Contacts of the strand formed by residues 92 - 97 (chain A) in PDB entry 1NPR
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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68A LEU* 4.5 0.2 - - - -
87A ARG 3.5 0.6 - - - +
88A ILE* 3.3 7.8 - - - +
89A GLU 3.1 28.0 + - - +
90A ASN* 3.0 22.6 + - - +
91A GLY* 1.3 79.6 - - - +
93A VAL* 1.3 68.3 + - - +
94A LYS* 6.0 0.4 - - + -
109A PRO* 3.1 34.2 - - + +
110A ILE 3.3 9.0 - - - +
111A SER* 4.2 11.9 - - - -
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Residues in contact with VAL 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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54A VAL* 3.6 36.3 - - + -
68A LEU* 3.7 8.7 - - + -
86A PHE* 4.5 7.6 - - + -
87A ARG 3.3 9.2 - - - +
88A ILE* 4.3 8.3 - - + -
92A GLU* 1.3 82.7 - - - +
94A LYS* 1.3 69.3 + - - +
109A PRO* 3.0 23.9 - - - +
110A ILE* 3.0 27.3 + - + +
117A ILE* 3.5 5.2 - - + +
126A ALA* 4.2 24.7 - - + -
128A ILE* 4.3 7.6 - - + -
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Residues in contact with LYS 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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86A PHE* 3.2 8.6 - - - +
87A ARG* 2.9 69.6 + - + +
89A GLU* 4.8 7.1 + - - -
92A GLU* 6.0 0.4 - - + -
93A VAL* 1.3 77.5 - - - +
95A VAL* 1.3 68.2 + - - +
96A VAL* 5.3 3.8 - - - +
107A ALA 4.9 4.3 - - - +
109A PRO* 3.9 25.6 - - + -
117A ILE* 3.7 11.0 - - + -
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Residues in contact with VAL 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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84A THR* 4.0 12.6 - - + -
85A THR 3.7 2.9 - - - +
86A PHE* 3.9 15.3 - - + +
94A LYS* 1.3 76.4 - - - +
96A VAL* 1.3 65.8 + - - +
97A GLU 3.7 20.6 - - - +
98A SER* 4.0 2.9 - - - -
104A CYS* 3.8 15.7 + - - +
105A VAL* 3.6 35.9 + - + +
107A ALA 5.3 1.6 + - - -
117A ILE* 3.5 31.7 - - + +
119A CYS* 3.9 13.7 - - - -
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Residues in contact with VAL 96 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A ASP* 3.9 11.7 - - - +
85A THR* 2.6 24.7 + - + +
86A PHE 4.0 0.9 - - - -
87A ARG* 3.3 61.5 - - + +
94A LYS* 3.6 5.4 + - + +
95A VAL* 1.3 73.2 - - - +
97A GLU* 1.3 71.7 + - + +
105A VAL* 3.8 8.9 - - - +
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Residues in contact with GLU 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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83A VAL* 3.5 21.8 - - - +
84A THR* 3.2 0.9 - - - +
85A THR* 2.7 54.3 + - - +
95A VAL* 3.4 5.9 - - - -
96A VAL* 1.3 91.4 - - + +
98A SER* 1.3 63.8 + - - +
105A VAL* 4.2 7.0 - - - -
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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