Contacts of the strand formed by residues 209 - 214 (chain F) in PDB entry 5DK3
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 209 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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117F PRO 5.6 1.6 - - - +
119F VAL* 4.3 23.7 - - + +
198F CYS 3.8 1.4 - - - +
199F GLU* 3.5 0.3 - - - -
200F VAL* 2.7 39.3 + - - +
205F LEU* 3.6 32.9 - - + +
207F SER 3.2 6.2 + - - +
208F PRO* 1.4 70.5 - - - +
210F THR* 1.3 59.0 + - - +
211F LYS* 4.2 26.9 - - + +
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Residues in contact with THR 210 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153F LYS* 6.5 0.7 - - + -
197F ALA* 3.9 26.0 - - + -
198F CYS 3.5 7.6 - - - +
199F GLU* 3.5 27.8 + - + +
208F PRO* 3.8 7.1 + - - +
209F VAL* 1.3 75.6 + - - +
211F LYS* 1.3 65.6 + - - +
212F SER* 4.0 4.8 + - - -
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Residues in contact with LYS 211 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119F VAL* 2.8 56.7 + - + +
120F PHE* 4.7 1.9 - - - -
121F ILE* 3.5 28.5 - - + +
197F ALA* 3.4 1.7 - - - -
198F CYS* 3.1 30.4 + - - +
209F VAL* 4.2 16.3 - - + +
210F THR* 1.3 74.7 - - - +
212F SER* 1.3 59.0 + - - +
140G GLU* 5.0 9.1 + - - -
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Residues in contact with SER 212 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269B GLU* 4.7 6.7 - - - +
121F ILE* 3.8 11.2 - - - +
195F VAL* 3.7 15.8 - - - +
196F TYR 3.0 16.0 + - - -
197F ALA* 3.6 10.3 - - - -
210F THR* 4.0 5.6 + - - -
211F LYS* 1.3 76.2 - - - +
213F PHE* 1.3 76.6 + - - +
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Residues in contact with PHE 213 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269B GLU* 4.8 8.5 - - - -
121F ILE* 3.6 29.4 - - + -
122F PHE 4.6 0.2 - - - -
123F PRO* 3.6 37.0 - - + -
124F PRO* 4.2 4.3 - - + -
136F VAL* 3.4 35.4 - - + -
190F TYR* 3.7 16.2 - - - -
194F LYS 4.0 0.2 - - - +
195F VAL* 3.8 2.8 - - - -
196F TYR* 3.1 53.4 + + + +
212F SER* 1.3 80.4 + - - +
214F ASN* 1.4 70.1 + - - +
215F ARG* 4.3 2.7 - - - -
218F CYS* 4.6 3.8 - - - -
134G CYS* 4.2 22.2 - - + -
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Residues in contact with ASN 214 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235B LEU* 6.1 0.6 - - - +
269B GLU* 4.8 11.2 + - - +
298B SER* 3.8 29.2 + - - -
299B THR* 6.1 0.8 - - - +
194F LYS* 3.4 14.3 - - - +
195F VAL* 3.3 26.6 - - + +
213F PHE* 1.4 76.4 - - - +
215F ARG* 1.4 68.7 + - - +
216F GLY* 4.3 4.2 - - - +
217F GLU* 2.9 50.1 + - + +
218F CYS* 4.2 3.1 - - - -
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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