Contacts of the strand formed by residues 90 - 98 (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 GLY 90 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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85B LYS* 3.3 15.5 - - - +
86B PHE 2.9 30.1 + - - +
88B ASP 3.6 2.6 - - - +
89B PHE* 1.3 80.0 - - - +
91B SER* 1.3 61.3 + - - -
136B TYR* 3.9 1.3 - - - -
137B ARG 3.1 15.0 - - - -
138B ASN* 3.7 8.6 - - - +
139B ASN 5.4 0.4 - - - -
415B LDA 3.4 6.0 - - - +
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Residues in contact with SER 91 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57B PHE* 4.3 13.8 - - - -
84B LEU 3.2 12.1 - - - -
85B LYS* 3.8 20.0 - - - -
90B GLY* 1.3 75.2 - - - -
92B ILE* 1.3 62.1 + - - +
93B ASP* 5.1 4.0 + - - -
135B THR 3.7 0.9 + - - +
136B TYR* 3.1 9.2 - - - -
137B ARG* 2.9 48.9 + - - +
415B LDA 4.1 1.3 - - - -
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Residues in contact with ILE 92 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57B PHE* 3.8 1.1 - - - -
83B GLY* 3.1 2.4 - - - -
84B LEU* 2.8 40.1 + - + +
91B SER* 1.3 74.1 - - - +
93B ASP* 1.3 63.2 + - - +
134B LEU* 3.9 25.8 - - + -
135B THR 3.3 17.7 - - - +
136B TYR* 3.7 25.4 - - + +
401B LDA 4.0 10.8 - - + -
415B LDA 4.1 11.2 - - + -
416B LDA 3.7 41.7 - - + +
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Residues in contact with ASP 93 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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348A LEU* 5.8 0.2 - - - -
57B PHE* 3.8 22.5 - - + -
81B TYR* 4.1 9.0 - - + +
82B ALA 3.3 14.4 - - - +
83B GLY* 3.9 0.4 - - - -
91B SER* 5.1 4.3 + - - -
92B ILE* 1.3 77.2 - - - +
94B TYR* 1.3 64.6 + - - +
97B ASN* 3.3 31.8 + - - +
133B LEU 4.6 1.4 - - - +
134B LEU* 3.4 7.4 - - - +
135B THR* 2.9 54.5 + - - +
137B ARG* 5.2 6.6 + - - +
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Residues in contact with TYR 94 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19A VAL* 3.6 21.5 - - + +
20A ARG 3.4 32.0 + - - -
21A HIS* 3.2 17.7 + - + -
36A ASP* 3.4 17.5 + - - +
38A SER* 4.0 6.3 - - - -
348A LEU* 5.4 1.7 - - + +
402A LDA 3.7 48.5 - - + -
81B TYR* 3.3 6.0 - - - +
82B ALA 2.9 31.1 + - - +
93B ASP* 1.3 76.4 - - - +
95B GLY* 1.3 59.5 + - - +
132B ASN* 2.9 37.7 + - - -
133B LEU 3.0 26.9 - - - -
134B LEU* 4.0 9.2 - - + -
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Residues in contact with GLY 95 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A VAL* 4.2 6.5 - - - -
36A ASP* 4.4 5.8 - - - -
38A SER* 4.7 2.2 - - - -
80B ALA 3.5 6.5 - - - -
81B TYR* 4.2 0.6 - - - +
93B ASP* 4.7 0.6 + - - -
94B TYR* 1.3 90.8 - - - +
96B ARG* 1.3 62.2 + - - -
97B ASN* 3.9 2.0 + - - -
130B ASN 3.8 0.7 - - - +
131B ARG 3.6 0.7 - - - -
132B ASN 3.0 26.1 + - - -
133B LEU* 3.0 16.3 + - - +
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Residues in contact with ARG 96 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38A SER* 6.0 0.2 - - - -
66A THR* 4.3 16.6 - - - +
68A LYS 4.0 14.5 + - - -
70A GLU* 3.0 29.1 + - - +
77B ASN* 3.1 24.0 + - - -
78B ARG 2.9 21.6 + - - +
79B LEU* 3.6 3.5 - - - +
80B ALA* 2.7 40.7 + - + +
81B TYR* 3.4 11.3 - - - +
95B GLY* 1.3 72.0 - - - -
97B ASN* 1.3 60.0 + - - +
122B THR* 3.5 6.7 - - - +
123B ASP* 2.7 31.7 + - - -
129B ARG* 3.3 16.8 + - - +
130B ASN* 3.1 14.8 - - - +
131B ARG* 3.6 19.7 - - - +
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Residues in contact with ASN 97 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79B LEU* 4.0 7.9 - - - +
81B TYR* 3.1 40.2 - - + -
93B ASP* 3.3 30.5 + - - +
95B GLY 3.9 2.5 + - - -
96B ARG* 1.3 73.4 - - - +
98B TYR* 1.3 89.5 + - - +
129B ARG* 4.0 4.0 - - - -
130B ASN 2.8 33.6 + - - +
133B LEU* 3.3 15.3 - - + +
135B THR* 5.3 3.5 + - - +
137B ARG* 6.2 1.1 - - - +
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Residues in contact with TYR 98 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59B ARG* 6.0 0.9 - - - -
61B GLU* 5.0 0.7 + - - -
78B ARG* 3.3 15.1 + - - -
79B LEU* 3.8 21.8 - - + -
97B ASN* 1.3 94.9 + - - +
99B GLY* 1.3 65.8 + - - +
102B TYR* 3.5 45.0 + + + -
103B ASP* 4.8 6.1 - - - +
128B SER* 3.8 4.9 - - - -
129B ARG* 3.1 52.9 + - + -
133B LEU* 4.0 1.5 - - - +
135B THR* 4.7 0.3 + - - +
137B ARG* 4.3 10.3 + - - +
153B GLN* 3.2 15.6 + - - -
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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