Contacts of the strand formed by residues 56 - 61 (chain E) in PDB entry 2NN6
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 THR 56 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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52E LYS* 3.1 6.4 - - - +
53E LEU* 2.5 81.8 + - + +
54E GLY 3.6 0.4 + - - -
55E HIS* 1.3 72.4 - - - +
57E ASP* 1.3 69.4 + - - +
58E ILE* 3.0 4.0 - - + +
143E GLU* 3.2 13.8 + - - -
144E CYS* 3.5 1.1 - - - -
145E GLY* 2.8 26.0 - - - +
148E LEU* 2.6 37.2 - - + +
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Residues in contact with ASP 57 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31B PHE* 3.8 19.4 - - - -
50E ARG* 5.1 8.7 + - + +
51E VAL 3.7 4.3 - - - +
52E LYS* 2.9 39.2 + - + +
56E THR* 1.3 77.4 + - - +
58E ILE* 1.3 64.6 + - - +
59E LEU* 4.9 2.5 - - + -
141E LEU* 3.2 4.0 - - - -
142E LEU* 2.5 55.8 + - + +
143E GLU* 3.4 32.7 + - - +
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Residues in contact with ILE 58 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49E ALA 3.6 0.3 - - - +
50E ARG* 3.3 1.6 - - - -
51E VAL 3.1 31.9 + - - +
56E THR* 3.0 26.7 - - - +
57E ASP* 1.3 77.2 - - - +
59E LEU* 1.3 75.3 + - - +
60E VAL* 4.3 3.1 - - + -
139E VAL* 3.8 18.8 - - + -
140E LEU 3.3 11.2 - - - +
141E LEU* 4.7 4.0 - - + -
148E LEU* 3.3 13.0 - - + -
151E ALA* 3.0 31.4 - - + +
152E ILE* 4.4 15.3 - - + -
155E ALA* 3.8 24.4 - - + +
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Residues in contact with LEU 59 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48B LEU* 6.2 0.2 - - + -
80B PHE* 5.6 7.5 - - + -
127B LEU* 5.2 9.2 - - + -
41E VAL* 6.0 5.2 - - + -
42E VAL* 5.0 17.5 - - + -
49E ALA 3.1 11.2 - - - +
50E ARG* 3.7 27.6 - - + +
57E ASP 4.6 0.2 - - - -
58E ILE* 1.3 97.7 - - - +
60E VAL* 1.3 67.1 + - - +
138E ASP 3.4 0.5 - - - +
139E VAL* 3.4 3.8 - - - +
140E LEU* 3.1 40.6 + - + +
142E LEU* 3.4 37.7 - - + -
155E ALA* 5.3 0.2 - - - -
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Residues in contact with VAL 60 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80B PHE* 5.0 1.6 - - - -
42E VAL* 5.7 2.8 - - - +
47E GLY 3.2 1.4 - - - +
48E SER* 3.0 27.2 + - - -
49E ALA 3.3 10.0 + - - -
58E ILE* 4.3 5.2 - - + -
59E LEU* 1.3 82.5 - - - +
61E GLY* 1.3 60.3 - - - +
62E VAL* 4.9 0.2 - - + -
137E VAL* 3.1 35.7 - - + -
138E ASP 3.0 16.4 - - - +
139E VAL* 4.0 15.5 - - + -
152E ILE* 5.8 1.6 - - + +
155E ALA* 3.7 36.8 - - + +
156E VAL* 4.5 7.4 - - + +
159E ALA* 3.7 6.0 - - + +
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Residues in contact with GLY 61 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80B PHE* 3.9 25.4 - - - -
42E VAL* 5.7 3.4 - - - -
45E THR* 4.8 3.1 - - - -
47E GLY 3.0 7.6 - - - -
48E SER* 4.6 1.8 - - - -
60E VAL* 1.3 74.9 - - - +
62E VAL* 1.3 70.4 + - - +
136E TYR 2.9 12.7 - - - +
137E VAL* 3.0 11.1 - - - -
138E ASP* 3.1 9.2 + - - -
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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