Contacts of the helix formed by residues 25 - 32 (chain A) in PDB entry 4TVQ
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 25 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21A PRO* 2.9 22.9 + - + +
24A ALA* 1.3 83.9 - - - +
26A MET* 1.3 71.8 + - - +
27A TYR 3.4 0.9 - - - -
28A PRO* 3.2 4.6 - - - +
29A VAL* 3.1 31.3 + - + +
63A ILE* 3.8 24.0 - - + -
66B ILE* 4.5 21.1 - - + +
69B LYS* 4.1 17.7 - - + +
72B VAL* 4.1 23.6 - - + -
73B GLU* 4.4 10.8 - - + +
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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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21A PRO 3.3 2.4 + - - +
22A LEU* 2.9 23.7 + - + +
25A VAL* 1.3 72.8 - - - +
27A TYR* 1.3 60.0 + - + +
29A VAL* 3.2 3.6 + - + +
30A PHE* 2.9 74.4 + - + -
48A PHE* 3.8 21.8 - - + -
59A THR* 3.6 29.4 - - + -
62A ILE* 6.5 0.4 - - - -
63A ILE* 4.2 15.3 - - + -
48B PHE* 5.5 0.4 - - + -
62B ILE* 4.4 9.2 - - + -
66B ILE* 4.0 29.4 - - + -
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Residues in contact with TYR 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 LEU* 2.9 23.2 + - + -
23A TYR* 3.1 57.2 - + - +
26A MET* 1.3 75.6 - - + +
28A PRO* 1.3 57.8 - - + +
30A PHE* 3.5 6.8 + + - +
31A ASN* 3.0 39.9 + - - -
45A ARG* 4.9 18.7 - - + +
49A ILE* 3.2 37.2 - - + +
27C TYR* 3.4 31.2 - + + -
28C PRO* 5.0 0.9 - - - +
31C ASN* 3.1 38.8 + - - +
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Residues in contact with PRO 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 TYR 3.1 19.1 - - - +
24A ALA 3.3 15.0 - - - +
25A VAL 3.2 17.5 - - - +
27A TYR* 1.3 88.2 - - + +
29A VAL* 1.3 57.6 + - - +
32A GLU* 2.8 45.3 + - - +
69B LYS* 3.9 13.5 - - + +
11C GLU* 3.4 34.6 - - + +
23C TYR* 4.3 11.0 - - + -
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Residues in contact with VAL 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 VAL* 3.1 23.8 + - + +
26A MET* 3.2 10.1 + - + +
28A PRO* 1.3 79.5 - - - +
30A PHE* 1.3 70.1 + - + +
32A GLU* 3.4 10.0 + - - +
33A LEU* 3.6 17.1 - - + +
62B ILE* 3.9 31.0 - - + +
65B LYS* 3.6 39.9 - - + +
66B ILE* 4.2 9.6 - - + +
69B LYS* 3.7 18.2 - - + +
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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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22A LEU* 5.9 0.2 - - + -
26A MET* 2.9 50.6 + - + +
27A TYR* 3.9 4.7 - + - +
29A VAL* 1.3 79.3 - - + +
31A ASN* 1.3 62.6 + - - +
33A LEU* 3.3 16.9 + - + +
34A GLU* 3.4 13.7 + - - +
41A ALA* 4.0 13.7 - - + +
44A LEU* 3.6 33.9 - - + -
45A ARG* 3.4 46.4 - - + +
48A PHE* 3.5 37.9 - + + -
48B PHE* 5.4 0.7 - + - -
62B ILE* 4.1 16.2 - - + -
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Residues in contact with ASN 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 TYR* 3.0 30.5 + - - +
28A PRO 3.6 0.2 - - - +
30A PHE* 1.3 77.5 - - - +
32A GLU* 1.3 59.1 + - - +
33A LEU 3.2 3.7 + - - -
34A GLU* 3.0 37.9 + - - +
45A ARG* 3.3 11.9 + - - -
3C MET* 3.7 21.1 - - + +
8C MET* 3.7 13.3 - - - +
11C GLU* 3.3 30.4 + - - +
27C TYR* 3.4 18.6 - - - -
45C ARG* 3.7 12.4 + - - +
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Residues in contact with GLU 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 PRO* 2.8 20.4 + - - +
29A VAL 3.4 2.0 + - - +
30A PHE 3.2 0.8 - - - -
31A ASN* 1.3 74.8 - - - +
33A LEU* 1.3 71.1 + - - +
65B LYS* 2.7 45.7 + - - +
69B LYS* 3.2 21.6 + - - -
8C MET* 3.5 40.1 - - + +
11C GLU* 3.1 25.4 - - - +
12C ALA* 3.3 28.8 + - - +
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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