Contacts of the strand formed by residues 129 - 132 (chain N) in PDB entry 6E0C
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 LEU 129 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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57N GLN* 3.6 29.6 - - + +
59N VAL* 3.9 14.1 - - + -
69N TRP* 5.4 3.1 - - + -
119N ALA* 3.7 22.9 - - + -
120N ARG 3.4 7.4 - - - -
121N LYS* 3.8 16.2 - - + -
128N THR* 1.3 76.8 + - - +
130N ASP* 1.3 59.9 + - - +
131N TYR 3.8 0.4 - - - -
132N TRP* 3.3 36.2 + - + -
194N TYR* 3.2 15.2 + - - +
204N THR* 2.9 17.7 + - - -
247N LEU* 3.8 20.9 - - + -
249N HIS* 6.2 0.9 - - + +
254N TYR* 4.9 7.0 - - + -
256N PHE* 4.2 1.3 - - + -
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Residues in contact with ASP 130 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105H GLU* 5.1 5.9 - - - +
54N TYR* 4.8 2.4 - - - -
120N ARG* 2.7 33.4 + - - +
122N SER* 4.2 12.0 + - - -
127N SER* 5.1 3.5 + - - -
128N THR* 3.0 29.1 + - - +
129N LEU* 1.3 72.2 - - - +
131N TYR* 1.3 84.4 + - + +
132N TRP* 3.7 5.8 - - - -
203N LYS* 5.7 0.2 - - - -
204N THR* 3.0 24.7 + - - +
207N TYR* 6.0 1.7 - - - -
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Residues in contact with TYR 131 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23N GLU* 5.8 5.4 - - + -
24N VAL* 3.7 51.1 - - + +
26N LEU* 3.7 8.9 - - + +
119N ALA* 3.3 2.3 - - - -
120N ARG* 2.9 63.3 + - + +
130N ASP* 1.3 89.8 - - + +
132N TRP* 1.3 64.2 + - - +
214N ASP* 4.9 15.2 + - - +
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Residues in contact with TRP 132 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26N LEU* 4.3 11.1 + - - +
59N VAL* 3.6 31.4 - - + -
67N LEU* 5.1 1.6 - - + -
117N TYR* 3.6 23.8 - + + -
118N CYS 3.5 4.3 - - - -
119N ALA* 3.9 12.1 - - + +
129N LEU* 3.3 42.6 + - + -
130N ASP 3.7 9.9 - - - -
131N TYR* 1.3 82.1 - - - +
133N GLY* 1.3 69.0 + - - +
134N GLN* 5.6 1.6 + - - -
194N TYR* 3.5 28.3 - + - -
201N SER* 4.1 10.3 + - - +
202N PRO* 3.3 50.6 + - + +
203N LYS* 5.1 0.2 - - - -
204N THR* 4.0 1.0 + - - -
256N PHE* 3.9 15.3 - + - -
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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