Contacts of the strand formed by residues 92 - 97 (chain B) in PDB entry 1NPP
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 GLU 92 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68B LEU* 4.0 1.1 - - - -
87B ARG 3.7 0.5 - - - +
88B ILE* 3.4 5.0 - - - +
89B GLU* 3.1 36.6 + - + +
90B ASN* 3.8 14.0 + - + +
91B GLY* 1.3 76.3 - - - +
93B VAL* 1.3 65.7 + - - +
94B LYS* 5.9 0.4 - - - +
109B PRO* 3.7 33.1 - - + +
110B ILE 3.1 15.5 - - - +
111B SER* 4.3 7.9 + - - -
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Residues in contact with VAL 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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54B VAL* 3.5 40.8 - - + -
56B ILE* 5.9 0.2 - - + -
68B LEU* 4.0 2.5 - - + -
86B PHE* 4.3 13.0 - - + -
87B ARG 3.3 10.3 - - - +
88B ILE* 4.4 7.0 - - + -
92B GLU* 1.3 78.1 - - - +
94B LYS* 1.3 68.9 + - - +
109B PRO* 3.1 7.0 - - - +
110B ILE* 2.9 37.9 + - + -
117B ILE* 3.7 5.6 - - + +
126B ALA* 4.0 22.7 - - + -
128B ILE* 3.6 14.1 - - + -
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Residues in contact with LYS 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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86B PHE* 3.4 7.4 - - - +
87B ARG* 2.8 62.2 + - + +
89B GLU* 3.9 22.5 + - - -
92B GLU 5.9 0.2 - - - +
93B VAL* 1.3 76.9 - - - +
95B VAL* 1.3 67.4 + - - +
96B VAL* 4.3 10.0 - - + +
105B VAL 6.0 0.7 - - - +
107B ALA 5.0 4.0 - - - +
109B PRO* 4.0 26.0 - - + -
117B ILE* 4.1 7.6 - - - -
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Residues in contact with VAL 95 (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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84B THR* 4.3 2.5 - - + -
85B THR 3.8 5.6 - - - +
86B PHE* 3.7 22.4 - - + +
94B LYS* 1.3 79.8 - - - +
96B VAL* 1.3 62.9 + - - +
97B GLU 3.6 23.1 - - - +
98B SER* 4.2 1.8 - - - -
104B CYS* 3.7 19.4 + - - +
105B VAL* 3.5 38.3 + - + +
107B ALA 5.4 1.2 + - - -
117B ILE* 3.8 18.4 - - + +
119B CYS* 3.6 24.2 - - - -
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Residues in contact with VAL 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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74B ASP* 4.4 12.8 - - - +
85B THR* 2.9 41.2 + - - +
86B PHE 4.4 2.9 - - - +
87B ARG* 3.4 51.8 - - + +
94B LYS* 4.3 10.5 - - - +
95B VAL* 1.3 76.4 - - - +
97B GLU* 1.3 62.0 + - + +
105B VAL* 4.8 5.0 - - - +
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Residues in contact with GLU 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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83B VAL* 5.0 9.5 - - - +
84B THR* 3.3 0.3 - - - -
85B THR* 2.8 50.7 + - + +
95B VAL* 3.5 6.1 - - - +
96B VAL* 1.3 83.4 - - + +
98B SER* 1.3 76.4 + - - +
105B VAL* 4.6 3.8 - - - -
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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