Contacts of the helix formed by residues 25 - 34 (chain A) in PDB entry 1NVD
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 TYR 25 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4A PRO* 6.5 1.1 - - + -
6A LYS* 4.6 14.0 + - - -
16A ILE* 4.3 24.0 - - + +
21A LEU* 2.8 45.5 + - + +
22A TRP 4.2 0.8 + - - -
23A ARG 4.0 0.2 - - - -
24A ASN* 1.3 77.1 - - - +
26A VAL* 1.3 68.3 + - - +
27A ALA* 3.6 2.5 - - - +
28A LYS* 3.5 9.1 + - + +
29A ASP* 2.9 54.3 + - + -
172A LYS* 5.6 0.7 + - - -
174A TYR* 4.2 11.9 - + - -
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Residues in contact with VAL 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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21A LEU* 3.0 19.8 + - + +
22A TRP* 3.7 31.4 + - + +
25A TYR* 1.3 77.6 - - - +
27A ALA* 1.3 66.6 + - - +
29A ASP* 2.9 5.0 + - - +
30A LEU* 2.8 43.7 + - + +
55A PHE* 3.7 20.2 - - + -
110A ILE* 5.6 0.9 - - + -
137A VAL* 4.8 2.5 - - + -
174A TYR* 3.8 39.7 - - + -
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Residues in contact with ALA 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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22A TRP 5.1 1.6 + - - +
25A TYR 3.6 1.5 - - - +
26A VAL* 1.3 78.6 - - - +
28A LYS* 1.3 63.8 + - - +
30A LEU* 3.2 4.7 + - - +
31A ILE* 3.2 29.1 + - - +
55A PHE* 3.6 19.0 - - + -
58A ALA* 3.7 41.7 - - + +
59A PHE* 3.9 11.0 - - - +
62A ARG* 4.4 1.6 - - + -
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Residues in contact with LYS 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 ASN 5.3 7.4 - - - +
25A TYR* 3.5 13.1 + - + +
26A VAL 3.2 0.4 - - - -
27A ALA* 1.3 79.8 - - - +
29A ASP* 1.3 61.6 + - - +
31A ILE* 3.5 4.0 + - - +
32A SER* 3.2 21.4 + - - +
62A ARG* 3.2 54.6 + - + +
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Residues in contact with ASP 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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16A ILE* 5.3 0.3 - - - +
25A TYR* 2.9 49.3 + - + +
26A VAL 3.5 3.1 - - - +
28A LYS* 1.3 74.8 - - - +
30A LEU* 1.3 61.3 + - - +
32A SER* 3.3 4.9 + - - -
33A ASP* 2.9 46.3 + - - +
34A CYS* 5.3 0.2 - - - -
172A LYS* 3.4 24.4 + - - -
174A TYR* 2.9 26.0 + - - +
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Residues in contact with LEU 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 VAL* 2.8 25.3 + - + +
27A ALA* 3.5 6.7 - - - +
29A ASP* 1.3 71.5 - - - +
31A ILE* 1.3 59.4 + - + +
34A CYS* 2.8 46.4 + - + +
39A TYR* 3.8 18.6 - - + -
55A PHE* 3.8 21.3 - - + -
59A PHE* 5.6 3.1 - - + -
108A VAL* 5.1 2.7 - - + -
110A ILE* 3.4 32.1 - - + -
135A VAL* 4.1 20.0 - - + -
174A TYR* 3.4 32.1 - - + +
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Residues in contact with ILE 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 ALA 3.2 15.2 + - - +
28A LYS 3.8 6.7 - - - +
30A LEU* 1.3 79.4 - - + +
32A SER* 1.3 59.0 + - - +
35A SER* 3.8 16.8 + - - -
39A TYR* 3.7 18.6 + - + +
59A PHE* 3.6 31.2 - - + -
62A ARG* 3.8 28.7 - - + +
63A ALA* 5.0 3.4 - - - -
66A ILE* 3.5 34.5 - - + -
70A PRO* 4.2 10.8 - - + -
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Residues in contact with SER 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 LYS* 3.2 16.1 + - - +
29A ASP* 3.3 9.7 + - - -
31A ILE* 1.3 82.7 - - - +
33A ASP* 1.3 73.9 + - - +
34A CYS 3.5 0.2 - - - -
35A SER* 4.4 7.8 + - - -
62A ARG* 5.3 8.1 - - - -
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Residues in contact with ASP 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 ASP* 2.9 25.5 + - - +
32A SER* 1.3 86.6 + - - +
34A CYS* 1.3 65.4 + - - +
35A SER 3.6 2.0 + - - -
133A ARG* 4.9 2.8 + - - -
171A THR* 5.1 4.3 - - - +
172A LYS* 3.8 31.3 + - - -
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Residues in contact with CYS 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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29A ASP 3.8 0.4 + - - -
30A LEU* 2.8 26.1 + - + +
33A ASP* 1.3 84.1 - - - +
35A SER* 1.3 60.1 + - - +
39A TYR* 2.6 28.1 + - - -
108A VAL* 3.8 23.6 - - + +
133A ARG* 4.0 11.4 - - - +
135A VAL* 4.2 21.5 - - - -
171A THR* 3.9 25.8 - - - -
172A LYS* 4.4 9.6 - - - -
174A TYR* 5.2 0.2 - - - -
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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