Contacts of the strand formed by residues 114 - 119 (chain D) in PDB entry 6VSU
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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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65D THR* 3.4 20.0 - - + -
67D LEU* 3.8 31.6 - - + -
93D ILE* 4.5 12.8 - - + -
94D TRP* 4.0 25.6 - - + -
108D LEU* 3.7 39.1 - - + +
109D LYS 5.4 0.3 - - - -
110D ASP 3.2 2.8 + - - +
111D PRO* 3.2 23.3 + - - +
113D VAL* 1.3 80.4 - - - +
115D THR* 1.3 75.4 + - - +
116D ASP* 6.1 0.2 - - + -
333D VAL* 5.4 2.7 - - + -
334D ARG* 5.8 1.1 - - + -
337D ALA* 4.1 9.2 - - + -
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Residues in contact with THR 115 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51D LYS* 3.9 33.0 - - + +
54D LEU* 4.9 2.9 - - + -
55D VAL* 4.2 6.5 - - + -
65D THR 2.9 7.2 + - - +
66D SER* 2.8 29.7 + - - -
67D LEU* 2.9 26.5 + - - +
111D PRO* 3.4 33.5 + - + +
114D LEU* 1.3 78.3 - - - +
116D ASP* 1.3 63.7 + - - +
152D LEU* 4.0 6.1 - - - +
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Residues in contact with ASP 116 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127A ASP* 4.0 16.1 - - - +
51D LYS* 3.2 24.2 + - - +
67D LEU* 3.4 22.6 - - + +
90D ARG* 2.7 43.4 + - - +
94D TRP* 5.8 1.7 + - - -
115D THR* 1.3 78.7 - - - +
117D VAL* 1.3 62.7 + - - +
118D GLY* 2.7 30.0 + - - -
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Residues in contact with VAL 117 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44D ILE* 3.8 12.0 - - + +
47D ARG* 2.5 40.4 + - + +
48D ALA* 3.7 38.8 - - + +
51D LYS* 4.1 8.1 - - + -
66D SER* 3.5 17.9 - - - +
67D LEU 2.9 21.1 + - - +
68D LEU* 3.8 23.3 - - + -
116D ASP* 1.3 72.8 - - - +
118D GLY* 1.3 50.5 + - - +
146D VAL* 3.9 20.4 - - + -
152D LEU* 4.9 1.8 - - + -
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Residues in contact with GLY 118 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124A GLU* 4.1 7.9 - - - -
47D ARG* 3.1 8.7 - - - -
68D LEU* 3.6 8.5 - - - +
69D GLY 2.8 26.9 + - - -
90D ARG* 3.3 13.1 + - - -
116D ASP* 2.7 17.5 + - - -
117D VAL* 1.3 80.8 - - - +
119D ASP* 1.3 53.3 + - - -
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Residues in contact with ASP 119 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124A GLU* 3.8 13.3 + - - +
44D ILE* 3.7 10.3 - - - +
47D ARG* 3.2 11.2 + - - +
69D GLY* 2.9 24.0 - - - +
71D PRO* 4.2 13.1 - - + +
86D PRO* 3.6 10.9 - - - +
87D PRO* 4.0 14.2 - - - +
90D ARG* 2.7 32.6 + - - -
118D GLY* 1.3 71.0 - - - -
120D VAL* 1.3 68.4 + - - +
121D PRO* 3.3 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