Contacts of the helix formed by residues 38 - 48 (chain A) in PDB entry 6WNX
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 CYS 38 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8A THR* 4.7 3.1 - - - -
35A GLU 3.7 0.9 - - - +
36A LEU 3.4 0.8 - - - -
37A VAL* 1.3 81.5 - - - +
39A LYS* 1.3 67.1 + - - +
40A GLU* 3.9 9.6 - - - -
41A TRP* 3.2 37.7 + - - +
42A GLN 3.1 17.5 + - - -
123B ILE* 3.7 16.4 - - + -
124B LYS 3.8 14.8 - - - +
126B ASP* 3.3 18.6 - - - +
127B PHE* 3.3 16.8 - - - -
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Residues in contact with LYS 39 (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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38A CYS* 1.3 71.2 - - - +
40A GLU* 1.3 51.4 + - - +
42A GLN* 3.1 30.8 + - - +
43A ARG* 2.8 34.5 + - - +
126B ASP* 2.7 40.1 + - - +
127B PHE* 3.6 17.8 - - + -
131B GLU* 3.0 30.0 + - - +
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Residues in contact with GLU 40 (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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7A ILE 4.5 3.1 - - - +
8A THR* 3.4 38.5 - - + +
11A PRO* 3.7 15.2 - - - +
38A CYS* 3.2 7.2 - - - -
39A LYS* 1.3 75.6 - - - +
41A TRP* 1.3 60.8 + - - +
43A ARG* 2.9 47.5 + - - +
44A VAL* 2.9 29.2 + - + +
126B ASP* 4.5 3.0 + - - +
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Residues in contact with TRP 41 (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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5A ASP* 2.7 33.9 + - - -
6A PHE 5.2 0.7 - - - -
7A ILE* 3.4 44.9 - - + +
8A THR* 3.9 7.2 - - - -
23A LEU* 4.8 2.5 - - + -
34A ALA* 3.4 40.8 - - + +
37A VAL* 3.7 9.4 - - + -
38A CYS* 3.2 26.6 + - - +
40A GLU* 1.3 71.3 - - - +
42A GLN* 1.3 66.6 + - - +
44A VAL* 3.2 3.1 + - - +
45A ILE* 3.0 30.7 + - + +
109B ILE* 3.9 23.8 - - + -
117B ILE* 3.7 28.0 - - + -
121B PHE* 4.2 9.2 - + - -
123B ILE* 3.6 17.7 - - + +
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Residues in contact with GLN 42 (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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35A GLU* 3.4 35.4 + - + +
38A CYS 3.1 6.3 + - - +
39A LYS* 3.1 39.6 + - - +
41A TRP* 1.3 76.8 - - - +
43A ARG* 1.3 54.2 + - - +
45A ILE* 3.4 4.1 + - - +
46A SER* 2.8 40.7 + - - -
93A ARG* 5.4 6.1 - - - +
127B PHE* 3.5 10.3 - - + -
131B GLU* 5.5 1.5 - - - +
135B VAL* 3.9 27.5 - - - +
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Residues in contact with ARG 43 (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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11A PRO* 4.0 5.5 - - - +
16A ASP* 3.2 25.7 + - - -
39A LYS 2.8 21.0 + - - +
40A GLU* 2.9 40.4 + - - +
41A TRP 3.2 0.4 - - - -
42A GLN* 1.3 74.0 - - - +
44A VAL* 1.3 68.2 + - - +
46A SER* 2.8 9.4 + - - +
47A GLU* 2.8 75.7 + - + +
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Residues in contact with VAL 44 (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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7A ILE* 3.9 26.9 - - + +
11A PRO* 4.0 7.6 - - + -
16A ASP* 5.0 3.4 - - + +
19A ALA* 4.3 9.4 - - + -
20A GLU* 4.2 19.8 - - + +
23A LEU* 3.7 22.2 - - + -
40A GLU* 2.9 20.6 + - - +
41A TRP 3.2 4.7 + - - +
43A ARG* 1.3 98.2 - - - +
45A ILE* 1.3 57.8 + - - +
47A GLU* 5.1 0.9 - - - -
48A GLY* 2.7 33.7 + - - +
50A LEU* 3.9 0.5 - - - +
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Residues in contact with ILE 45 (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 LEU* 3.8 17.5 - - + -
31A LEU* 3.9 16.2 - - + +
34A ALA* 3.7 17.5 - - + -
35A GLU* 3.4 46.4 - - + +
41A TRP* 3.0 20.6 + - + +
42A GLN* 3.6 6.3 - - - +
44A VAL* 1.3 74.1 - - - +
46A SER* 1.3 64.6 + - - +
49A MET 3.3 2.9 + - - -
50A LEU* 3.2 39.5 + - + -
51A TRP* 3.9 30.1 - - + +
89A ASN* 4.1 2.2 - - - +
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Residues in contact with SER 46 (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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42A GLN* 2.8 20.4 + - - -
43A ARG* 2.8 22.2 + - - +
45A ILE* 1.3 78.7 - - - +
47A GLU* 1.3 66.2 + - - +
49A MET* 3.3 7.8 + - - +
89A ASN* 3.2 40.6 - - - +
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Residues in contact with GLU 47 (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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20A GLU* 4.5 3.3 - - - +
43A ARG* 2.8 56.1 + - + +
44A VAL* 4.5 1.1 - - - +
46A SER* 1.3 73.6 + - - +
48A GLY* 1.3 61.2 + - - +
49A MET* 3.1 19.3 + - - +
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Residues in contact with GLY 48 (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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20A GLU* 3.3 29.7 + - - -
44A VAL 2.7 22.5 + - - -
47A GLU* 1.3 69.1 - - - +
49A MET* 1.3 66.0 + - - +
50A LEU* 3.3 8.6 - - - +
53A LYS* 2.5 31.2 + - - +
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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