Contacts of the strand formed by residues 114 - 118 (chain M) 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 M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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112M ASP 5.5 0.2 - - - +
113M LYS* 1.3 76.9 - - - +
115M VAL* 1.3 60.9 + - - +
135M LYS* 4.2 20.4 - - + -
136M LYS* 3.4 16.4 - - + +
138M PHE* 4.1 23.1 - - + -
176M VAL* 4.5 13.5 - - + -
178M LYS 4.9 1.6 - - - +
179M VAL* 3.3 25.5 - - + +
180M ASP* 3.0 37.0 + - - +
181M ILE 3.3 5.5 + - - -
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Residues in contact with VAL 115 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110M PHE* 3.9 18.6 - - + -
113M LYS* 4.2 3.4 - - + +
114M VAL* 1.3 80.3 - - - +
116M LEU* 1.3 62.7 + - - +
129M ALA* 4.1 7.0 - - + -
134M ALA* 3.8 25.6 - - + -
136M LYS 2.9 12.9 + - - +
137M VAL* 3.3 9.4 - - + +
138M PHE* 2.8 30.5 + - - +
179M VAL* 4.2 2.0 - - - -
181M ILE* 3.3 20.6 - - + +
183M ILE* 3.9 39.3 - - + -
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Residues in contact with LEU 116 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115M VAL* 1.3 76.3 - - - +
117M ASP* 1.3 59.7 + - - +
118M VAL* 3.6 24.4 + - + -
138M PHE* 3.3 19.1 - - + +
140M ILE* 3.8 28.0 - - + -
174M LEU* 4.1 13.9 - - + -
179M VAL* 3.8 17.9 - - + +
181M ILE 2.9 7.9 + - - -
182M ILE* 3.4 17.3 - - + +
183M ILE 2.9 26.6 + - - +
203M ALA* 4.1 2.9 - - + -
207M TRP* 3.8 33.7 - - + -
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Residues in contact with ASP 117 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115M VAL* 4.0 1.2 + - - +
116M LEU* 1.3 71.4 - - - +
118M VAL* 1.3 69.0 + - - +
119M GLY 3.4 3.6 + - - +
120M SER* 3.5 26.4 + - - +
125M LEU* 3.3 18.6 - - - +
126M SER* 2.8 42.5 + - - +
137M VAL* 4.7 1.3 - - + +
138M PHE 2.7 13.4 + - - +
139M GLY* 3.5 2.5 - - - -
140M ILE 3.1 25.8 + - - +
183M ILE* 3.5 19.2 - - + +
401M SAH 4.0 5.7 + - - -
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Residues in contact with VAL 118 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116M LEU* 3.7 29.8 - - + -
117M ASP* 1.3 69.9 - - - +
119M GLY* 1.3 65.1 + - - +
140M ILE 4.5 0.4 - - - +
169M VAL* 4.1 9.6 - - + -
182M ILE* 4.0 16.6 - - + -
183M ILE 3.0 7.3 + - - -
184M SER* 2.8 38.5 + - - +
185M GLU 4.6 1.7 + - - +
196M MET* 3.4 9.0 - - + +
199M THR* 3.9 29.8 - - + +
200M VAL* 4.0 14.1 - - + -
203M ALA* 3.8 14.1 - - + -
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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