Contacts of the strand formed by residues 54 - 65 (chain C) 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 LEU 54 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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312B PHE* 4.3 13.5 - - + -
406B LDA 4.2 27.1 - - + -
50C ILE* 3.0 35.0 + - + +
51C THR* 3.0 41.4 + - + +
53C GLN* 1.3 78.9 - - - +
55C THR* 1.3 60.0 + - - +
84C LEU* 4.1 20.4 - - + -
85C LYS 3.5 14.4 - - - +
86C PHE* 3.9 22.4 - - + -
406C LDA 4.3 18.6 - - + -
439C LDA 5.0 1.1 - - - -
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Residues in contact with THR 55 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47C ASP* 5.3 9.5 + - + +
48C THR 3.1 15.0 - - - +
49C GLN* 3.4 35.9 - - - +
50C ILE* 3.8 4.0 - - - -
53C GLN 4.0 2.1 + - - +
54C LEU* 1.3 72.7 - - - +
56C GLY* 1.3 64.6 + - - +
57C PHE* 4.4 1.0 - - - -
84C LEU* 3.3 4.7 - - - +
85C LYS* 2.9 54.9 + - - +
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Residues in contact with GLY 56 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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316B MET* 4.0 6.5 - - - -
47C ASP* 3.3 4.7 - - - +
48C THR* 2.7 51.4 + - - +
50C ILE* 3.4 5.2 - - - +
55C THR* 1.3 77.1 - - - +
57C PHE* 1.3 61.7 + - - +
83C GLY 3.4 7.6 - - - -
84C LEU* 3.8 11.0 - - - -
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Residues in contact with PHE 57 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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316B MET* 4.2 2.6 - - - +
350B TYR* 4.0 9.4 - - - +
46C GLY 3.1 13.0 - - - +
47C ASP* 4.6 11.0 - - - +
55C THR* 4.4 1.6 - - - -
56C GLY* 1.3 77.2 - - - +
58C GLY* 1.3 60.2 + - - +
81C TYR* 3.9 22.9 - + - -
82C ALA* 3.3 4.3 - - - +
83C GLY* 2.9 59.5 + - - +
84C LEU 3.6 15.7 - - - -
85C LYS* 4.0 16.6 - - + -
91C SER* 4.3 12.1 - - - -
92C ILE 3.8 8.5 - - - -
93C ASP* 3.7 23.3 - - + -
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Residues in contact with GLY 58 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17B VAL* 4.4 6.1 - - - -
350B TYR* 3.8 22.9 - - - -
44C VAL 4.7 0.2 - - - -
45C LYS* 3.3 4.2 - - - +
46C GLY 2.8 32.7 + - - +
57C PHE* 1.3 77.9 - - - +
59C ARG* 1.3 61.1 + - - +
81C TYR 3.4 10.3 - - - -
82C ALA* 4.2 0.2 - - - -
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Residues in contact with ARG 59 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17B VAL* 4.0 8.2 - - - +
14C TYR* 3.0 22.3 + - - +
44C VAL 3.3 11.2 - - - +
45C LYS* 4.0 25.4 - - + +
58C GLY* 1.3 75.0 - - - +
60C PHE* 1.3 68.7 + - - +
61C GLU* 2.8 24.7 + - - -
79C LEU* 3.4 23.0 - - + +
80C ALA* 3.2 6.2 + - - -
81C TYR* 3.0 73.1 + - + +
98C TYR* 6.1 0.6 - - - -
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Residues in contact with PHE 60 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17B VAL* 4.5 4.7 - - + +
40B VAL* 3.7 39.7 - - + -
42B LEU* 4.1 16.8 - - + -
62B TRP* 4.0 28.9 - + - -
64B THR* 4.1 4.5 - - + -
66B THR* 4.6 0.7 - - + -
14C TYR* 4.0 1.9 + - - -
42C LEU 5.6 0.9 - - - -
43C GLY* 3.2 4.0 - - - -
44C VAL* 2.8 52.3 + - + +
59C ARG* 1.3 76.1 - - - +
61C GLU* 1.3 72.6 + - - +
62C TRP* 3.9 24.7 - - + -
77C ASN* 3.7 31.2 - - + -
79C LEU 3.2 10.1 - - - -
80C ALA* 4.3 0.4 - - + -
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Residues in contact with GLU 61 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14C TYR* 2.6 31.4 + - + +
41C ARG* 4.0 25.0 + - + -
42C LEU 3.6 8.1 - - - +
59C ARG* 2.8 18.0 + - - +
60C PHE* 1.3 77.9 - - - +
62C TRP* 1.3 58.6 + - - +
77C ASN* 3.6 2.6 - - - -
78C ARG* 2.6 69.8 + - + +
79C LEU* 2.8 36.0 + - + +
98C TYR* 5.1 0.7 + - - -
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Residues in contact with TRP 62 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60A PHE* 3.9 25.6 - + - -
62A TRP* 4.4 16.6 - + - -
77A ASN* 4.5 0.2 - - - -
414A CA 4.5 15.5 - - - -
62B TRP* 4.5 13.3 - + - -
75B ASN* 5.0 1.2 + - - +
40C VAL* 5.0 2.7 - - + -
41C ARG* 3.2 8.2 - - - +
42C LEU* 2.8 65.1 + - + +
60C PHE* 3.9 21.3 - + + -
61C GLU* 1.3 74.0 - - - +
63C GLU* 1.3 65.6 + - - +
64C THR* 3.5 29.8 - - + -
75C ASN* 3.6 39.4 + - - +
76C LYS 3.3 20.2 - - - +
77C ASN* 3.6 18.1 + - - -
78C ARG* 4.6 1.1 - - - -
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Residues in contact with GLU 63 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16C LYS* 4.5 2.6 - - - -
39C ARG* 4.1 27.5 + - + +
40C VAL 3.1 17.0 - - - +
41C ARG* 2.8 43.3 + - - +
62C TRP* 1.3 80.2 - - - +
64C THR* 1.3 66.6 + - - +
65C LYS* 5.0 1.0 - - + +
75C ASN* 3.7 0.3 - - - -
76C LYS* 2.7 66.4 + - + +
78C ARG* 3.7 23.1 + - - +
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Residues in contact with THR 64 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60A PHE* 4.0 9.2 - - + -
77A ASN* 2.9 35.6 + - - +
39C ARG* 3.2 5.2 - - - +
40C VAL* 2.9 38.9 + - + -
62C TRP* 3.5 33.8 - - + -
63C GLU* 1.3 75.3 - - - +
65C LYS* 1.3 63.0 + - - +
66C THR* 3.9 6.2 - - + +
74C GLU 3.3 5.7 + - - -
75C ASN* 3.1 17.2 + - - -
76C LYS* 5.4 0.4 - - - -
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Residues in contact with LYS 65 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77A ASN* 3.0 19.4 + - - -
37C ASP* 2.9 29.0 + - - -
38C SER 3.6 14.1 + - - -
39C ARG* 3.6 34.9 - - + +
63C GLU* 5.0 2.0 - - - +
64C THR* 1.3 76.9 + - - +
66C THR* 1.3 60.7 + - - +
67C ASN* 3.5 20.1 + - - +
68C LYS* 5.4 1.5 + - + -
72C GLU* 5.6 5.1 - - + +
73C GLY 5.8 0.2 + - - -
74C GLU* 3.1 41.5 + - + +
76C LYS* 3.9 24.5 - - + +
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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