Contacts of the strand formed by residues 208 - 215 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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178A LYS* 3.6 11.6 - - - -
179A VAL* 3.6 17.5 - - - +
180A ASP 3.7 18.2 - - - +
181A ILE 4.4 0.2 - - - -
182A ILE* 4.1 17.6 - - + +
203A ALA 3.7 1.4 + - - -
204A ARG* 2.8 49.6 + - + +
205A ASP 4.9 1.6 - - - +
207A TRP* 1.3 74.7 - - - +
209A LYS* 1.3 70.7 + - - +
210A PRO* 4.0 0.7 - - - +
212A GLY* 3.8 19.1 - - - +
213A LEU 3.8 10.3 - - - +
214A MET* 3.9 21.5 - - + -
281A TYR* 4.8 4.0 - - + -
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Residues in contact with LYS 209 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113A LYS* 3.8 17.2 - - - +
178A LYS* 3.6 17.5 - - + -
179A VAL 3.0 18.6 + - - +
180A ASP* 2.8 37.5 + - - +
207A TRP 3.3 1.4 + - - -
208A LEU* 1.3 79.1 - - - +
210A PRO* 1.3 87.2 - - + +
211A GLY 3.3 4.2 + - - -
212A GLY* 2.8 32.7 + - - +
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Residues in contact with PRO 210 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178A LYS* 4.8 9.9 - - + -
208A LEU 4.0 2.0 - - - +
209A LYS* 1.3 100.1 - - + +
211A GLY* 1.3 61.7 + - - +
212A GLY 3.2 0.2 + - - -
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Residues in contact with GLY 211 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209A LYS* 3.3 6.0 + - - -
210A PRO* 1.3 71.4 - - - +
212A GLY* 1.3 65.7 + - - +
213A LEU* 4.0 11.8 - - - +
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Residues in contact with GLY 212 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180A ASP 3.4 14.8 - - - -
208A LEU* 3.8 13.8 - - - +
209A LYS* 2.8 27.8 + - - -
210A PRO 3.1 1.4 + - - -
211A GLY* 1.3 83.4 - - - +
213A LEU* 1.3 62.2 + - - +
281A TYR* 3.5 17.5 - - - -
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Residues in contact with LEU 213 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109A VAL* 3.4 34.8 - - + -
113A LYS* 6.6 0.4 - - - -
180A ASP 3.2 5.8 + - - +
181A ILE* 3.5 13.5 - - + -
182A ILE 3.1 22.9 + - - -
208A LEU* 3.8 2.1 - - - +
211A GLY 4.0 9.6 - - - +
212A GLY* 1.3 79.8 - - - +
214A MET* 1.3 66.5 + - - +
215A PHE* 4.3 10.8 - - + -
281A TYR* 3.7 4.0 - - - +
317A LYS* 3.7 44.4 - - + -
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Residues in contact with MET 214 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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182A ILE* 3.4 25.6 - - + +
200A VAL* 3.5 31.2 - - + -
204A ARG* 3.8 32.1 - - + -
208A LEU* 3.9 8.3 - - + -
213A LEU* 1.3 81.5 - - - +
215A PHE* 1.3 68.3 + - - +
216A PRO* 3.4 12.1 - - - +
217A ASP* 3.2 28.2 - - + +
280A ILE* 3.6 29.6 - - + +
281A TYR* 3.1 26.7 + - + -
315A PHE* 5.3 1.0 - - - +
317A LYS* 5.1 0.5 - - - +
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Residues in contact with PHE 215 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99A TYR* 4.0 3.8 - - + -
102A SER* 3.4 44.6 - - - +
103A MET* 4.7 2.7 - - + -
106A ASN* 5.5 0.7 - - + -
109A VAL* 4.2 21.5 - - + -
110A PHE* 3.7 28.9 - + - -
181A ILE* 4.0 19.3 - - + -
182A ILE 2.9 8.5 + - - +
183A ILE* 3.4 16.2 - - + -
184A SER* 3.1 24.8 + - - +
213A LEU* 4.3 11.0 - - + -
214A MET* 1.3 81.1 - - - +
216A PRO* 1.3 64.0 - - - +
315A PHE* 3.6 17.0 - + + -
317A LYS* 4.8 11.7 - - + -
318A CYS* 4.0 13.2 - - - -
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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