Contacts of the strand formed by residues 208 - 215 (chain N) 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 LEU 208 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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178N LYS* 3.7 12.6 - - - -
179N VAL* 3.6 15.9 - - - +
180N ASP 3.8 17.9 - - - +
181N ILE 4.3 0.2 - - - +
182N ILE* 4.1 18.8 - - + +
203N ALA 3.8 1.4 + - - -
204N ARG* 2.9 46.5 + - + +
205N ASP 4.6 1.9 - - - +
207N TRP* 1.3 79.1 - - - +
209N LYS* 1.3 71.8 + - - +
210N PRO* 4.4 0.2 - - - +
212N GLY* 3.8 19.7 - - - +
213N LEU 4.0 8.3 - - - +
214N MET* 3.9 20.6 - - + -
281N TYR* 4.8 4.0 - - + -
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Residues in contact with LYS 209 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113N LYS* 3.9 18.2 - - - +
178N LYS* 3.7 17.9 - - + -
179N VAL 3.0 19.2 + - - +
180N ASP* 2.9 37.3 + - - +
207N TRP 3.4 1.8 + - - -
208N LEU* 1.3 82.8 - - - +
210N PRO* 1.3 87.7 - - + +
211N GLY 3.3 5.0 + - - -
212N GLY* 3.0 29.5 + - - +
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Residues in contact with PRO 210 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178N LYS* 4.9 9.0 - - + -
208N LEU 4.4 1.6 - - - +
209N LYS* 1.3 98.8 - - + +
211N GLY* 1.3 61.8 + - - +
212N GLY 3.4 0.3 + - - -
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Residues in contact with GLY 211 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209N LYS* 3.3 8.0 + - - -
210N PRO* 1.3 72.5 - - - +
212N GLY* 1.3 65.3 + - - +
213N LEU* 4.0 11.7 + - - +
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Residues in contact with GLY 212 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180N ASP 3.4 15.0 - - - -
208N LEU* 3.8 16.9 - - - +
209N LYS* 3.0 25.5 + - - +
210N PRO 3.2 1.2 + - - -
211N GLY* 1.3 83.6 - - - +
213N LEU* 1.3 62.3 + - - +
281N TYR* 3.5 17.3 - - - -
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Residues in contact with LEU 213 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109N VAL* 3.3 35.4 - - + -
180N ASP 3.3 7.7 + - - +
181N ILE* 3.4 11.5 - - + +
182N ILE 3.0 24.3 + - - -
208N LEU* 4.0 1.0 - - - +
211N GLY 4.1 9.9 - - - +
212N GLY* 1.3 78.3 - - - +
214N MET* 1.3 67.4 + - - +
215N PHE* 4.1 13.7 - - + -
281N TYR* 3.8 4.0 - - - +
317N LYS* 3.8 42.8 - - + -
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Residues in contact with MET 214 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182N ILE* 3.3 25.1 - - + +
200N VAL* 3.5 32.3 - - + -
204N ARG* 3.8 30.7 - - + -
208N LEU* 3.9 12.8 - - + -
213N LEU* 1.3 82.4 - - - +
215N PHE* 1.3 69.2 + - - +
216N PRO* 3.3 15.3 - - - +
217N ASP* 3.1 25.4 - - + +
280N ILE* 3.6 29.4 - - + +
281N TYR* 3.3 21.0 + - + -
315N PHE* 5.2 0.9 - - - -
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Residues in contact with PHE 215 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99N TYR* 4.0 3.8 - - + -
102N SER* 3.6 44.2 - - - +
103N MET* 4.7 3.1 - - + -
106N ASN* 5.6 0.7 - - + -
109N VAL* 4.2 16.2 - - + -
110N PHE* 3.9 26.2 - + - -
181N ILE* 3.9 16.6 - - + -
182N ILE 2.9 7.5 + - - +
183N ILE* 3.4 19.6 - - + -
184N SER* 3.0 26.2 + - - +
213N LEU* 4.1 20.9 - - + -
214N MET* 1.3 81.1 - - - +
216N PRO* 1.3 61.7 - - - +
315N PHE* 3.6 16.6 - + + -
317N LYS* 4.8 12.8 - - + -
318N CYS* 4.2 12.1 - - - -
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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