Contacts of the strand formed by residues 39 - 47 (chain A) in PDB entry 1WXQ
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 39 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2A GLU* 5.4 0.2 - - - +
17A PHE* 4.1 2.9 - - - -
37A ALA 3.2 14.9 + - - +
38A ASN* 1.3 97.3 - - - +
40A GLY* 1.3 67.9 + - - +
74A LYS* 3.5 34.8 - - + +
75A MSE 3.4 7.6 - - - +
76A VAL* 4.2 15.0 - - + -
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Residues in contact with GLY 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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17A PHE* 3.7 2.5 - - - -
21A THR* 3.7 18.2 - - - -
39A VAL* 1.3 79.6 - - - +
41A VAL* 1.3 61.9 + - - +
74A LYS* 3.5 7.3 - - - +
75A MSE 2.8 31.0 + - - -
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Residues in contact with VAL 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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20A ALA 3.9 1.4 - - - +
21A THR* 3.7 25.7 + - - +
22A LEU 5.4 0.9 - - - -
40A GLY* 1.3 75.0 - - - +
42A THR* 1.3 74.5 + - - +
43A TYR* 4.6 17.6 - - + +
72A PRO* 3.7 23.8 - - + -
73A VAL 3.4 10.5 - - - +
74A LYS* 5.3 0.7 - - + -
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Residues in contact with THR 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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20A ALA* 3.0 22.8 + - - +
40A GLY 4.3 0.2 - - - -
41A VAL* 1.3 78.6 - - - +
43A TYR* 1.3 78.0 + - - +
73A VAL* 2.9 50.3 + - + +
75A MSE 3.8 34.0 - - + +
258A ARG* 5.0 3.3 + - - +
306A GLN* 5.5 0.7 + - - -
309A ILE* 3.1 29.6 - - + +
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Residues in contact with TYR 43 (chain A).
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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41A VAL* 4.6 16.0 - - + +
42A THR* 1.3 87.6 + - - +
44A ALA* 1.3 59.2 + - - +
45A ILE* 3.9 9.4 - - + -
62A TYR* 5.7 0.8 - - - -
63A GLU* 4.4 19.3 + - + +
65A ARG* 5.9 2.5 - - - -
70A LEU* 3.5 32.3 - - + -
71A ILE 3.4 5.4 - - - -
72A PRO* 3.2 48.6 - - + +
73A VAL* 4.6 1.8 - - - +
258A ARG* 5.7 8.8 - - - +
306A GLN* 3.3 20.6 + - - +
309A ILE* 3.6 13.9 - - - +
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Residues in contact with ALA 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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43A TYR* 1.3 73.1 - - - +
45A ILE* 1.3 62.8 + - - +
46A THR 3.7 0.7 + - - -
69A ALA 2.9 14.1 - - - +
71A ILE* 2.6 39.4 + - + +
73A VAL* 4.3 13.7 - - + -
309A ILE* 4.9 0.9 - - - -
310A ASN* 4.1 6.5 - - - +
313A VAL* 4.3 25.1 - - + -
314A PHE* 4.3 12.0 - - + -
344A LEU* 5.3 1.3 - - + -
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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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43A TYR* 4.5 7.0 - - + +
44A ALA* 1.3 72.5 - - - +
46A THR* 1.3 65.6 + - - +
68A LEU* 3.8 31.4 - - + -
69A ALA 3.2 2.7 - - - -
70A LEU* 3.5 41.3 - - + -
267A GLU 4.4 14.4 - - - +
268A TYR 4.5 6.1 - - - +
269A ILE* 5.6 7.0 - - + -
306A GLN* 3.5 37.2 - - + +
310A ASN* 3.1 30.7 + - - +
314A PHE* 4.5 0.2 - - - -
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Residues in contact with THR 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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44A ALA 4.7 2.2 - - - +
45A ILE* 1.3 76.7 - - - +
47A ASP* 1.3 72.9 + - - +
68A LEU* 3.4 11.5 - - - +
69A ALA* 2.7 36.6 + - + +
71A ILE* 4.7 2.0 - - + -
314A PHE* 3.6 28.6 - - + -
321A PRO* 4.0 21.3 - - + -
386A PHE* 3.5 19.6 - - + -
387A ASN* 5.4 0.2 - - - +
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Residues in contact with ASP 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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46A THR* 1.3 81.5 + - - +
48A HIS* 1.3 62.1 + - - +
49A PRO 3.5 0.5 - - - -
51A LYS* 4.0 30.8 + - + +
67A GLY 4.0 5.4 - - - +
68A LEU* 3.3 20.1 - - - +
69A ALA* 4.4 1.0 - - - +
386A PHE* 6.1 0.2 - - + -
387A ASN* 3.0 32.5 + - - +
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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