Contacts of the strand formed by residues 114 - 119 (chain A) in PDB entry 3N51
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 114 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100A VAL* 4.3 26.9 - - + +
103A LEU* 4.0 41.5 + - + +
104A LYS* 3.8 13.9 - - + +
112A MET* 3.6 6.5 + - + +
113A LYS* 1.3 93.2 + - - +
115A TYR* 1.3 62.1 + - - +
116A GLU 4.2 9.4 - - - +
126A LEU* 4.2 10.3 - - + -
127A VAL 3.4 27.1 - - - +
128A GLY* 4.5 0.7 - - - +
701A BK3 4.0 27.1 - - + -
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Residues in contact with TYR 115 (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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51A TYR* 5.2 3.1 - - - +
75A GLN* 5.2 13.5 + - + -
76A GLU 5.3 3.6 - - - -
77A CYS* 4.5 8.5 - - + -
104A LYS* 3.5 20.5 - - - +
113A LYS* 3.5 29.0 - - + +
114A LEU* 1.3 75.4 - - - +
116A GLU* 1.3 71.7 + - + +
127A VAL* 2.7 21.5 + - + +
128A GLY* 3.6 19.1 - - - -
129A GLU* 3.6 45.2 + - + +
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Residues in contact with GLU 116 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A ARG* 2.9 30.4 + - - -
51A TYR* 2.7 29.5 + - - +
104A LYS* 4.5 12.8 - - - +
114A LEU* 3.9 8.7 - - - +
115A TYR* 1.3 87.4 - - + +
117A PHE* 1.3 61.3 + - - +
118A PHE* 3.1 32.1 - - + -
126A LEU* 3.7 2.4 - - - -
127A VAL* 2.8 39.1 + - + +
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Residues in contact with PHE 117 (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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93A LYS* 6.1 0.2 - - + -
96A LEU* 4.2 14.6 - - + -
97A LEU* 3.4 32.3 - - + -
100A VAL* 3.5 31.9 - - + -
104A LYS* 5.0 6.0 - - + +
116A GLU* 1.3 78.2 - - - +
118A PHE* 1.3 77.0 + - - +
119A GLU* 4.2 16.2 - - + -
124A PHE* 3.3 41.5 - + - -
125A TYR 3.4 3.1 - - - -
126A LEU* 3.4 28.0 - - + +
202A PHE* 6.0 0.4 - + - -
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Residues in contact with PHE 118 (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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45A ALA* 3.7 27.8 - - + +
46A ILE* 3.7 17.5 - - - -
47A PHE* 3.4 33.9 - + + +
50A ARG* 4.5 8.7 - - + -
51A TYR* 3.8 23.3 - + - -
116A GLU* 3.1 43.7 - - + -
117A PHE* 1.3 85.6 - - - +
119A GLU* 1.3 62.2 + - - +
124A PHE* 3.4 5.4 - - - +
125A TYR* 2.7 55.7 + - + -
127A VAL* 4.0 5.8 - - + -
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Residues in contact with GLU 119 (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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45A ALA 5.0 6.5 + - - +
46A ILE* 6.0 1.6 - - - +
84A LYS* 2.5 37.3 + - - +
93A LYS* 2.6 40.7 + - - +
97A LEU* 5.4 1.0 - - - +
117A PHE* 4.2 12.3 - - + -
118A PHE* 1.3 79.5 - - - +
120A ASP* 1.3 66.7 + - - +
123A TYR 3.4 5.6 - - - +
124A PHE* 3.5 19.5 - - + -
125A TYR* 4.5 3.4 - - - -
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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