Contacts of the strand formed by residues 199 - 204 (chain F) in PDB entry 1DE4
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 SER 199 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197F GLN 4.9 3.2 + - - -
198F ASN* 1.3 73.0 - - - +
200F VAL* 1.3 64.4 + - - +
201F ILE* 3.9 18.8 - - - +
214F GLU 3.4 5.4 - - - -
215F ASN* 3.0 26.2 - - - -
216F PRO* 4.1 2.7 - - - +
335F GLN* 5.8 0.4 - - - +
375F LEU* 3.5 5.4 - - - +
376F THR* 2.7 70.9 + - - +
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Residues in contact with VAL 200 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199F SER* 1.3 72.8 - - - +
201F ILE* 1.3 67.6 + - - +
212F LEU 3.7 0.3 - - - -
213F VAL* 2.8 43.4 + - + -
214F GLU* 3.0 18.4 + - + +
216F PRO* 4.9 1.6 - - + -
280F LEU* 3.7 24.5 - - + -
335F GLN* 4.7 3.8 - - + -
337F ILE* 3.9 18.8 - - + -
345F LEU* 4.1 17.5 - - + -
373F VAL* 5.0 5.8 - - + -
374F LYS 3.7 3.8 - - - +
375F LEU* 3.6 26.7 - - + -
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Residues in contact with ILE 201 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199F SER* 3.9 19.1 - - - +
200F VAL* 1.3 79.6 - - - +
202F ILE* 1.3 78.4 + - - +
203F VAL* 3.7 8.0 + - + -
209F LEU* 3.8 19.5 - - + -
212F LEU* 3.5 37.5 - - + +
213F VAL* 4.1 1.3 - - - +
373F VAL* 3.3 4.2 - - - +
374F LYS* 2.7 63.8 + - + +
376F THR* 5.1 0.4 - - + -
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Residues in contact with ILE 202 (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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201F ILE* 1.3 86.2 - - - +
203F VAL* 1.3 64.5 + - - +
210F VAL* 3.3 26.9 + - + +
211F TYR* 3.4 28.0 + - + -
212F LEU 3.9 4.0 - - - +
213F VAL* 3.7 22.2 - - + +
344F LYS 4.4 3.4 - - - +
345F LEU* 4.0 16.4 - - + -
348F ASN* 3.4 43.7 - - + +
371F LYS* 4.3 20.2 - - + -
372F ASN 3.7 8.5 - - - +
373F VAL* 4.2 5.6 - - + +
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Residues in contact with VAL 203 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201F ILE* 3.7 10.7 + - + +
202F ILE* 1.3 80.4 - - - +
204F ASP* 1.3 78.5 + - - +
205F LYS* 5.2 0.4 - - - -
207F GLY* 3.3 28.9 - - - +
208F ARG 3.2 14.4 - - - +
209F LEU* 4.6 1.3 - - - -
210F VAL* 4.1 4.0 - - - -
229F THR* 5.1 4.7 - - + +
371F LYS* 4.0 5.9 - - - +
372F ASN* 2.7 50.0 + - - +
374F LYS* 4.3 29.6 - - + +
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Residues in contact with ASP 204 (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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203F VAL* 1.3 80.0 - - - +
205F LYS* 1.3 59.9 + - - +
206F ASN* 2.3 23.3 + - - +
207F GLY 2.5 17.5 + - - -
208F ARG* 3.1 21.1 + - + +
210F VAL* 3.6 19.8 - - + +
370F SER* 4.1 12.0 - - - +
371F LYS* 5.3 4.8 - - - +
372F ASN* 5.0 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