Contacts of the strand formed by residues 64 - 72 (chain A) in PDB entry 3NX4
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 ASP 64 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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37A SER* 2.8 20.9 + - - -
38A SER* 3.0 16.0 + - - +
40A ASN* 2.7 27.2 + - - -
43A ASP* 5.1 0.2 + - - -
62A GLY* 4.3 0.2 - - - -
63A ILE* 1.3 84.4 - - - +
65A PHE* 1.3 68.5 + - - +
85A LEU* 3.1 6.7 - - - +
86A THR* 3.4 9.7 - - - +
97A GLY* 3.4 8.2 - - - -
122A MSE 3.5 19.1 - - + -
125A GLY* 3.4 2.1 - - - -
126A THR* 2.5 43.0 + - - -
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Residues in contact with PHE 65 (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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32A VAL* 3.8 25.8 - - + -
34A VAL* 4.0 18.8 - - + -
36A TRP 3.4 12.6 - - - +
64A ASP* 1.3 78.1 - - - +
66A ALA* 1.3 66.2 + - - +
83A VAL* 4.8 2.9 - - + -
84A LEU* 3.4 1.4 - - - -
85A LEU* 2.8 76.1 + - + +
90A VAL* 4.8 4.7 - - + -
97A GLY* 3.7 26.5 - - - +
102A ALA* 3.7 24.2 - - + -
104A VAL* 4.1 10.3 - - + -
109A LEU* 4.0 16.2 - - + -
122A MSE 3.4 10.1 - - - +
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Residues in contact with ALA 66 (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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34A VAL* 3.8 1.3 - - - -
35A HIS* 2.9 21.8 + - - +
36A TRP* 2.9 14.6 + - + +
65A PHE* 1.3 78.6 - - - +
67A GLY* 1.3 59.2 + - - +
83A VAL 3.4 12.6 - - - +
84A LEU* 4.3 4.3 - - + -
112A LEU* 5.6 0.4 - - + -
118A SER* 3.4 28.2 + - - +
121A ALA* 4.6 1.8 - - + -
122A MSE 3.7 23.8 - - + -
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Residues in contact with GLY 67 (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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32A VAL* 3.9 12.8 - - - +
33A ASP 3.2 14.4 - - - -
34A VAL* 4.2 0.2 - - - -
35A HIS* 3.9 11.0 - - - -
65A PHE* 4.5 0.2 - - - -
66A ALA* 1.3 75.3 - - - +
68A THR* 1.3 62.1 + - - -
82A GLU* 3.6 7.5 - - - +
83A VAL* 2.9 33.8 + - - +
118A SER* 4.1 3.4 + - - -
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Residues in contact with THR 68 (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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32A VAL* 4.1 2.5 - - - -
33A ASP* 2.8 35.6 + - - +
35A HIS* 3.1 23.5 - - - -
67A GLY* 1.3 72.1 - - - -
69A VAL* 1.3 68.5 + - - +
70A HIS 3.2 0.3 + - - -
80A GLY* 3.5 36.3 - - - +
81A GLN 3.3 3.8 - - - +
82A GLU* 2.7 22.8 + - - +
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Residues in contact with VAL 69 (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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30A VAL* 4.0 20.6 - - + -
31A THR 3.6 6.5 - - - +
32A VAL* 4.4 1.3 - - + +
67A GLY 4.3 0.2 - - - -
68A THR* 1.3 73.7 - - - +
70A HIS* 1.3 62.1 + - - +
71A ALA 3.5 28.5 - - - +
72A SER* 4.1 3.6 - - - -
77A PHE* 4.5 6.1 - - + -
78A HIS 3.2 31.0 - - - +
79A ALA* 4.0 0.4 - - - +
80A GLY 2.9 26.2 + - - -
81A GLN* 2.9 21.1 + - + +
83A VAL* 3.8 26.2 - - + -
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Residues in contact with HIS 70 (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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22A GLU* 4.8 7.4 - - - -
31A THR* 2.8 28.0 + - + +
33A ASP* 3.7 31.2 + - - +
68A THR 3.2 3.2 + - - -
69A VAL* 1.3 75.2 - - - +
71A ALA* 1.3 69.3 + - + +
79A ALA* 3.5 17.4 - - - +
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Residues in contact with ALA 71 (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 ASP 4.5 0.4 - - - -
30A VAL* 3.7 0.2 - - - -
31A THR* 2.9 36.0 + - - +
69A VAL* 3.5 6.1 - - - +
70A HIS* 1.3 93.3 - - + +
72A SER* 1.3 63.1 + - - +
79A ALA* 4.9 4.3 - - - -
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Residues in contact with SER 72 (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 ASP 3.4 5.8 - - - -
30A VAL* 3.9 4.1 - - - +
69A VAL* 4.1 9.2 - - - +
71A ALA* 1.3 79.1 - - - +
73A GLU* 1.3 60.5 + - - +
74A ASP* 2.8 34.4 + - - +
77A PHE* 3.1 30.4 + - - +
78A HIS* 4.4 2.5 - - - -
79A ALA 5.3 1.6 - - - +
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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