Contacts of the strand formed by residues 108 - 113 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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51A SER* 3.6 22.9 - - - +
52A VAL 4.1 8.5 - - - -
53A ILE* 3.8 41.7 - - + -
73A SER* 5.8 1.8 - - - -
75A THR* 3.7 21.6 - - - +
104A ILE* 4.9 0.7 - - + -
106A GLY 3.5 18.8 - - - -
107A LYS* 1.3 79.8 - - - +
109A ASP* 1.3 66.2 + - - +
110A THR 4.2 1.6 - - - +
135A THR* 3.1 8.7 + - - +
136A SER* 3.2 30.0 - - - +
137A MSE 3.5 2.1 + - - -
51B SER* 4.3 4.5 - - - -
72B GLU* 2.6 38.4 + - - +
73B SER* 3.2 27.3 + - - -
107B LYS* 4.4 10.7 - - - +
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Residues in contact with ASP 109 (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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50A ARG* 3.6 23.2 - - + -
51A SER* 2.9 37.5 + - - +
108A TYR* 1.3 72.3 - - - +
110A THR* 1.3 67.8 + - - +
137A MSE 3.1 15.2 + - - +
138A TRP* 2.9 31.0 + - + -
105B SER 4.8 1.0 - - - +
106B GLY* 3.2 6.6 - - - -
107B LYS* 2.9 38.0 + - - +
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Residues in contact with THR 110 (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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41A ILE* 4.3 3.6 - - + -
46A ASN* 2.7 37.4 + - - +
47A ILE* 4.8 0.2 - - + -
51A SER 3.1 2.6 + - - -
52A VAL* 3.4 10.5 - - + +
53A ILE* 2.8 34.1 + - - +
108A TYR* 4.2 0.3 - - - +
109A ASP* 1.3 88.3 + - - +
111A TRP* 1.3 58.4 + - - +
112A ILE* 4.1 16.2 - - + -
136A SER* 4.0 4.3 - - - -
138A TRP* 3.4 5.3 - - + +
140A TYR* 3.8 31.6 - - + -
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Residues in contact with TRP 111 (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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53A ILE* 3.5 34.8 - - + -
55A ALA* 3.4 25.8 - - + +
77A PHE* 4.1 10.1 - + - -
101A VAL* 4.1 1.1 - - + -
104A ILE* 4.5 2.0 - - + -
110A THR* 1.3 72.5 - - - +
112A ILE* 1.3 70.7 + - - +
113A MSE 3.5 29.0 - - + +
128A PHE* 3.5 23.8 - + - -
131A LYS* 3.5 31.9 - - + -
132A ALA* 3.6 20.0 - - + +
135A THR* 3.2 26.9 - - - -
136A SER* 3.3 20.6 - - - +
138A TRP 2.8 11.2 + - - +
139A ILE* 3.5 14.3 - - + -
140A TYR* 2.8 27.9 + - - +
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Residues in contact with ILE 112 (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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37A PHE* 3.6 26.9 - - + -
38A LEU* 4.1 5.8 - - + -
41A ILE* 3.8 26.5 - - + -
47A ILE* 4.0 8.1 - - + -
52A VAL* 3.8 15.9 - - + -
53A ILE 2.9 10.0 + - - +
54A ASP* 3.3 10.5 - - + +
55A ALA* 2.9 28.1 + - - +
62A LEU* 3.7 21.3 - - + +
66A SER* 3.6 23.3 - - - +
110A THR* 4.1 7.9 - - + -
111A TRP* 1.3 79.9 - - - +
113A MSE 1.3 66.4 + - - +
140A TYR* 3.5 3.8 - - + -
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Residues in contact with MSE 113 (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 ASP* 4.6 1.1 - - - -
55A ALA* 4.0 16.2 - - + +
62A LEU* 4.8 1.3 - - - -
111A TRP* 3.5 24.5 - - - +
112A ILE* 1.3 82.9 - - - +
114A ASN* 1.3 62.6 + - - +
115A PRO* 3.4 36.3 - - + -
117A PHE* 3.9 8.3 - - + -
128A PHE* 4.1 24.7 - - + +
129A ILE* 3.8 31.6 - - + -
132A ALA* 5.2 1.6 - - - -
139A ILE* 5.2 1.1 - - - -
140A TYR 3.0 15.0 + - - +
141A SER* 3.3 15.6 - - - +
142A ILE* 3.2 25.3 + - - +
151A LEU* 5.2 0.4 - - + -
155A PHE* 4.9 2.5 - - + -
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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