Contacts of the strand formed by residues 108 - 113 (chain B) in PDB entry 1NE2
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 TYR 108 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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51A SER* 4.1 13.7 - - - -
72A GLU* 2.6 43.0 + - - +
73A SER* 3.6 15.4 - - - -
107A LYS* 4.5 2.2 - - - -
51B SER* 3.5 22.9 - - - +
52B VAL 4.2 8.5 - - - -
53B ILE* 3.6 35.9 - - + -
73B SER* 5.6 1.8 - - - -
75B THR* 3.7 22.4 - - - +
104B ILE* 4.8 0.2 - - + -
106B GLY 3.6 12.3 - - - -
107B LYS* 1.3 86.6 + - - +
109B ASP* 1.3 65.4 + - - +
110B THR 4.2 1.3 - - - +
135B THR* 3.2 22.5 + - + +
136B SER* 3.1 30.0 - - - +
137B MSE 3.7 1.7 + - - +
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Residues in contact with ASP 109 (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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105A SER 4.9 0.4 - - - +
106A GLY* 3.3 5.4 - - - -
107A LYS* 2.9 46.9 + - - +
50B ARG* 3.5 22.4 + - + -
51B SER* 2.8 40.7 + - - +
108B TYR* 1.3 71.7 - - - +
110B THR* 1.3 67.2 + - - +
137B MSE 3.1 20.5 + - - +
138B TRP* 2.9 35.0 + - + -
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Residues in contact with THR 110 (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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41B ILE* 4.2 3.8 - - + -
46B ASN* 2.8 36.4 + - - +
50B ARG* 4.5 0.3 - - - +
51B SER 3.1 2.0 + - - -
52B VAL* 3.4 11.9 - - + +
53B ILE* 2.9 29.6 + - - +
108B TYR* 4.2 0.3 - - - +
109B ASP* 1.3 88.2 + - - +
111B TRP* 1.3 63.5 - - - +
112B ILE* 4.2 13.9 - - + -
136B SER* 3.8 3.6 - - - -
138B TRP* 3.3 13.0 - - + +
140B TYR* 3.8 26.2 - - + -
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Residues in contact with TRP 111 (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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53B ILE* 3.4 24.9 - - + -
55B ALA* 3.4 25.4 - - + -
77B PHE* 4.1 12.6 - + - -
101B VAL* 4.1 1.1 - - + -
104B ILE* 4.4 8.3 - - + -
110B THR* 1.3 72.3 - - - +
112B ILE* 1.3 70.3 + - - +
113B MSE 3.5 29.2 - - + +
128B PHE* 3.6 23.8 - + - -
131B LYS* 3.4 35.0 - - + -
132B ALA* 3.5 25.1 - - + +
135B THR* 3.9 18.4 - - + -
136B SER* 3.3 17.2 + - - +
138B TRP 2.8 10.3 + - - +
139B ILE* 3.5 14.9 - - + -
140B TYR* 2.8 28.9 + - - +
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Residues in contact with ILE 112 (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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37B PHE* 3.6 29.6 - - + -
38B LEU* 4.1 7.0 - - + -
41B ILE* 4.0 24.7 - - + -
47B ILE* 4.2 6.5 - - + -
52B VAL* 3.8 16.6 - - + -
53B ILE 2.9 8.9 + - - +
54B ASP* 3.2 11.6 - - + +
55B ALA* 2.8 30.1 + - - +
62B LEU* 3.8 19.7 - - + +
66B SER* 3.6 24.5 - - - +
110B THR* 4.2 8.5 - - + -
111B TRP* 1.3 79.7 - - - +
113B MSE 1.3 65.3 + - - +
140B TYR* 3.5 2.9 - - + -
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Residues in contact with MSE 113 (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 ASP* 4.6 1.1 - - - -
55B ALA* 3.8 15.5 - - + +
62B LEU* 4.9 0.9 - - - -
111B TRP* 3.5 23.8 - - - +
112B ILE* 1.3 83.8 - - - +
114B ASN* 1.3 61.8 + - - +
115B PRO* 3.1 28.9 - - + -
117B PHE* 4.5 9.4 - - + -
128B PHE* 3.4 42.8 - - + +
129B ILE* 4.9 6.7 - - + +
132B ALA* 5.1 2.2 - - - -
139B ILE* 5.4 2.2 - - - -
140B TYR 3.1 13.7 + - - +
141B SER* 3.3 19.0 - - - +
142B ILE* 3.1 23.9 + - - +
151B LEU* 6.2 0.2 - - + -
155B PHE* 5.1 9.9 - - + -
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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