Contacts of the helix formed by residues 34 - 43 (chain B) in PDB entry 2WLV
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 GLU 34 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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33A ALA* 3.9 19.6 - - + +
34A GLU* 3.4 36.2 - - + +
25B LEU* 4.7 2.5 - - + +
29B LYS* 3.7 45.7 - - + +
32B GLY* 3.6 6.4 - - - -
33B ALA* 1.3 81.7 + - - +
35B VAL* 1.4 60.2 + - - +
36B VAL 3.0 2.2 - - - -
37B PRO* 3.2 11.3 - - - +
38B GLY* 2.9 28.6 + - - -
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Residues in contact with VAL 35 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B TRP* 3.7 16.5 - - + -
25B LEU* 4.4 19.3 - - + +
26B VAL* 5.0 4.0 - - - -
29B LYS* 4.2 15.5 - - + +
31B PHE* 3.9 31.0 - - + +
32B GLY 3.1 19.5 + - - +
34B GLU* 1.4 76.0 - - - +
36B VAL* 1.3 61.9 + - + +
38B GLY* 5.0 0.7 - - - -
39B PHE* 2.9 31.0 + - - +
137B LEU* 4.1 20.0 - - + +
141B VAL* 3.8 17.3 - - + -
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Residues in contact with VAL 36 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B ALA* 3.2 8.9 + - - +
34B GLU 3.0 0.8 - - - -
35B VAL* 1.3 78.4 - - - +
37B PRO* 1.3 71.6 - - + +
39B PHE* 3.3 5.5 + - - +
40B GLN* 3.0 20.4 + - - +
134B GLN* 3.9 32.3 + - + +
137B LEU* 4.0 14.4 - - + -
138B GLN* 3.9 40.4 - - + +
141B VAL* 4.1 12.3 - - + -
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Residues in contact with PRO 37 (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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28A GLU* 3.4 26.6 - - + +
29A LYS* 3.8 18.6 - - + +
34A GLU* 3.6 26.7 - - - +
33B ALA 3.2 13.7 - - - +
34B GLU* 3.2 21.3 - - - +
36B VAL* 1.3 95.3 - - + +
38B GLY* 1.3 61.7 + - - +
40B GLN* 3.2 3.7 + - + -
41B ALA* 2.9 22.5 + - - +
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Residues in contact with GLY 38 (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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25A LEU* 4.0 13.0 - - - -
34A GLU* 4.3 2.6 - - - +
22B TRP* 4.4 4.7 - - - -
25B LEU* 3.9 21.1 - - - -
34B GLU 2.9 18.4 + - - -
35B VAL 3.9 0.2 - - - -
37B PRO* 1.3 80.0 - - - +
39B PHE* 1.3 61.2 + - - +
41B ALA* 3.4 0.7 + - - +
42B LEU* 3.0 29.6 + - - +
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Residues in contact with PHE 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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22B TRP* 3.6 24.0 - + + -
35B VAL 2.9 19.5 + - - +
36B VAL 3.7 3.1 - - - +
38B GLY* 1.3 76.7 - - - +
40B GLN* 1.3 64.9 + - - +
42B LEU 4.6 0.2 - - - +
43B SER* 2.7 63.2 + - - -
51B ILE* 4.1 17.3 - - + -
54B MET* 3.8 26.7 - - + -
55B LEU* 5.7 2.2 - - + -
130B ARG* 3.8 22.0 - - + -
133B ILE* 3.5 32.3 - - + -
134B GLN* 4.7 5.2 - - + -
137B LEU* 3.4 22.7 - - + -
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Residues in contact with GLN 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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28A GLU* 3.4 25.8 - - - +
36B VAL 3.0 13.3 + - - +
37B PRO* 3.2 9.4 + - + +
39B PHE* 1.3 84.1 - - - +
41B ALA* 1.3 64.8 + - - +
43B SER* 3.4 4.9 + - - -
44B GLU* 3.5 5.5 + - - +
130B ARG* 2.8 54.0 + - - +
131B ARG* 6.0 0.2 - - - -
134B GLN* 3.6 34.9 + - - +
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Residues in contact with ALA 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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21A ALA* 5.4 1.9 - - - -
24A LYS* 3.6 35.2 - - - +
25A LEU* 3.6 23.6 - - + +
28A GLU* 4.2 9.9 - - + -
37B PRO 2.9 16.5 + - - +
38B GLY 3.8 3.4 - - - +
40B GLN* 1.3 78.4 - - - +
42B LEU* 1.3 62.7 + - + +
44B GLU* 3.3 25.2 + - - +
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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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21A ALA* 4.1 25.6 - - + +
25A LEU* 4.3 16.8 - - + -
42A LEU* 5.2 2.2 - - + -
14B LEU* 3.9 21.8 - - - +
18B THR* 4.1 26.1 - - + +
21B ALA* 4.0 15.9 - - + -
22B TRP* 3.6 36.8 - - + +
25B LEU* 4.1 12.3 - - + -
38B GLY 3.0 22.0 + - - +
41B ALA* 1.3 76.6 - - - +
43B SER* 1.3 58.7 + - - +
44B GLU 3.3 2.0 + - - +
46B CYS* 4.1 0.2 - - - -
54B MET* 4.0 16.5 - - + +
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Residues in contact with SER 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 PHE* 2.7 47.0 + - - -
40B GLN* 3.4 2.3 + - - -
42B LEU* 1.3 75.1 - - - +
44B GLU* 1.3 66.9 + - - +
45B GLY 3.3 0.3 + - - -
46B CYS* 3.1 26.2 + - - +
51B ILE* 4.6 2.5 - - - -
54B MET* 3.9 11.7 - - - -
130B ARG* 2.8 36.2 + - - -
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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