Contacts of the helix formed by residues 22 - 34 (chain V) in PDB entry 4ADV
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 ASP 22 (chain V).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20V LEU* 4.7 1.2 - - - +
21V ASN* 1.3 78.6 - - - +
23V GLN* 1.3 58.5 + - - +
24V PHE* 3.0 23.4 + - - +
25V VAL* 2.9 44.2 + - + +
26V ILE* 2.9 31.0 + - - +
179V SER 5.2 0.9 - - - +
180V ALA* 3.2 23.5 + - + -
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Residues in contact with GLN 23 (chain V).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21V ASN 3.3 5.2 + - - -
22V ASP* 1.3 73.0 + - - +
24V PHE* 1.3 67.8 + - + +
26V ILE* 3.3 23.6 + - - +
27V ASP* 2.7 65.2 + - - +
54V PRO* 6.1 0.6 - - - +
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Residues in contact with PHE 24 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22V ASP* 3.0 14.3 + - - +
23V GLN* 1.3 81.4 - - + +
25V VAL* 1.3 68.2 + - + +
27V ASP* 3.3 15.5 + - + +
28V SER* 3.0 23.7 + - - -
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Residues in contact with VAL 25 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20V LEU* 4.0 16.2 - - + -
22V ASP* 2.9 35.8 + - + +
24V PHE* 1.3 75.6 - - + +
26V ILE* 1.3 65.0 + - - +
28V SER* 2.6 28.0 + - - +
29V ILE* 3.0 21.9 + - + +
174V LEU* 4.6 1.3 - - + -
175V GLU 6.1 0.2 - - - +
176V VAL* 3.8 29.2 - - + -
177V PRO* 5.1 6.3 - - + -
180V ALA* 4.0 12.3 - - + -
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Residues in contact with ILE 26 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20V LEU* 3.9 28.9 - - + +
21V ASN 4.3 5.6 - - - +
22V ASP 2.9 25.1 + - - +
23V GLN* 3.4 28.5 - - - +
25V VAL* 1.3 76.2 - - - +
27V ASP* 1.3 62.4 + - - +
29V ILE* 3.3 4.0 + - - +
30V VAL* 3.0 24.7 + - + +
50V ALA* 3.5 41.7 - - + +
51V LEU* 4.1 9.5 - - + +
54V PRO* 4.1 14.4 - - + -
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Residues in contact with ASP 27 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23V GLN* 2.7 47.9 + - - +
24V PHE* 3.5 17.6 - - + +
26V ILE* 1.3 75.6 - - - +
28V SER* 1.3 57.7 + - - +
30V VAL* 3.3 6.7 + - - +
31V SER* 2.9 31.5 + - - -
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Residues in contact with SER 28 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24V PHE 3.0 10.4 + - - -
25V VAL* 2.6 26.9 + - - -
27V ASP* 1.3 78.2 - - - +
29V ILE* 1.3 54.6 + - - +
31V SER* 3.6 7.1 - - - -
32V ALA* 3.0 27.0 + - - +
174V LEU* 3.0 36.2 - - - +
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Residues in contact with ILE 29 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20V LEU* 3.7 30.3 - - + -
25V VAL* 3.0 16.9 + - + +
26V ILE 3.7 5.6 - - - +
27V ASP 3.3 0.2 - - - -
28V SER* 1.3 74.1 - - - +
30V VAL* 1.3 60.4 + - - +
32V ALA* 3.2 6.6 + - + +
33V ILE* 2.8 50.1 + - + +
51V LEU* 3.8 19.5 - - + -
137V HIS* 6.2 0.2 - - + -
139V MET* 3.9 10.3 - - + -
174V LEU* 3.6 17.5 - - + -
191V VAL* 3.8 32.3 - - + -
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Residues in contact with VAL 30 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26V ILE* 3.0 23.9 + - + +
27V ASP* 3.7 6.3 - - - +
29V ILE* 1.3 75.2 - - - +
31V SER* 1.3 58.4 + - - +
33V ILE* 3.3 6.2 + - - +
34V ASN* 2.8 26.7 + - - -
35V PRO* 3.6 10.3 - - + +
51V LEU* 4.4 6.7 - - + -
54V PRO* 3.6 46.9 - - + +
55V VAL* 4.3 12.6 - - + -
58V ARG* 3.7 26.0 + - - +
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Residues in contact with SER 31 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27V ASP 2.9 17.3 + - - -
28V SER* 3.6 9.0 - - - -
30V VAL* 1.3 77.9 - - - +
32V ALA* 1.3 61.6 + - - +
34V ASN* 3.4 14.6 + - - +
58V ARG* 4.6 9.0 - - - +
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Residues in contact with ALA 32 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28V SER 3.0 15.7 + - - +
29V ILE* 3.2 10.0 + - + +
31V SER* 1.3 77.7 - - - +
33V ILE* 1.3 63.5 + - - +
34V ASN* 3.3 4.0 + - - +
137V HIS* 4.0 16.6 + - + +
173V VAL* 3.6 31.0 - - + -
191V VAL* 5.9 0.2 - - + -
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Residues in contact with ILE 33 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29V ILE* 2.8 42.1 + - + +
30V VAL* 3.8 4.3 - - - +
32V ALA* 1.3 72.2 - - - +
34V ASN* 1.3 66.3 + - - +
35V PRO* 4.0 11.4 - - + -
41V MET* 3.8 29.8 - - + -
51V LEU* 4.9 1.6 - - + -
55V VAL* 4.6 12.6 - - + -
109V ARG* 2.9 30.7 + - - +
111V PHE* 3.9 33.9 - - + -
137V HIS* 3.7 32.8 - - + +
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Residues in contact with ASN 34 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30V VAL 2.8 14.1 + - - -
31V SER 3.6 12.8 - - - +
32V ALA 3.2 3.5 - - - +
33V ILE* 1.3 80.3 - - - +
35V PRO* 1.3 69.7 - - - +
36V GLN* 2.7 38.5 + - - +
39V GLN* 3.9 1.2 + - - +
58V ARG* 3.2 12.8 + - - +
109V ARG* 3.5 5.5 + - - -
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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