Contacts of the strand formed by residues 75 - 86 (chain A) 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 A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A TRP* 3.6 26.6 - - - +
63A GLU 3.7 3.8 - - - -
64A THR* 3.1 22.2 + - - -
73A GLY* 2.9 24.7 + - - +
74A GLU* 1.3 74.9 + - - +
76A LYS* 1.3 63.5 + - - +
77A ASN* 6.0 0.4 - - - +
62B TRP* 5.0 0.9 + - - +
75B ASN* 3.4 17.1 + - - +
77B ASN* 4.8 2.8 + - - +
70C GLU 3.7 0.7 - - - +
71C ASN* 3.2 26.5 - - - +
73C GLY* 4.9 13.7 + - - -
75C ASN* 3.4 24.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 76 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A TRP* 3.3 10.6 - - - +
63A GLU* 2.7 60.4 + - + +
65A LYS* 3.8 29.5 - - + +
74A GLU* 3.4 30.9 + - + +
75A ASN* 1.3 80.5 - - - +
77A ASN* 1.3 64.1 + - - +
78A ARG* 3.5 4.6 + - + -
70C GLU* 3.3 26.9 - - + +
71C ASN* 4.0 12.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 77 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A PHE* 3.6 7.8 - - + -
61A GLU 3.7 4.0 - - - -
62A TRP* 3.6 19.8 + - - -
75A ASN* 6.0 1.5 - - - +
76A LYS* 1.3 68.3 - - - +
78A ARG* 1.3 61.3 + - - +
79A LEU 3.6 1.1 - - - -
80A ALA* 5.6 0.4 - - + -
96A ARG* 3.1 16.6 + - - -
62C TRP* 4.5 0.5 - - - -
64C THR* 2.9 41.1 + - - +
65C LYS 3.0 17.2 + - - -
66C THR* 4.1 17.7 - - + +
70C GLU* 2.8 32.1 + - - +
72C GLU* 6.2 0.8 - - - +
73C GLY* 5.1 7.9 - - - +
75C ASN* 4.8 4.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 78 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A ARG* 3.1 36.1 - - - +
61A GLU* 2.6 47.3 + - - +
63A GLU* 3.7 41.9 + - + +
76A LYS* 3.5 4.9 + - + +
77A ASN* 1.3 73.3 - - - +
79A LEU* 1.3 60.9 + - - +
96A ARG* 2.9 22.4 + - - +
98A TYR* 3.3 24.0 + - - -
129A ARG* 3.3 42.3 - - - +
70C GLU* 3.3 22.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 79 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A ARG* 3.4 46.9 - - + +
60A PHE* 3.2 8.0 - - - -
61A GLU* 2.8 49.0 + - + +
78A ARG* 1.3 88.8 - - + +
80A ALA* 1.3 63.7 + - - +
81A TYR* 4.2 12.8 - - + -
96A ARG* 3.6 4.0 - - - +
97A ASN* 4.0 22.0 - - - +
98A TYR* 3.9 19.7 - - + -
129A ARG* 3.8 22.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 80 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A ARG 3.3 6.7 - - - -
60A PHE* 4.3 2.0 - - + +
77A ASN* 5.6 0.7 - - + -
79A LEU* 1.3 73.7 - - - +
81A TYR* 1.3 55.6 + - - +
95A GLY* 3.5 4.3 - - - -
96A ARG* 2.7 38.4 + - + +
17C VAL* 4.2 5.8 - - + -
19C VAL* 3.9 5.2 - - + +
38C SER* 5.3 0.9 - - - -
40C VAL* 3.9 13.9 - - + -
66C THR* 3.6 41.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 81 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A PHE* 3.9 32.1 - + - -
58A GLY* 3.4 1.9 - - - -
59A ARG* 3.0 81.1 + - + -
79A LEU* 4.2 11.7 - - + -
80A ALA* 1.3 77.5 - - - +
82A ALA* 1.3 61.6 + - - +
93A ASP* 4.2 9.9 - - + +
94A TYR 3.3 19.5 - - - +
95A GLY 4.3 0.2 - - - +
96A ARG 3.4 14.8 - - - +
97A ASN* 3.1 40.6 - - - +
17C VAL* 3.4 8.7 - - - +
19C VAL* 4.0 2.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 82 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A PHE* 3.3 13.7 - - - +
81A TYR* 1.3 76.9 - - - +
83A GLY* 1.3 58.4 + - - +
93A ASP* 3.3 5.6 - - - -
94A TYR 2.9 31.2 + - - +
17C VAL* 4.5 4.5 - - + -
19C VAL* 4.0 14.7 - - + +
316C MET* 4.8 0.7 - - + -
348C LEU* 3.7 27.3 - - + +
350C TYR* 4.3 17.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 83 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A GLY* 3.4 0.5 - - - -
57A PHE* 2.9 46.2 + - - -
82A ALA* 1.3 76.5 - - - +
84A LEU* 1.3 59.6 + - - -
92A ILE 3.1 12.8 - - - -
93A ASP* 3.9 0.4 - - - -
316C MET* 3.2 11.7 - - - +
348C LEU* 3.7 11.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 84 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A ILE* 3.6 31.0 - - + -
54A LEU* 4.1 17.5 - - + -
55A THR 3.4 7.6 - - - +
56A GLY* 4.2 0.2 - - - -
57A PHE* 3.7 2.7 - - - -
83A GLY* 1.3 74.6 - - - -
85A LYS* 1.3 60.4 + - - +
90A GLY 4.3 0.2 - - - +
91A SER* 3.2 2.9 - - - -
92A ILE* 2.8 51.0 + - + +
312C PHE* 3.7 34.1 - - + -
316C MET* 3.9 20.6 - - + -
348C LEU* 5.4 5.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 85 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A GLN 3.4 3.6 - - - +
54A LEU* 3.5 4.4 - - - +
55A THR* 2.9 46.9 + - - +
57A PHE* 4.0 15.9 - - + -
84A LEU* 1.3 76.1 - - - +
86A PHE* 1.3 68.0 + - - +
87A ALA* 5.1 3.8 - - - +
88A ASP* 4.7 6.7 - - - +
90A GLY* 3.3 36.4 - - - +
91A SER* 3.8 8.5 - - - -
138A ASN* 5.7 0.6 - - - +
139A ASN* 5.3 14.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 86 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A THR* 5.1 2.0 - - - -
53A GLN* 3.3 39.9 - - + -
54A LEU* 3.9 24.0 - - + -
84A LEU 4.3 0.2 - - - -
85A LYS* 1.3 77.5 + - - +
87A ALA* 1.3 77.0 + - - +
88A ASP 3.2 0.9 + - - -
89A PHE* 2.9 48.1 + + + -
90A GLY 2.9 16.4 + - - +
----------------------------------------------------------
Back to top of page
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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
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