Contacts of the strand formed by residues 129 - 138 (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 ARG 129 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A GLU* 2.7 36.0 + - - -
78B ARG* 3.3 54.3 - - - +
79B LEU* 3.8 15.3 - - + -
96B ARG* 3.3 14.8 + - - +
97B ASN 3.2 8.1 - - - +
98B TYR* 3.1 51.2 + - + -
121B GLN 4.6 0.2 - - - +
122B THR* 3.3 20.3 + - + -
123B ASP 2.9 25.6 + - - -
128B SER* 1.3 86.6 + - - +
130B ASN* 1.3 60.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 130 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96B ARG* 3.1 13.9 - - - +
97B ASN 2.8 32.8 + - - +
123B ASP* 3.5 12.6 - - - +
124B ASN 3.3 18.2 - - - +
125B PHE 2.8 34.7 + - - +
128B SER 3.4 1.3 + - - +
129B ARG* 1.3 73.1 - - - +
131B ARG* 1.3 102.6 + - - +
133B LEU* 3.6 12.0 - - + +
155B GLN* 3.3 20.2 - - - +
172B ASN* 4.1 2.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 131 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A ASP* 4.0 5.8 - - - +
66A THR 3.9 20.6 - - - +
67A ASN* 3.4 17.9 + - - +
68A LYS 3.4 17.3 + - - +
95B GLY 3.7 4.3 - - - +
96B ARG* 3.6 10.6 - - + +
123B ASP* 3.9 8.9 - - - +
130B ASN* 1.3 106.9 + - - +
132B ASN* 1.3 71.4 + - + +
133B LEU* 3.4 2.1 + - - +
155B GLN* 3.1 21.5 + - - -
158B ASN* 3.2 29.6 + - - +
164B SER* 2.9 27.2 + - - -
166B ALA* 3.4 14.9 - - - +
170B LYS 2.7 23.8 + - - -
171B ASP* 3.0 25.5 + - - -
172B ASN* 4.2 0.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 132 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A HIS* 2.9 21.4 + - - -
35A GLY* 4.3 0.2 - - - -
36A ASP* 3.2 22.4 + - + +
402A LDA 5.2 0.9 - - - +
94B TYR* 2.9 25.3 + - - -
95B GLY 3.0 6.9 + - - -
131B ARG* 1.3 78.5 - - - +
133B LEU* 1.3 58.9 + - - +
134B LEU 4.1 0.2 + - - -
154B TYR 3.6 1.2 - - - +
155B GLN* 3.2 5.7 - - - +
156B GLY* 2.9 46.0 + - - +
157B LYS 3.1 11.7 + - - -
158B ASN* 2.9 29.7 + - - +
164B SER* 3.8 5.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 133 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93B ASP* 3.7 2.4 - - - +
94B TYR* 3.0 9.1 - - - -
95B GLY 3.0 31.9 + - - +
97B ASN* 3.3 35.2 - - + +
98B TYR 4.0 4.0 - - - +
99B GLY* 3.9 19.7 - - - +
126B MET* 4.0 13.7 - - + -
130B ASN* 3.6 20.0 - - + +
131B ARG 3.9 2.2 - - - +
132B ASN* 1.3 76.7 - - - +
134B LEU* 1.3 58.5 + - - +
135B THR* 4.1 11.2 + - - +
153B GLN* 4.1 7.4 - - - +
154B TYR 3.5 0.7 - - - +
155B GLN* 3.5 43.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 134 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
402A LDA 4.2 37.9 - - + -
92B ILE* 3.9 25.6 - - + -
93B ASP 3.4 13.7 - - - +
94B TYR* 4.0 20.1 - - + -
132B ASN 4.1 0.2 + - - -
133B LEU* 1.3 72.5 - - - +
135B THR* 1.3 61.2 + - - +
136B TYR 4.2 0.2 - - - -
152B LEU 4.0 0.2 - - - +
153B GLN* 3.2 5.5 - - - +
154B TYR* 2.8 43.8 + - + +
401B LDA 4.3 20.9 - - + +
416B LDA 6.0 3.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 135 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91B SER* 3.7 1.4 + - - +
92B ILE* 3.3 6.7 - - - -
93B ASP* 2.9 52.7 + - - +
97B ASN* 5.3 3.0 - - - +
98B TYR 4.7 1.4 + - - +
100B VAL* 4.4 4.9 - - + -
133B LEU* 4.2 5.4 - - - +
134B LEU* 1.3 77.0 + - - +
136B TYR* 1.3 66.2 + - - +
137B ARG* 3.8 32.4 + - + +
152B LEU 3.4 9.0 - - - +
153B GLN* 2.7 32.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 136 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89B PHE 2.4 29.7 + - - -
90B GLY 4.2 0.4 - - - -
91B SER 3.1 27.1 - - - -
92B ILE* 3.7 20.3 - - + +
135B THR* 1.3 73.7 - - - +
137B ARG* 1.3 70.9 + - - +
138B ASN* 2.8 19.6 + - + -
142B PHE* 3.5 12.9 - + - -
150B PHE* 3.8 25.4 - + - -
151B ALA* 3.2 4.0 - - - +
152B LEU* 2.7 59.4 + - + +
401B LDA 3.8 14.7 - - + +
415B LDA 4.6 12.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 137 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85B LYS* 5.7 0.3 + - - -
90B GLY* 3.1 4.7 - - - -
91B SER* 2.9 45.5 + - - +
93B ASP* 5.2 6.7 + - - +
97B ASN* 6.2 1.0 - - - +
98B TYR* 4.3 13.3 + - - +
100B VAL* 4.0 12.7 - - - +
103B ASP* 2.8 42.6 + - - -
135B THR* 3.8 17.2 - - + +
136B TYR* 1.3 83.3 - - - +
138B ASN* 1.3 60.7 + - - +
150B PHE 3.6 4.2 - - - +
151B ALA* 3.5 15.5 - - + +
179B SER* 4.4 0.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 138 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88B ASP 4.1 1.2 + - - -
89B PHE* 3.4 18.0 + - - +
90B GLY* 4.4 3.6 - - - -
136B TYR* 2.8 23.8 + - + +
137B ARG* 1.3 75.2 - - - +
139B ASN* 1.3 71.5 + - - +
140B ASN* 3.3 5.1 - - - +
141B ALA 3.1 7.0 + - - -
142B PHE* 3.0 40.8 + - - +
149B SER* 3.3 6.2 - - - -
150B PHE* 3.0 60.8 + - + +
----------------------------------------------------------
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