Contacts of the strand formed by residues 75 - 86 (chain B) in PDB entry 5NXR
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 ASN 75 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70A GLU 3.9 0.4 - - - +
71A ASN* 3.3 26.2 - - - +
73A GLY* 5.1 12.4 + - - -
75A ASN* 3.4 14.7 - - - +
62B TRP* 3.6 26.9 + - - +
63B GLU 3.6 3.8 - - - -
64B THR* 3.1 22.0 + - - -
73B GLY* 2.9 24.6 + - - +
74B GLU* 1.3 75.3 + - - +
76B LYS* 1.3 63.6 + - - +
77B ASN* 4.3 0.9 - - - +
62C TRP* 5.0 0.9 + - - +
75C ASN* 3.4 24.5 - - - +
77C ASN* 4.7 3.0 + - - +
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Residues in contact with LYS 76 (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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70A GLU* 3.4 29.6 - - + +
71A ASN* 4.1 11.2 - - + +
62B TRP* 3.3 10.7 - - - +
63B GLU* 2.7 60.9 + - + +
65B LYS* 3.8 29.9 - - + +
74B GLU* 3.3 29.5 + - - +
75B ASN* 1.3 80.6 - - - +
77B ASN* 1.3 62.8 + - - +
78B ARG* 3.5 4.2 + - + -
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Residues in contact with ASN 77 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A TRP* 4.5 0.3 - - - -
64A THR* 2.9 41.8 + - - +
65A LYS 3.1 17.0 + - - -
66A THR* 3.9 18.3 - - + +
69A ALA 5.5 2.6 + - - +
70A GLU* 2.9 31.4 + - - +
73A GLY* 5.1 8.5 - - - +
75A ASN* 4.8 4.4 + - - +
60B PHE* 3.7 7.6 - - + -
61B GLU 3.9 3.6 - - - -
62B TRP* 3.6 18.5 + - - -
75B ASN* 6.0 0.4 - - - +
76B LYS* 1.3 70.2 - - - +
78B ARG* 1.3 60.3 + - - +
79B LEU 3.6 1.6 - - - -
80B ALA* 5.7 0.7 - - + -
96B ARG* 3.1 16.8 + - - -
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Residues in contact with ARG 78 (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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70A GLU* 3.5 18.3 + - - +
41B ARG* 3.1 36.8 - - - +
61B GLU* 2.6 48.6 + - - +
63B GLU* 3.7 43.2 + - + +
76B LYS* 3.5 4.0 + - + +
77B ASN* 1.3 73.5 - - - +
79B LEU* 1.3 61.2 + - - +
96B ARG* 2.9 22.4 + - - +
98B TYR* 3.3 24.0 + - - -
129B ARG* 3.3 46.1 - - - +
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Residues in contact with LEU 79 (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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59B ARG* 3.4 48.7 - - + +
60B PHE* 3.2 7.8 - - - -
61B GLU* 2.8 51.2 + - + +
77B ASN 5.1 0.4 - - - -
78B ARG* 1.3 86.5 - - + +
80B ALA* 1.3 63.0 + - - +
81B TYR* 4.3 10.8 - - + -
96B ARG* 3.6 4.5 - - - +
97B ASN* 4.0 22.4 - - - +
98B TYR* 3.8 20.0 - - + -
129B ARG* 3.8 22.2 - - + -
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Residues in contact with ALA 80 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A VAL* 4.2 5.6 - - + -
19A VAL* 3.9 5.4 - - + +
38A SER* 5.3 0.5 - - - -
40A VAL* 3.8 15.0 - - + -
66A THR* 3.7 40.4 + - + +
59B ARG 3.2 6.7 - - - -
60B PHE* 4.2 1.6 - - + +
77B ASN* 5.7 0.4 - - + -
79B LEU* 1.3 75.6 - - - +
81B TYR* 1.3 56.0 + - - +
95B GLY* 3.5 4.0 - - - -
96B ARG* 2.7 38.5 + - + +
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Residues in contact with TYR 81 (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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17A VAL* 3.6 8.1 - - - +
19A VAL* 4.0 2.2 - - - -
57B PHE* 3.8 33.9 - + - -
58B GLY* 3.4 1.7 - - - -
59B ARG* 3.0 79.2 + - + +
79B LEU* 4.3 11.4 - - + -
80B ALA* 1.3 77.2 - - - +
82B ALA* 1.3 63.1 - - - +
93B ASP* 4.1 9.2 - - - +
94B TYR 3.3 18.8 - - - +
95B GLY 4.3 0.2 - - - +
96B ARG 3.4 14.6 - - - +
97B ASN* 3.1 40.4 - - - +
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Residues in contact with ALA 82 (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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17A VAL* 4.6 4.0 - - + +
19A VAL* 4.0 13.8 - - + +
316A MET* 4.6 0.7 - - + -
348A LEU* 3.7 28.0 - - + +
350A TYR* 4.3 18.4 - - + +
57B PHE* 3.3 13.5 - - - +
58B GLY* 4.2 0.2 - - - -
81B TYR* 1.3 76.5 - - - +
83B GLY* 1.3 58.6 + - - +
93B ASP* 3.3 5.1 - - - -
94B TYR 2.9 31.9 + - - +
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Residues in contact with GLY 83 (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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316A MET* 3.2 8.5 - - - +
348A LEU* 3.7 10.0 - - - +
56B GLY* 3.4 0.5 - - - -
57B PHE* 2.9 45.6 + - - -
82B ALA* 1.3 76.9 - - - +
84B LEU* 1.3 64.5 + - - -
92B ILE 3.1 13.0 - - - -
93B ASP* 3.9 0.2 - - - -
416B LDA 6.2 0.2 - - - -
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Residues in contact with LEU 84 (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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312A PHE* 4.2 18.6 - - + -
316A MET* 3.7 22.7 - - + -
348A LEU* 4.1 13.7 - - + -
50B ILE* 3.6 31.2 - - + -
54B LEU* 4.1 15.9 - - + -
55B THR 3.4 1.8 - - - +
56B GLY* 3.8 3.1 - - - -
57B PHE* 3.5 2.9 - - - -
83B GLY* 1.3 82.8 - - - +
85B LYS* 1.3 60.8 - - - +
86B PHE 4.3 0.2 - - - -
91B SER* 3.2 2.8 - - - -
92B ILE* 2.8 36.6 + - + +
415B LDA 3.8 4.9 - - + +
416B LDA 3.9 42.0 - - + -
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Residues in contact with LYS 85 (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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53B GLN 3.4 3.3 - - - +
54B LEU* 3.5 3.7 - - - +
55B THR* 2.9 49.2 + - - +
57B PHE* 4.1 9.9 - - + -
84B LEU* 1.3 75.5 - - - +
86B PHE* 1.3 67.4 + - - +
87B ALA* 5.1 4.3 - - - +
88B ASP 5.5 2.4 - - - +
90B GLY* 3.3 28.7 - - - +
91B SER* 3.8 12.8 - - - +
137B ARG 5.7 0.2 + - - -
139B ASN* 4.5 23.2 - - - +
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Residues in contact with PHE 86 (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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51B THR* 5.1 0.2 - - + -
53B GLN* 3.3 38.4 - - + -
54B LEU* 3.9 21.8 - - + -
85B LYS* 1.3 76.4 - - - +
87B ALA* 1.3 76.3 + - - +
88B ASP 3.2 1.0 + - - -
89B PHE* 2.9 26.7 + + + -
90B GLY 2.9 15.6 + - - +
415B LDA 3.6 70.7 - - + +
416B LDA 3.9 38.6 - - + -
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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