Contacts of the helix formed by residues 38 - 46 (chain B) in PDB entry 3VZD
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 38 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33B LEU 3.5 0.2 + - - -
34B PHE* 3.0 47.5 + - + +
37B HIS* 1.3 80.6 - - - +
39B GLN* 1.3 65.6 + - - +
40B PRO 3.5 0.9 - - - -
41B LEU* 3.2 8.7 + - - +
42B LEU* 3.1 32.7 + - + +
78B MET* 4.2 1.8 - - - -
108B LEU* 3.9 21.1 - - + -
135B LEU* 3.8 24.5 - - + -
139B THR* 3.5 23.6 - - + +
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Residues in contact with GLN 39 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34B PHE* 2.8 26.7 + - + +
35B ARG* 3.0 49.4 + - - +
38B VAL* 1.3 72.6 - - - +
40B PRO* 1.4 71.5 - - + +
42B LEU* 3.0 19.3 + - - +
43B ALA* 3.0 16.6 + - + +
49B PHE* 3.9 22.0 - - + -
24C ARG* 5.9 4.4 - - - +
55C GLU* 4.0 4.4 + - - -
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Residues in contact with PRO 40 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35B ARG 3.3 14.1 - - - +
36B SER* 3.6 20.2 - - - +
37B HIS 4.4 1.8 - - - +
38B VAL 3.6 3.4 - - - +
39B GLN* 1.4 96.3 - - + +
41B LEU* 1.3 68.0 + - + +
43B ALA* 3.7 8.2 + - + +
44B GLU* 3.4 20.4 + - - +
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Residues in contact with LEU 41 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37B HIS 3.6 15.5 - - - +
38B VAL 3.2 8.2 + - - +
40B PRO* 1.3 82.7 - - + +
42B LEU* 1.3 66.7 + - - +
44B GLU* 3.3 8.1 + - + +
45B ALA 3.1 17.3 + - - -
136B THR* 4.2 18.8 - - + +
139B THR* 3.5 32.1 - - + -
140B LEU* 4.4 22.7 - - + -
143B CYS* 3.5 15.9 - - - -
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Residues in contact with LEU 42 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17B VAL* 5.8 0.7 - - + -
19B VAL* 5.1 3.8 - - + -
34B PHE* 3.9 13.0 - - + -
38B VAL* 3.1 37.5 + - + +
39B GLN* 3.0 7.8 + - - +
41B LEU* 1.3 76.5 - - - +
43B ALA* 1.3 56.7 + - - +
45B ALA* 3.1 2.9 + - - +
46B GLU 2.9 24.4 + - - -
47B ILE* 3.0 42.9 + - + +
49B PHE* 3.8 33.2 - - + -
76B VAL* 6.5 0.2 - - + -
139B THR* 4.5 2.9 - - + -
142B LEU* 3.7 31.6 - - + -
143B CYS* 4.4 9.2 - - - -
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Residues in contact with ALA 43 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39B GLN* 3.0 17.0 + - + +
40B PRO* 3.7 9.2 - - + +
42B LEU* 1.3 77.4 - - - +
44B GLU* 1.3 61.0 + - - +
46B GLU* 3.2 16.2 + - - +
47B ILE 4.9 2.2 - - - -
49B PHE* 6.0 0.8 - - + -
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Residues in contact with GLU 44 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13B ARG* 4.1 10.6 + - - -
40B PRO 3.4 10.1 + - - +
41B LEU* 3.3 10.9 + - + +
43B ALA* 1.3 78.9 - - - +
45B ALA* 1.3 60.4 + - - +
46B GLU* 3.5 4.5 + - - +
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Residues in contact with ALA 45 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13B ARG* 3.6 12.3 - - - +
41B LEU 3.1 16.9 + - - +
42B LEU 3.1 3.6 + - - +
44B GLU* 1.3 78.5 - - + +
46B GLU* 1.3 65.9 + - - +
47B ILE* 3.9 11.0 - - + -
143B CYS* 3.7 30.7 - - + +
145B ARG* 2.7 34.5 + - - +
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Residues in contact with GLU 46 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209A ARG* 4.4 5.9 + - - -
330A GLU* 4.4 14.5 - - - +
13B ARG* 2.6 34.5 + - + +
14B PRO* 3.3 37.0 - - + +
15B CYS 3.3 3.1 + - - +
42B LEU 2.9 4.2 + - - -
43B ALA* 3.2 11.7 + - - +
44B GLU 4.1 6.5 - - - +
45B ALA* 1.3 81.2 - - - +
47B ILE* 1.3 60.4 + - - +
48B SER 3.8 0.8 + - - -
145B ARG* 3.1 12.7 + - - +
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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