Contacts of the strand formed by residues 114 - 118 (chain D) in PDB entry 5DST
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 VAL 114 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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113D LYS* 1.3 75.4 - - - +
115D VAL* 1.3 62.5 + - - +
135D LYS* 4.0 22.9 - - - -
136D LYS* 3.5 14.4 - - + +
138D PHE* 3.9 31.0 - - + -
176D VAL* 4.5 11.7 - - + -
178D LYS 4.9 2.0 - - - +
179D VAL* 3.4 18.7 - - + +
180D ASP* 3.0 43.4 + - - +
181D ILE 3.3 7.8 + - - -
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Residues in contact with VAL 115 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110D PHE* 4.0 19.1 - - + -
113D LYS* 4.2 3.6 - - + +
114D VAL* 1.3 79.0 - - - +
116D LEU* 1.3 59.4 + - - +
117D ASP 4.1 0.2 - - - -
129D ALA* 4.2 6.1 - - + -
134D ALA* 3.8 25.1 - - + -
136D LYS 3.0 9.4 + - - +
137D VAL* 3.3 9.8 - - + +
138D PHE* 2.7 35.7 + - - +
179D VAL* 4.3 1.8 - - - -
181D ILE* 3.3 20.6 - - + +
183D ILE* 3.9 39.7 - - + -
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Residues in contact with LEU 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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115D VAL* 1.3 76.2 - - - +
117D ASP* 1.3 57.0 + - - +
118D VAL* 3.7 23.0 + - + -
138D PHE* 3.4 18.8 - - + +
140D ILE* 3.7 28.7 - - + -
174D LEU* 4.2 12.1 - - + -
179D VAL* 3.8 17.4 - - + +
181D ILE 2.8 8.9 + - - -
182D ILE* 3.3 18.2 - - + +
183D ILE 2.8 31.9 + - - +
203D ALA* 4.1 2.9 - - + -
207D TRP* 3.7 36.8 - - + -
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Residues in contact with ASP 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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115D VAL* 4.1 1.6 - - - +
116D LEU* 1.3 70.1 - - - +
118D VAL* 1.3 69.9 + - - +
119D GLY 3.3 6.6 + - - +
120D SER* 3.5 21.7 + - - +
125D LEU* 3.2 22.3 - - - +
126D SER* 2.8 42.3 + - - +
137D VAL* 4.8 1.3 - - + +
138D PHE 2.7 12.2 + - - +
139D GLY* 3.5 2.8 - - - -
140D ILE* 3.1 26.0 + - - +
183D ILE* 3.3 20.3 - - + +
401D SAH 4.0 3.1 + - - -
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Residues in contact with VAL 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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116D LEU* 3.9 18.8 - - + -
117D ASP* 1.3 70.2 - - - +
119D GLY* 1.3 65.8 + - - +
140D ILE* 4.6 1.6 - - + +
169D VAL* 4.0 11.0 - - + -
182D ILE* 4.0 16.8 - - + -
183D ILE 3.0 7.5 + - - -
184D SER* 2.9 38.6 + - - +
185D GLU 4.6 1.4 + - - +
196D MET* 3.5 7.6 - - + +
199D THR* 3.9 28.9 - - + +
200D VAL* 4.1 15.5 - - + -
203D ALA* 3.8 24.5 - - + -
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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