* 3.0 26.3 + - - +
28A VAL* 3.3 11.7 + - - +
29A TYR 3.1 0.6 - - - -
30A GLN* 1.3 77.4 - - + +
32A ALA* 1.3 59.5 + - - +
34A LEU* 3.7 11.5 - - - +
35A SER* 3.2 21.5 + - - -
208A THR* 3.9 3.8 - - - +
210A ASN* 3.5 24.2 + - - +
212A TYR* 2.9 27.9 + - - +
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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 VAL 3.1 7.9 + - - +
29A TYR* 2.9 9.9 + - + +
31A GLN* 1.3 76.3 - - - +
33A ARG* 1.3 59.6 + - - +
34A LEU 3.3 2.0 - - - -
35A SER* 4.0 5.6 - - - -
36A ASN* 2.8 35.2 + - - +
127A LEU* 4.2 13.9 - - + -
131A THR* 4.6 7.6 - - + +
207A ILE* 3.7 8.5 - - + +
208A THR* 3.4 30.5 - - - +
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Residues in contact with ARG 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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29A TYR* 2.6 52.4 + - + +
30A GLN* 3.1 34.4 + - - +
31A GLN 3.6 0.2 - - - -
32A ALA* 1.3 75.4 - - - +
34A LEU* 1.3 80.4 + - - +
36A ASN* 4.3 2.4 + - - +
39A LEU* 4.3 23.4 - - + +
40A ARG* 5.1 5.0 - - - +
127A LEU* 3.9 9.7 - - - +
431A GLU* 4.1 9.4 + - - -
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Residues in contact with LEU 34 (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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30A GLN 3.4 18.4 - - - +
31A GLN* 3.7 13.7 - - - +
33A ARG* 1.3 98.0 - - - +
35A SER* 1.3 67.3 + - - +
36A ASN 3.7 0.4 - - - -
40A ARG* 3.2 31.8 + - - +
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Residues in contact with SER 35 (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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31A GLN 3.2 14.4 + - - -
32A ALA 3.2 3.4 + - - -
34A LEU* 1.3 86.9 - - - +
36A ASN* 1.3 62.3 + - - +
37A PRO* 3.3 2.9 - - - +
40A ARG* 4.1 6.8 + - - +
208A THR 3.1 19.8 + - - -
336C GLU* 5.2 0.2 - - - +
339C GLU* 4.9 4.0 - - - +
343C ARG* 2.6 38.5 + - - -
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Residues in contact with ASN 36 (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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32A ALA 2.8 17.8 + - - +
33A ARG 4.3 1.4 + - - +
34A LEU 3.7 1.0 - - - -
35A SER* 1.3 75.9 - - - +
37A PRO* 1.3 69.3 - - - +
38A GLU* 3.1 27.4 + - - +
39A LEU* 3.0 27.8 + - + +
40A ARG* 3.2 27.1 + - - +
127A LEU* 3.6 29.7 - - + +
207A ILE* 3.0 30.5 + - - +
343C ARG* 4.0 2.7 - - - +
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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