Contacts of the strand formed by residues 129 - 138 (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 ARG 129 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70B GLU* 2.6 38.4 + - - -
78C ARG* 3.3 52.6 - - - +
79C LEU* 3.8 16.6 - - + -
96C ARG* 3.4 13.5 + - - +
97C ASN 3.2 7.9 - - - +
98C TYR* 3.1 51.2 + - + +
122C THR* 3.3 19.9 + - + +
123C ASP 3.0 25.3 + - - -
124C ASN 4.6 0.2 + - - -
128C SER* 1.3 86.3 + - - +
130C ASN* 1.3 59.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 130 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96C ARG* 3.1 13.1 - - - +
97C ASN 2.8 32.3 + - - +
123C ASP* 3.5 12.0 - - - +
124C ASN 3.3 18.6 - - - +
125C PHE 2.8 34.7 + - - +
128C SER 3.4 1.1 + - - +
129C ARG* 1.3 73.8 - - - +
131C ARG* 1.3 101.2 + - - +
133C LEU* 3.6 11.9 - - + +
155C GLN* 3.3 19.8 - - - +
170C LYS 4.8 0.2 + - - -
172C ASN* 4.2 2.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 131 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36B ASP* 4.0 4.5 - - - +
66B THR 3.9 20.6 - - - +
67B ASN* 3.3 17.4 + - - +
68B LYS 3.4 16.9 + - - +
69B ALA 4.9 0.2 - - - -
95C GLY 3.7 4.5 - - - +
96C ARG* 3.5 10.0 - - + +
123C ASP* 3.9 8.9 - - - +
130C ASN* 1.3 107.8 + - - +
132C ASN* 1.3 70.2 + - + +
133C LEU* 3.4 2.9 + - - +
155C GLN* 3.1 21.3 + - - -
158C ASN* 3.2 28.8 + - - +
164C SER* 2.9 27.5 + - - -
166C ALA* 3.4 15.2 - - - +
170C LYS 2.7 24.2 + - - -
171C ASP* 3.0 25.1 + - - -
172C ASN* 4.2 0.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 132 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B HIS* 2.8 35.9 + - - -
35B GLY* 4.2 0.4 - - - -
36B ASP* 3.1 23.4 + - + +
94C TYR* 2.9 12.0 + - - -
95C GLY 3.0 7.2 + - - -
131C ARG* 1.3 75.7 - - - +
133C LEU* 1.3 59.2 + - - +
134C LEU 4.1 0.2 + - - -
154C TYR 3.6 1.2 - - - +
155C GLN* 3.2 5.5 - - - -
156C GLY* 2.9 46.1 + - - +
157C LYS 3.1 11.9 + - - -
158C ASN* 2.9 28.8 + - - +
164C SER* 3.8 4.9 + - - -
407C LDA 5.0 0.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 133 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93C ASP* 3.7 2.4 - - - +
94C TYR* 3.2 7.7 - - - -
95C GLY 3.0 30.9 + - - +
97C ASN* 3.3 37.4 - - + +
98C TYR 4.0 0.2 - - - +
99C GLY* 3.9 17.3 - - - +
126C MET* 4.0 13.7 - - + -
130C ASN* 3.6 19.1 - - + +
131C ARG 3.9 2.5 - - - +
132C ASN* 1.3 75.8 - - - +
134C LEU* 1.3 59.4 + - - +
135C THR* 4.1 4.3 + - - +
153C GLN* 3.9 18.8 - - - +
154C TYR 3.5 0.9 - - - +
155C GLN* 3.5 42.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 134 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92C ILE* 3.9 27.1 - - + -
93C ASP 3.4 13.2 - - - +
94C TYR* 4.0 15.0 - - + -
132C ASN 4.1 0.4 + - - -
133C LEU* 1.3 72.5 - - - +
135C THR* 1.3 62.6 + - - +
136C TYR 4.3 0.2 - - - -
153C GLN* 3.2 4.5 - - - +
154C TYR* 2.8 43.1 + - + +
406C LDA 4.0 18.6 - - + -
407C LDA 4.1 30.5 - - + -
408C LDA 3.9 16.4 - - + +
409C LDA 4.2 24.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 135 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91C SER* 3.7 1.2 + - - +
92C ILE* 3.3 6.9 - - - -
93C ASP* 2.9 52.1 + - - +
97C ASN* 5.3 3.1 - - - +
98C TYR 4.7 1.8 + - - +
100C VAL* 4.3 6.5 - - + -
133C LEU* 4.2 4.9 - - - +
134C LEU* 1.3 78.0 + - - +
136C TYR* 1.3 67.1 + - - +
137C ARG* 3.9 34.1 + - + +
152C LEU 3.4 9.4 - - - +
153C GLN* 2.8 29.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 136 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89C PHE 2.4 29.7 + - - -
90C GLY 4.2 0.4 - - - -
91C SER 3.1 28.3 - - - -
92C ILE* 3.7 18.2 - - + -
135C THR* 1.3 73.4 - - - +
137C ARG* 1.3 69.5 + - - +
138C ASN* 2.8 21.0 + - + -
142C PHE* 3.5 12.9 - + - -
150C PHE* 3.8 26.9 - + - -
151C ALA* 3.2 4.3 - - - +
152C LEU* 2.7 60.5 + - + +
408C LDA 3.7 14.1 - - + +
439C LDA 4.4 15.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 137 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85C LYS* 5.8 0.5 + - - -
90C GLY* 3.1 4.5 - - - -
91C SER* 2.9 45.8 + - - +
93C ASP* 5.1 7.0 + - - +
97C ASN* 6.2 0.8 - - - +
98C TYR* 4.2 13.1 + - - +
100C VAL* 4.0 11.9 - - - +
103C ASP* 2.8 43.2 + - - -
135C THR* 3.9 17.5 - - + +
136C TYR* 1.3 83.9 - - - +
138C ASN* 1.3 60.7 + - - +
150C PHE 3.7 4.9 - - - +
151C ALA* 3.5 15.7 - - + +
179C SER* 4.4 0.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 138 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88C ASP 4.2 2.7 + - - +
89C PHE* 3.4 18.2 + - - +
90C GLY* 4.4 3.6 - - - -
136C TYR* 2.8 23.6 + - + +
137C ARG* 1.3 73.8 - - - +
139C ASN* 1.3 72.3 + - - +
140C ASN 3.4 2.1 + - - -
141C ALA 3.1 6.6 + - - -
142C PHE* 3.0 41.8 + - - +
149C SER* 3.3 5.5 - - - -
150C PHE* 3.0 61.9 + - + +
----------------------------------------------------------
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