Contacts of the strand formed by residues 39 - 47 (chain A) in PDB entry 1WF8
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 39 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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30A GLY 4.7 0.2 - - - -
31A VAL* 2.9 43.7 + - + +
32A GLY 3.7 1.5 + - - +
37A LEU 4.4 6.5 - - - +
38A GLU* 1.3 76.3 - - - +
40A LEU* 1.3 68.5 + - - +
74A VAL* 3.7 28.7 + - + -
75A GLY* 3.8 13.4 - - - +
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Residues in contact with LEU 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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28A GLY* 3.7 12.8 - - - -
29A MET* 2.6 55.4 - - - +
30A GLY* 3.5 9.8 - - - -
38A GLU* 3.9 17.9 + - + +
39A LYS* 1.3 71.3 - - - +
41A GLY* 1.3 63.1 - - - +
42A ILE* 3.9 7.2 - - + -
73A LEU 4.0 2.1 - - - +
74A VAL* 3.8 4.9 - - - +
75A GLY* 2.8 32.2 + - - -
76A VAL 3.1 34.5 + - - +
77A THR* 4.4 6.3 - - - +
78A GLN 4.5 3.6 - - - +
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Residues in contact with GLY 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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29A MET 2.5 26.8 + - - -
31A VAL* 3.1 23.3 - - - +
40A LEU* 1.3 73.8 - - - +
42A ILE* 1.3 60.3 - - - -
43A PHE* 2.8 27.9 + - - -
64A GLN* 4.7 9.2 - - - -
73A LEU 4.9 0.9 - - - -
74A VAL* 5.7 0.4 - - - -
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Residues in contact with ILE 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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26A ILE* 3.7 30.1 - - + -
27A ILE 3.6 6.1 - - - +
28A GLY* 4.5 0.2 - - - -
40A LEU* 3.9 11.7 - - + -
41A GLY* 1.3 68.7 - - - +
43A PHE* 1.3 61.6 + - - +
64A GLN* 3.6 6.5 - - - +
65A ILE* 3.0 29.6 + - + +
73A LEU* 3.4 34.3 + - + +
76A VAL* 3.5 25.1 - - + +
78A GLN* 3.8 16.6 - - + -
81A ALA* 3.3 36.1 - - + -
85A LEU* 5.1 0.2 - - + -
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Residues in contact with PHE 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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26A ILE* 3.0 7.6 - - - +
27A ILE* 2.5 49.5 + - + -
29A MET* 3.5 32.5 - - + -
31A VAL* 3.8 22.4 - - + -
41A GLY* 2.8 37.0 - - - -
42A ILE* 1.3 74.9 - - - +
44A VAL* 1.3 61.3 - - - +
62A ASN* 3.8 15.0 - - - +
63A ASP 2.9 13.7 - - - +
64A GLN* 3.7 29.6 - - + -
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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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24A ILE* 4.9 6.3 - - + -
25A SER 3.1 8.5 - - - +
26A ILE* 4.6 0.4 - - + -
27A ILE* 3.8 1.8 - - - +
43A PHE* 1.3 69.8 - - - +
45A LYS* 1.3 62.6 + - - +
46A THR 3.3 23.6 - - - +
47A VAL* 3.8 7.9 - - + -
59A ILE* 4.3 9.6 - - + -
60A GLN 3.4 21.8 - - - +
61A VAL* 3.6 8.5 - - - -
62A ASN* 2.5 31.5 + - - +
63A ASP* 2.6 28.5 + - + +
65A ILE* 3.6 28.7 - - + -
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Residues in contact with LYS 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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25A SER* 2.9 13.0 + - - -
26A ILE 3.7 14.6 - - - +
27A ILE* 3.3 42.2 - - + +
43A PHE 3.4 0.4 + - - -
44A VAL* 1.3 72.2 - - - +
46A THR* 1.3 73.4 + - + +
61A VAL* 3.1 14.2 - - - +
62A ASN* 4.9 0.7 - - - +
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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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25A SER* 2.9 44.9 + - - +
44A VAL* 3.2 8.6 - - - +
45A LYS* 1.3 87.9 - - + +
47A VAL* 1.3 80.1 + - - +
61A VAL* 3.4 16.3 - - - +
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Residues in contact with VAL 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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23A GLY 4.2 1.1 - - - +
24A ILE* 3.5 22.9 - - + -
44A VAL* 3.8 10.1 - - + -
46A THR* 1.3 93.2 + - - +
48A THR* 1.3 68.5 + - - +
49A GLU* 3.3 4.3 + - - +
53A ALA 4.0 1.1 - - - -
54A GLN* 3.3 49.2 - - + +
59A ILE* 4.4 9.0 - - + +
60A GLN* 4.1 10.5 - - - -
61A VAL* 3.4 20.0 - - + +
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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