Contacts of the helix formed by residues 29 - 38 (chain E) in PDB entry 3VZC
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 LYS 29 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23E PRO 4.8 0.2 - - - -
25E GLY 2.6 14.6 + - - -
26E GLY* 3.1 17.6 + - - +
27E LYS 4.3 3.4 - - - +
28E GLY* 1.3 85.0 - - - +
30E ALA* 1.3 63.3 + - - -
31E LEU 3.2 3.4 - - - -
32E GLN* 2.9 47.6 + - + +
33E LEU* 2.9 23.9 + - + +
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Residues in contact with ALA 30 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21E LEU* 4.0 11.7 - - + -
22E ASN 3.4 17.7 - - - +
23E PRO* 4.3 1.5 + - + -
25E GLY 2.6 32.2 + - - +
26E GLY* 3.5 6.8 - - - +
28E GLY 3.9 0.2 - - - -
29E LYS* 1.3 70.4 - - - +
31E LEU* 1.3 56.9 + - - +
33E LEU* 3.4 4.6 + - - -
34E PHE* 2.9 24.8 + - - +
78E MET* 3.4 12.5 - - + +
110E ALA* 3.7 18.6 - - + -
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Residues in contact with LEU 31 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21E LEU* 3.9 28.7 - - + +
23E PRO* 4.7 11.9 + - + +
29E LYS 3.2 1.4 - - - -
30E ALA* 1.3 76.0 - - - +
32E GLN* 1.3 65.8 + - - +
34E PHE* 3.2 5.6 + - + +
35E ARG* 3.0 36.7 + - - +
51E LEU* 4.2 22.7 - - + -
53E LEU* 4.5 16.2 - - + -
31F LEU* 3.7 29.8 - - + -
53F LEU* 4.8 7.6 - - + -
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Residues in contact with GLN 32 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29E LYS* 2.9 46.3 + - + +
31E LEU* 1.3 77.9 - - - +
33E LEU* 1.3 61.4 + - + +
35E ARG* 3.2 10.4 + - + +
36E SER* 3.0 34.2 + - - +
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Residues in contact with LEU 33 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26E GLY* 4.2 25.6 - - - +
29E LYS* 2.9 21.3 + - + +
30E ALA* 3.5 8.7 - - - +
32E GLN* 1.3 80.2 - - + +
34E PHE* 1.3 54.2 + - - +
36E SER* 3.3 3.5 + - - +
37E HIS* 2.8 52.5 + - + +
38E VAL 3.6 0.3 + - - -
78E MET* 4.2 3.8 - - + -
109E PRO 5.4 0.4 - - - +
110E ALA* 5.0 8.5 - - + +
131E ASN 6.4 1.1 - - - -
132E GLU* 3.7 25.8 - - - +
135E LEU* 3.8 22.4 - - + -
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Residues in contact with PHE 34 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19E VAL* 4.0 25.8 - - + -
21E LEU* 3.8 13.2 - - + -
30E ALA 2.9 15.1 + - - +
31E LEU* 3.4 9.2 - - + +
33E LEU* 1.3 75.1 - - - +
35E ARG* 1.3 65.7 + - - +
38E VAL* 3.0 38.3 + - + -
39E GLN* 2.8 44.8 + - + -
42E LEU* 3.9 17.0 - - + -
49E PHE* 3.6 40.2 - + - -
51E LEU* 3.8 16.4 - - + -
78E MET* 3.6 15.1 - - - +
108E LEU* 5.4 1.3 - - + -
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Residues in contact with ARG 35 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31E LEU* 3.0 22.7 + - - +
32E GLN* 3.2 13.2 + - + +
34E PHE* 1.3 81.5 - - - +
36E SER* 1.3 61.8 + - - +
39E GLN* 3.0 33.2 + - - +
40E PRO* 3.4 18.9 - - - +
49E PHE* 3.9 7.3 - - - -
51E LEU* 3.9 18.6 - - - +
23F PRO* 4.3 20.0 - - - +
24F ARG* 5.6 0.8 - - - +
53F LEU* 4.3 6.3 - - - +
55F GLU* 2.8 38.5 + - - -
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Residues in contact with SER 36 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32E GLN* 3.0 20.5 + - - +
33E LEU* 3.3 4.3 + - - +
35E ARG* 1.3 77.9 - - - +
37E HIS* 1.3 85.7 + - - +
40E PRO* 3.5 19.1 - - - +
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Residues in contact with HIS 37 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33E LEU* 2.8 27.3 + - + +
36E SER* 1.3 100.7 + - - +
38E VAL* 1.3 61.5 + - - +
40E PRO* 4.3 1.8 - - - -
41E LEU* 4.2 21.7 - - - +
132E GLU* 3.8 34.3 - - + +
135E LEU* 4.0 20.6 - - + -
136E THR* 3.7 27.0 + - + +
139E THR* 4.4 4.0 + - - -
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Residues in contact with VAL 38 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34E PHE* 3.0 35.6 + - + +
37E HIS* 1.3 82.4 - - - +
39E GLN* 1.3 66.3 + - - +
40E PRO* 3.5 0.7 - - - -
41E LEU* 3.3 8.8 + - - +
42E LEU* 3.2 37.9 + - + +
78E MET* 3.9 9.0 - - + -
108E LEU* 3.8 19.1 - - + -
135E LEU* 3.9 22.7 - - + -
139E THR* 3.8 24.2 - - + +
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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