Contacts of the helix formed by residues 25 - 38 (chain A) in PDB entry 2YVC
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 THR 25 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23A ASN 4.2 7.4 - - - +
24A THR* 1.3 74.0 - - - +
26A GLY* 1.3 58.0 + - - +
27A LYS* 3.8 5.1 + - - +
28A GLN* 2.6 65.9 + - - +
29A LEU 3.1 8.8 + - - -
61A LEU 4.0 10.3 - - - -
62A ASN* 5.8 0.4 - - - -
63A LYS 3.7 10.1 - - - +
64A LYS* 4.2 10.3 - - + +
65A VAL* 4.4 0.9 - - - -
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Residues in contact with GLY 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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25A THR* 1.3 67.4 - - - +
27A LYS* 1.3 56.8 + - - +
29A LEU* 3.1 5.2 + - - +
30A PHE* 2.8 29.3 + - - +
59A LEU* 3.6 26.2 - - - +
60A LYS 3.8 3.4 - - - -
61A LEU* 3.8 10.8 - - - +
63A LYS 2.9 18.4 + - - -
65A VAL* 3.7 12.2 - - - +
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Residues in contact with LYS 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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25A THR* 2.8 9.0 + - - +
26A GLY* 1.3 71.4 - - - +
28A GLN* 1.3 54.9 + - + +
30A PHE* 3.1 7.1 + - - +
31A ASP* 2.7 69.7 + - - +
61A LEU* 2.9 54.6 + - + +
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Residues in contact with GLN 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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23A ASN 4.6 1.5 + - - +
24A THR* 3.3 31.8 + - + +
25A THR* 2.6 47.5 + - - +
27A LYS* 1.3 75.0 - - + +
29A LEU* 1.3 55.3 + - - +
31A ASP* 3.4 10.8 + - - +
32A GLN* 3.0 30.5 + - - +
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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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7A VAL* 3.9 11.7 - - + -
9A VAL* 4.5 4.0 - - + -
18A PHE* 3.6 33.9 - - + -
20A ILE* 4.0 12.6 - - + -
24A THR* 4.1 9.5 - - + +
25A THR 3.1 7.7 + - - +
26A GLY* 3.3 9.0 - - - +
28A GLN* 1.3 72.9 - - - +
30A PHE* 1.3 66.9 + - - +
32A GLN* 2.9 17.2 + - - +
33A VAL* 3.2 13.7 + - + +
47A LEU* 3.5 24.7 - - + -
59A LEU* 4.4 0.7 - - + -
65A VAL* 3.5 30.1 - - + -
78A PHE* 4.1 20.2 - - + -
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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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26A GLY 2.8 15.6 + - - +
27A LYS* 3.5 9.0 - - - +
29A LEU* 1.3 71.9 - - - +
31A ASP* 1.3 75.6 + - - +
33A VAL* 3.3 5.2 + - - +
34A VAL* 3.1 45.7 + - + +
42A VAL* 3.6 39.0 - - + -
45A PHE* 3.8 21.8 - - + -
46A GLY* 4.1 5.8 - - - -
47A LEU* 4.0 26.2 - - + +
61A LEU* 3.7 33.7 - - + -
80A PHE* 3.7 18.6 - + - -
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Residues in contact with ASP 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 LYS* 2.7 68.8 + - - +
28A GLN* 3.4 9.8 + - - +
30A PHE* 1.3 82.1 - - - +
32A GLN* 1.3 63.1 + - - +
34A VAL* 3.7 4.6 + - - +
35A LYS* 3.0 26.3 + - - +
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Residues in contact with GLN 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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18A PHE* 3.2 47.8 - - + +
19A ALA 5.3 1.8 + - - -
20A ILE* 4.4 13.7 - - - +
24A THR* 6.0 0.4 - - - +
28A GLN 3.0 13.3 + - - +
29A LEU* 2.9 10.0 + - - +
31A ASP* 1.3 77.1 - - - +
33A VAL* 1.3 50.6 + - - +
35A LYS* 3.1 31.0 + - - +
36A THR* 2.8 43.1 + - - +
149B ASN* 5.0 1.0 - - - +
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Residues in contact with VAL 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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9A VAL* 3.8 36.1 - - + -
11A THR* 4.9 9.2 - - + -
16A LEU* 4.6 10.7 - - + +
18A PHE* 4.0 17.5 - - + -
29A LEU* 3.2 13.9 + - + +
30A PHE* 3.6 9.0 - - - +
32A GLN* 1.3 77.8 - - - +
34A VAL* 1.3 63.7 - - - +
36A THR* 3.1 7.0 + - - -
37A VAL* 3.0 27.3 + - + +
47A LEU* 4.9 3.6 - - + -
80A PHE* 3.7 32.3 - - + -
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Residues in contact with VAL 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 PHE* 3.1 45.3 + - + +
31A ASP* 4.0 5.6 - - - +
33A VAL* 1.3 79.9 - - - +
35A LYS* 1.3 60.3 + - + +
37A VAL* 3.8 2.4 - - - -
38A GLY* 2.8 24.3 + - - -
39A LEU* 2.8 46.4 + - + +
42A VAL* 3.4 16.6 - - + -
80A PHE* 3.9 20.4 - - + -
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Residues in contact with LYS 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 ASP 3.0 20.5 + - - +
32A GLN* 3.4 30.6 + - - +
34A VAL* 1.3 78.8 - - + +
36A THR* 1.3 74.0 + - - +
38A GLY* 3.3 12.1 + - - -
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Residues in contact with THR 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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16A LEU* 4.0 19.3 - - + +
18A PHE* 5.1 1.0 - - - -
32A GLN* 2.8 23.3 + - - +
33A VAL 3.1 4.5 + - - -
35A LYS* 1.3 90.9 + - - +
37A VAL* 1.3 62.0 + - + +
149B ASN* 3.2 36.8 + - - +
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Residues in contact with VAL 37 (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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11A THR* 4.3 24.2 - - + +
14A ALA* 5.6 4.5 - - + -
16A LEU* 4.8 14.1 - - + -
33A VAL* 3.0 21.1 + - + +
34A VAL* 4.0 4.0 - - - +
36A THR* 1.3 78.2 - - + +
38A GLY* 1.3 60.5 - - - +
39A LEU* 4.2 12.3 - - + -
80A PHE* 6.1 2.0 - - + -
97A ILE* 3.7 31.2 - - + +
100A ARG* 6.1 0.9 - - - +
101A LEU* 4.9 10.3 - - + -
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Residues in contact with GLY 38 (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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34A VAL 2.8 9.9 + - - -
35A LYS* 3.3 12.5 + - - -
37A VAL* 1.3 80.4 - - - +
39A LEU* 1.3 58.3 + - - -
40A ARG* 5.4 1.8 - - - -
95A GLN* 3.8 9.1 + - - -
97A ILE* 3.6 19.9 - - - +
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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