Contacts of the strand formed by residues 179 - 184 (chain G) 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 179 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114G VAL* 3.4 20.6 - - + +
116G LEU* 3.8 21.3 - - + +
138G PHE* 4.9 3.1 - - + -
174G LEU* 4.5 8.7 - - + -
176G VAL* 4.0 14.6 - - + -
178G LYS* 1.3 79.5 - - - +
180G ASP* 1.3 65.2 + - - +
181G ILE 3.2 29.2 - - - +
182G ILE* 4.6 5.2 - - + -
207G TRP* 2.7 26.8 + - + +
208G LEU* 3.8 2.2 - - + +
209G LYS* 3.1 27.0 + - - +
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Residues in contact with ASP 180 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112G ASP 4.9 0.2 - - - +
113G LYS* 3.5 28.3 - - + +
114G VAL* 2.8 42.2 + - - +
179G VAL* 1.3 74.1 - - - +
181G ILE* 1.3 62.8 + - + +
208G LEU* 3.7 1.7 - - - +
209G LYS* 2.8 37.7 + - - +
212G GLY* 3.3 9.2 - - - -
213G LEU* 3.2 21.1 + - - +
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Residues in contact with ILE 181 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109G VAL* 3.4 34.1 - - + +
110G PHE* 3.6 41.1 - - + -
113G LYS* 4.4 13.0 - - + -
114G VAL 3.3 1.8 + - - -
115G VAL* 3.3 9.4 - - + -
116G LEU 2.9 25.1 + - - -
179G VAL* 3.2 5.6 - - - +
180G ASP* 1.3 87.9 - - + +
182G ILE* 1.3 65.1 + - - +
183G ILE* 4.0 15.0 - - + -
208G LEU* 4.4 0.9 - - - -
213G LEU* 3.4 21.3 - - + +
215G PHE* 4.0 13.5 - - + -
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Residues in contact with ILE 182 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116G LEU* 3.4 26.0 - - + +
118G VAL* 4.1 12.3 - - + -
179G VAL* 4.6 3.1 - - + -
181G ILE* 1.3 78.5 - - - +
183G ILE* 1.3 74.4 + - - +
184G SER* 4.8 4.7 - - - -
200G VAL* 4.9 1.8 - - + -
203G ALA* 3.9 9.4 - - + +
204G ARG* 3.6 36.1 - - - +
207G TRP 5.2 0.2 - - - -
208G LEU* 4.0 19.9 - - + +
213G LEU 3.0 7.5 + - - -
214G MET* 3.3 29.5 - - + -
215G PHE* 2.9 24.6 + - - +
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Residues in contact with ILE 183 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99G TYR* 5.5 0.9 - - + -
103G MET* 3.8 20.4 - - + -
110G PHE* 4.3 5.6 - - + -
115G VAL* 3.8 25.4 - - + -
116G LEU 2.9 8.1 + - - +
117G ASP* 3.4 22.8 - - + +
118G VAL 3.0 24.4 + - - -
125G LEU* 3.7 35.9 - - + +
126G SER* 4.2 0.9 - - - +
129G ALA* 4.1 6.3 - - + -
181G ILE* 4.0 8.0 - - + -
182G ILE* 1.3 78.9 - - - +
184G SER* 1.3 63.2 + - - +
215G PHE* 3.4 25.8 - - + +
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Residues in contact with SER 184 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99G TYR* 2.6 26.9 + - - -
117G ASP* 4.6 2.7 - - - -
118G VAL* 3.0 26.2 + - - +
125G LEU* 4.3 1.3 - - - +
182G ILE* 4.8 4.7 - - - +
183G ILE* 1.3 78.6 - - - +
185G GLU* 1.3 53.7 + - - +
186G TRP* 3.6 14.5 - - - +
196G MET* 3.8 3.3 - - - +
200G VAL* 3.4 32.2 - - - +
215G PHE 3.0 7.2 + - - -
216G PRO* 3.3 12.4 - - - +
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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
------------------------------------------------------------
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