Contacts of the strand formed by residues 90 - 98 (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 GLY 90 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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85A LYS* 3.3 17.6 - - - +
86A PHE* 2.9 30.6 + - - +
88A ASP 3.6 1.6 - - - -
89A PHE* 1.3 81.2 - - - +
91A SER* 1.3 61.1 + - - -
136A TYR* 3.9 3.8 - - - -
137A ARG 3.1 15.0 - - - -
138A ASN* 3.8 9.6 - - - +
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Residues in contact with SER 91 (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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57A PHE* 4.3 13.6 - - - -
84A LEU 3.2 11.7 - - - -
85A LYS* 3.8 18.8 - - - -
90A GLY* 1.3 75.6 - - - -
92A ILE* 1.3 61.7 + - - +
93A ASP* 5.1 3.3 + - - -
135A THR 3.7 0.3 + - - +
136A TYR* 3.1 10.6 - - - -
137A ARG* 2.9 50.5 + - - +
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Residues in contact with ILE 92 (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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57A PHE* 3.8 1.3 - - - -
83A GLY* 3.1 2.3 - - - -
84A LEU* 2.8 54.6 + - + +
91A SER* 1.3 74.8 - - - +
93A ASP* 1.3 62.5 + - - +
134A LEU* 3.9 21.1 - - + -
135A THR 3.3 19.1 - - - +
136A TYR* 3.7 24.5 - - + +
405A LDA 3.8 14.6 - - + -
407A LDA 5.4 5.4 - - + -
413A LDA 4.8 15.9 - - + -
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Residues in contact with ASP 93 (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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57A PHE* 3.8 21.3 - - + -
81A TYR* 4.2 9.6 - - + +
82A ALA 3.3 14.1 - - - +
83A GLY* 3.9 0.4 - - - -
91A SER* 5.1 3.3 + - - -
92A ILE* 1.3 77.6 - - - +
94A TYR* 1.3 64.1 + - - +
97A ASN* 3.3 32.1 + - - +
133A LEU 4.6 1.2 - - - +
134A LEU* 3.4 7.4 - - - +
135A THR* 2.9 54.7 + - - +
137A ARG* 4.7 9.2 - - - -
348C LEU* 5.9 0.2 - - - -
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Residues in contact with TYR 94 (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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81A TYR* 3.3 6.8 - - - +
82A ALA 2.9 31.2 + - - +
93A ASP* 1.3 75.8 - - - +
95A GLY* 1.3 58.9 + - - +
132A ASN* 2.9 29.6 + - - -
133A LEU 3.0 38.6 - - - -
134A LEU* 3.9 13.0 - - + -
19C VAL* 3.6 24.9 - - + +
20C ARG 3.4 33.2 + - - -
21C HIS* 3.3 17.0 + - + -
36C ASP* 3.3 17.2 + - - +
38C SER* 4.1 5.8 - - - -
348C LEU* 5.4 2.2 - - + +
401C LDA 3.8 41.7 - - + -
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Residues in contact with GLY 95 (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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80A ALA 3.5 7.0 - - - -
81A TYR* 4.2 0.6 - - - +
93A ASP* 4.8 0.2 + - - -
94A TYR* 1.3 91.5 - - - +
96A ARG* 1.3 59.9 + - - -
97A ASN* 3.9 1.6 + - - -
130A ASN 3.8 1.0 - - - +
131A ARG 3.6 0.7 - - - -
132A ASN 3.0 26.0 + - - -
133A LEU* 3.0 17.0 + - - +
19C VAL* 4.1 6.5 - - - -
36C ASP* 4.3 6.3 - - - -
38C SER* 4.6 1.8 - - - -
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Residues in contact with ARG 96 (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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77A ASN* 3.1 24.0 + - - -
78A ARG 2.9 21.9 + - - +
79A LEU* 3.6 2.6 - - - +
80A ALA* 2.7 42.6 + - + +
81A TYR* 3.4 9.2 - - - -
95A GLY* 1.3 72.0 - - - -
97A ASN* 1.3 62.7 + - - +
122A THR* 3.4 7.5 - - - +
123A ASP* 2.7 30.9 + - - -
129A ARG 3.4 16.0 + - - -
130A ASN* 3.1 15.9 - - - +
131A ARG* 3.6 18.6 - - - +
38C SER* 6.0 0.2 - - - -
66C THR* 4.3 19.7 - - - +
68C LYS 3.9 14.6 + - - -
70C GLU* 2.8 28.6 + - - +
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Residues in contact with ASN 97 (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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79A LEU* 4.0 9.0 - - - +
81A TYR* 3.1 40.1 - - + -
93A ASP* 3.3 31.5 + - - +
95A GLY 3.9 2.9 + - - -
96A ARG* 1.3 72.8 - - - +
98A TYR* 1.3 90.1 + - - +
129A ARG* 3.2 4.0 - - - -
130A ASN 2.8 33.4 + - - +
133A LEU* 3.3 15.2 - - + +
135A THR* 5.3 3.5 + - - +
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Residues in contact with TYR 98 (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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59A ARG* 6.1 0.2 - - - -
61A GLU* 5.1 0.7 + - - -
78A ARG* 3.3 14.6 + - - -
79A LEU* 3.9 22.2 - - + -
97A ASN* 1.3 94.3 + - - +
99A GLY* 1.3 67.4 - - - +
100A VAL 3.8 0.2 + - - -
102A TYR* 3.5 43.8 + + + -
103A ASP* 4.8 6.5 - - - +
128A SER* 3.8 4.7 - - - -
129A ARG* 3.1 53.5 + - + -
133A LEU* 4.0 1.5 - - - +
135A THR* 4.7 0.7 + - - +
137A ARG* 4.6 9.3 + - - +
153A GLN* 3.2 14.7 + - - -
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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