Contacts of the strand formed by residues 114 - 118 (chain H) 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 H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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112H ASP 5.4 0.2 - - - +
113H LYS* 1.3 75.6 - - - +
115H VAL* 1.3 62.5 + - - +
135H LYS* 4.2 21.5 - - - -
136H LYS* 3.4 14.8 - - + +
138H PHE* 3.9 31.6 - - + -
176H VAL* 4.6 10.8 - - + -
178H LYS 4.9 1.3 - - - +
179H VAL* 3.5 20.5 - - + +
180H ASP* 3.1 38.7 + - - +
181H ILE 3.3 8.0 + - - -
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Residues in contact with VAL 115 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110H PHE* 4.0 19.5 - - + -
113H LYS* 4.2 3.6 - - + +
114H VAL* 1.3 79.5 - - - +
116H LEU* 1.3 57.9 + - - +
129H ALA* 4.1 7.0 - - + -
134H ALA* 3.8 24.5 - - + -
136H LYS 2.9 9.2 + - - +
137H VAL* 3.3 10.0 - - + +
138H PHE* 2.7 35.2 + - - +
179H VAL* 4.3 2.7 - - - -
181H ILE* 3.3 18.4 - - + +
183H ILE* 3.9 40.4 - - + -
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Residues in contact with LEU 116 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115H VAL* 1.3 75.4 - - - +
117H ASP* 1.3 60.4 + - - +
118H VAL* 3.7 22.6 + - + -
138H PHE* 3.3 23.8 - - + +
140H ILE* 3.8 27.6 - - + -
174H LEU* 4.2 9.4 - - + -
179H VAL* 3.9 17.2 - - + +
181H ILE 2.9 9.3 + - - -
182H ILE* 3.5 19.6 - - + +
183H ILE 2.8 29.6 + - - +
203H ALA* 4.2 1.3 - - + -
207H TRP* 3.7 37.0 - - + -
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Residues in contact with ASP 117 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115H VAL* 4.1 1.4 + - - +
116H LEU* 1.3 71.3 - - - +
118H VAL* 1.3 65.1 + - - +
119H GLY 3.4 11.8 + - - +
120H SER* 3.4 21.2 + - - +
125H LEU* 3.3 20.7 - - - +
126H SER* 2.8 42.3 + - - +
137H VAL* 4.8 0.9 - - + -
138H PHE 2.7 12.3 + - - +
139H GLY* 3.5 2.6 - - - -
140H ILE 3.0 25.6 + - - +
183H ILE* 3.4 19.3 - - + +
401H SAH 4.1 2.8 + - - -
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Residues in contact with VAL 118 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116H LEU* 3.9 20.4 - - + -
117H ASP* 1.3 69.2 - - - +
119H GLY* 1.3 65.4 + - - +
140H ILE* 4.5 0.9 - - - -
169H VAL* 4.1 11.2 - - + -
182H ILE* 4.0 17.3 - - + -
183H ILE 3.0 6.3 + - - -
184H SER* 2.6 39.1 + - - +
185H GLU 4.6 1.2 + - - +
196H MET* 3.4 8.7 - - + +
199H THR* 4.0 25.4 - - + +
200H VAL* 4.0 18.8 - - + -
203H ALA* 3.8 22.7 - - + -
401H SAH 6.0 0.2 - - + -
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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