Contacts of the strand formed by residues 75 - 86 (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 ASN 75 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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62A TRP* 4.9 0.9 + - - +
75A ASN* 3.4 25.3 + - - +
77A ASN* 4.8 3.0 + - - +
70B GLU 3.9 0.3 - - - +
71B ASN* 3.3 26.2 - - - +
73B GLY* 4.9 13.4 + - - -
75B ASN* 3.4 14.7 - - - +
62C TRP* 3.6 26.2 + - - +
63C GLU 3.7 3.4 - - - -
64C THR* 3.1 22.0 + - - -
73C GLY* 2.9 24.2 + - - +
74C GLU* 1.3 74.9 + - - +
76C LYS* 1.3 63.6 + - - +
77C ASN* 4.4 1.1 - - - +
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Residues in contact with LYS 76 (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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70B GLU* 3.3 29.5 + - + +
71B ASN* 3.9 14.4 - - + +
39C ARG* 6.1 0.2 - - - +
62C TRP* 3.3 11.0 - - - +
63C GLU* 2.7 64.2 + - + +
65C LYS* 3.9 26.4 - - + +
74C GLU* 3.7 28.5 - - + +
75C ASN* 1.3 81.4 - - - +
77C ASN* 1.3 63.5 + - - +
78C ARG* 3.5 4.1 + - + +
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Residues in contact with ASN 77 (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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62B TRP* 4.6 0.5 - - - -
64B THR* 2.9 40.2 + - - +
65B LYS 3.1 16.2 + - - -
66B THR* 4.1 18.1 - - + +
69B ALA 5.4 3.0 + - - +
70B GLU* 2.8 23.9 + - - +
72B GLU* 6.0 0.2 - - - +
73B GLY* 4.9 9.7 - - - +
75B ASN* 4.7 4.6 + - - +
60C PHE* 3.7 7.8 - - + -
61C GLU 3.9 4.0 - - - -
62C TRP* 3.6 19.4 + - - -
75C ASN* 4.4 0.8 - - - +
76C LYS* 1.3 70.0 + - - +
78C ARG* 1.3 60.7 + - - +
79C LEU 3.6 1.3 - - - -
80C ALA* 5.7 0.9 - - + -
96C ARG* 3.1 23.5 + - - -
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Residues in contact with ARG 78 (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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70B GLU* 3.4 19.0 + - - +
41C ARG* 3.1 36.6 - - - +
61C GLU* 2.6 48.0 + - - +
63C GLU* 3.7 40.6 + - + +
76C LYS* 3.5 4.5 + - + +
77C ASN* 1.3 73.4 - - - +
79C LEU* 1.3 61.3 + - - +
96C ARG* 2.9 22.0 + - - +
98C TYR* 3.3 24.0 + - - -
129C ARG* 3.3 46.0 - - - +
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Residues in contact with LEU 79 (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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59C ARG* 3.4 46.2 - - + +
60C PHE* 3.2 8.3 - - - -
61C GLU* 2.8 50.9 + - + +
77C ASN 5.1 0.2 - - - -
78C ARG* 1.3 89.9 - - + +
80C ALA* 1.3 62.9 + - - +
81C TYR* 4.2 13.0 - - + -
96C ARG* 3.6 4.5 - - - +
97C ASN* 3.9 22.2 - - - +
98C TYR* 3.9 20.0 - - + -
129C ARG* 3.8 22.2 - - + -
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Residues in contact with ALA 80 (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* 4.1 6.1 - - + -
19B VAL* 3.9 5.2 - - + +
38B SER* 5.3 0.3 - - - -
40B VAL* 3.8 14.4 - - + -
66B THR* 3.7 40.9 + - + +
59C ARG 3.2 6.5 - - - -
60C PHE* 4.3 1.6 - - + +
77C ASN* 5.7 0.4 - - + -
79C LEU* 1.3 75.2 - - - +
81C TYR* 1.3 55.6 - - - +
95C GLY* 3.5 4.5 - - - -
96C ARG* 2.7 38.8 + - + +
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Residues in contact with TYR 81 (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* 3.5 8.6 - - - +
19B VAL* 4.0 2.0 - - - -
57C PHE* 3.9 31.9 - + - -
58C GLY* 3.4 1.9 - - - -
59C ARG* 3.0 81.2 + - + -
79C LEU* 4.2 12.6 - - + -
80C ALA* 1.3 77.2 - - - +
82C ALA* 1.3 61.8 + - - +
93C ASP* 4.2 10.1 - - + +
94C TYR 3.3 18.8 - - - +
96C ARG 3.4 16.2 - - - +
97C ASN* 3.1 40.6 - - - +
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Residues in contact with ALA 82 (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 6.3 - - + -
19B VAL* 4.0 13.0 - - + +
316B MET* 4.6 0.7 - - + -
348B LEU* 3.7 26.3 - - + +
350B TYR* 4.3 18.6 - - + +
57C PHE* 3.3 13.9 - - - +
81C TYR* 1.3 76.1 - - - +
83C GLY* 1.3 58.8 + - - +
93C ASP* 3.3 5.5 - - - -
94C TYR* 2.9 31.4 + - - +
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Residues in contact with GLY 83 (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* 3.3 8.5 - - - +
348B LEU* 3.6 11.0 - - - +
56C GLY* 3.4 0.7 - - - -
57C PHE* 2.9 45.2 + - - -
82C ALA* 1.3 77.0 - - - +
84C LEU* 1.3 64.9 + - - -
92C ILE 3.1 12.8 - - - -
93C ASP* 3.9 0.4 - - - -
406C LDA 5.8 0.4 - - - -
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Residues in contact with LEU 84 (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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312B PHE* 4.3 14.6 - - + -
316B MET* 3.8 21.8 - - + -
348B LEU* 4.2 12.8 - - + -
50C ILE* 3.6 31.0 - - + -
54C LEU* 4.1 15.9 - - + -
55C THR 3.3 3.4 - - - +
56C GLY* 3.8 3.1 - - - -
57C PHE* 3.7 2.5 - - - -
83C GLY* 1.3 83.5 - - - +
85C LYS* 1.3 60.2 + - - +
86C PHE 4.3 0.2 - - - -
91C SER* 3.2 2.8 - - - -
92C ILE* 2.8 39.9 + - + +
406C LDA 3.6 44.9 - - + -
439C LDA 4.6 3.2 - - - -
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Residues in contact with LYS 85 (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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53C GLN 3.4 2.6 - - - +
54C LEU* 3.5 4.3 - - - +
55C THR* 2.9 48.4 + - - +
57C PHE* 4.0 16.2 - - + -
84C LEU* 1.3 75.3 - - - +
86C PHE* 1.3 66.4 - - - +
87C ALA* 5.1 2.9 - - - +
88C ASP 6.0 1.1 - - - +
90C GLY* 3.3 27.6 - - - +
91C SER* 3.8 11.0 + - - -
137C ARG 5.8 0.4 + - - -
139C ASN* 4.3 21.6 - - - +
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Residues in contact with PHE 86 (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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51C THR* 5.1 1.8 - - - -
53C GLN* 3.3 40.2 - - + -
54C LEU* 3.9 18.6 - - + -
84C LEU 4.3 0.2 - - - -
85C LYS* 1.3 79.0 - - - +
87C ALA* 1.3 78.1 + - - +
88C ASP 3.2 0.5 + - - -
89C PHE* 2.9 43.1 + + + -
90C GLY 2.9 15.2 + - - +
406C LDA 4.1 33.0 - - + -
439C LDA 3.9 31.7 - - - -
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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