Contacts of the strand formed by residues 129 - 138 (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 ARG 129 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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78A ARG* 3.3 54.5 - - - +
79A LEU* 3.8 16.6 - - + -
96A ARG* 3.4 14.6 + - - +
97A ASN 3.2 7.6 - - - +
98A TYR* 3.1 50.1 + - + -
122A THR* 3.3 20.5 + - + -
123A ASP 2.9 25.1 + - - -
124A ASN 4.6 0.2 + - - -
128A SER* 1.3 86.0 + - - +
130A ASN* 1.3 59.4 - - - +
70C GLU* 2.7 35.3 + - - +
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Residues in contact with ASN 130 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96A ARG* 3.1 13.9 - - - +
97A ASN 2.8 32.9 + - - +
123A ASP* 3.5 11.7 - - - +
124A ASN 3.3 18.0 - - - +
125A PHE 2.8 35.1 + - - +
128A SER 3.4 0.6 + - - +
129A ARG* 1.3 72.7 - - - +
131A ARG* 1.3 100.5 + - - +
133A LEU* 3.6 12.2 - - + +
155A GLN* 3.3 21.7 + - - +
170A LYS 4.8 0.2 + - - -
172A ASN* 4.2 2.4 + - - -
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Residues in contact with ARG 131 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95A GLY 3.7 3.6 - - - -
96A ARG* 3.6 11.8 - - + +
123A ASP* 4.0 8.4 - - - +
130A ASN* 1.3 108.9 + - - +
132A ASN* 1.3 70.4 + - + +
133A LEU* 3.4 2.1 - - - +
155A GLN* 3.1 22.0 + - - -
158A ASN* 3.2 29.2 + - - +
164A SER* 3.0 26.7 + - - -
166A ALA* 3.3 15.0 - - - +
170A LYS 2.7 24.0 + - - -
171A ASP* 3.0 27.3 + - - -
172A ASN* 4.1 1.0 + - - -
36C ASP* 4.0 5.6 - - - +
66C THR 3.9 20.0 - - - +
67C ASN* 3.4 17.4 + - - +
68C LYS 3.5 16.2 + - - +
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Residues in contact with ASN 132 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94A TYR* 2.9 24.9 + - - -
95A GLY 3.0 7.1 + - - -
131A ARG* 1.3 75.7 - - - +
133A LEU* 1.3 58.6 + - - +
154A TYR 3.6 1.0 - - - +
155A GLN* 3.2 6.1 - - - -
156A GLY* 2.9 46.0 + - - +
157A LYS 3.1 11.9 + - - -
158A ASN* 2.9 28.0 + - - +
164A SER* 3.8 4.9 + - - -
21C HIS* 3.0 21.8 + - - -
35C GLY* 4.2 0.2 - - - -
36C ASP* 3.1 25.8 + - + +
401C LDA 5.0 1.2 - - - +
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Residues in contact with LEU 133 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93A ASP* 3.7 2.4 - - - +
94A TYR* 3.0 9.1 - - - -
95A GLY 3.0 30.4 + - - +
97A ASN* 3.3 34.9 - - + +
98A TYR 4.0 4.0 - - - +
99A GLY* 3.9 20.2 - - - +
126A MET* 4.0 13.7 - - + -
130A ASN* 3.6 14.6 - - + +
131A ARG 3.9 6.5 - - - +
132A ASN* 1.3 76.7 - - - +
134A LEU* 1.3 59.7 + - - +
135A THR* 4.2 10.0 + - - +
153A GLN* 4.1 7.4 - - - +
154A TYR 3.5 1.1 - - - +
155A GLN* 3.5 42.6 - - + +
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Residues in contact with LEU 134 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92A ILE* 3.9 26.2 - - + -
93A ASP 3.4 14.6 - - - +
94A TYR* 4.1 18.8 - - + -
133A LEU* 1.3 71.2 - - - +
135A THR* 1.3 62.8 + - - +
136A TYR 4.3 0.2 - - - -
152A LEU 4.0 0.2 - - - +
153A GLN* 3.2 4.7 - - - +
154A TYR* 2.9 39.5 + - + +
405A LDA 4.3 13.8 - - + +
412A LDA 3.6 29.8 - - + -
413A LDA 4.8 3.8 - - + -
401C LDA 4.4 24.7 - - + +
437C LDA 4.3 19.5 - - + -
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Residues in contact with THR 135 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91A SER 3.7 1.6 - - - +
92A ILE* 3.3 6.3 - - - -
93A ASP* 2.9 53.5 + - - +
97A ASN* 5.3 2.6 - - - +
98A TYR 4.7 1.9 + - - +
100A VAL* 4.3 5.2 - - + -
133A LEU* 4.2 4.5 - - - +
134A LEU* 1.3 79.5 + - - +
136A TYR* 1.3 61.9 + - - +
137A ARG* 4.0 36.4 + - + +
152A LEU 3.4 10.3 - - - +
153A GLN* 2.7 32.7 + - - +
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Residues in contact with TYR 136 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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89A PHE 2.4 31.9 + - - -
90A GLY 4.2 0.4 - - - -
91A SER 3.1 26.9 - - - -
92A ILE* 3.7 10.2 - - + +
135A THR* 1.3 74.1 - - - +
137A ARG* 1.3 70.8 + - - +
138A ASN* 3.7 10.0 - - + -
142A PHE* 3.5 21.8 - + - -
150A PHE* 3.8 27.1 - + - -
151A ALA* 3.2 4.3 - - - +
152A LEU* 2.7 52.8 + - + +
405A LDA 3.7 21.2 - - + +
407A LDA 3.8 42.0 - - + -
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Residues in contact with ARG 137 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90A GLY* 3.1 5.0 - - - -
91A SER* 2.9 46.7 + - - +
93A ASP* 4.7 10.3 - - - -
98A TYR* 4.6 9.3 + - - +
100A VAL* 4.0 6.5 - - - +
103A ASP* 2.8 43.3 + - - +
135A THR* 4.0 23.6 - - + +
136A TYR* 1.3 82.5 - - - +
138A ASN* 1.3 61.1 + - - +
150A PHE 3.7 4.7 - - - +
151A ALA* 3.8 12.5 - - + +
179A SER* 4.7 0.2 + - - -
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Residues in contact with ASN 138 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85A LYS* 5.7 1.0 - - - +
88A ASP 4.1 4.9 + - - -
89A PHE 4.0 2.6 - - - -
90A GLY* 3.8 20.1 - - - +
136A TYR* 3.7 12.1 - - - +
137A ARG* 1.3 75.1 - - - +
139A ASN* 1.3 69.1 + - - +
140A ASN* 3.5 14.9 + - - -
141A ALA 4.2 1.3 - - - -
142A PHE* 3.1 34.8 + - - -
149A SER* 3.3 5.9 - - - -
150A PHE* 3.0 66.2 + - + +
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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