Contacts of the strand formed by residues 199 - 202 (chain A) in PDB entry 3DDN
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 PHE 199 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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111A LEU* 4.0 31.0 - - + -
115A SER* 3.6 22.2 - - - -
138A THR* 3.9 21.5 - - + -
139A GLU 4.0 2.5 - - - -
140A ILE* 3.9 22.2 - - + -
143A LYS* 3.7 28.7 - - + -
144A THR 3.2 2.4 + - - -
145A VAL* 3.9 28.7 - - + -
146A GLY 2.7 32.2 + - - -
197A ALA* 3.3 5.7 - - - +
198A ASP* 1.3 87.2 - - + +
200A ILE* 1.3 60.0 + - - +
227A ILE* 3.3 34.1 - - + +
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Residues in contact with ILE 200 (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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111A LEU* 5.8 1.1 - - - -
145A VAL* 5.6 0.2 - - - -
146A GLY 3.3 3.6 - - - +
148A VAL* 3.9 26.9 - - + -
193A LEU* 4.3 4.3 - - + -
194A LEU* 4.0 17.9 - - + +
197A ALA* 3.7 16.4 - - + -
199A PHE* 1.3 82.2 - - - +
201A SER* 1.3 60.3 + - - +
202A VAL* 4.4 9.9 - - + -
214A ILE* 5.7 5.6 - - + -
222A THR* 3.8 28.7 - - + -
226A VAL* 4.2 11.0 - - + -
227A ILE 2.9 7.9 + - - +
228A ILE* 3.4 23.2 - - + -
229A VAL* 2.7 34.8 + - - +
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Residues in contact with SER 201 (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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107A ALA* 4.1 11.3 - - - +
111A LEU* 5.3 8.1 - - - +
145A VAL* 5.2 6.4 - - - +
146A GLY 2.9 9.4 + - - -
147A VAL* 3.5 4.6 - - - -
148A VAL 2.9 24.3 + - - -
157A VAL* 4.2 12.3 - - - +
199A PHE 4.3 0.2 - - - -
200A ILE* 1.3 75.6 - - - +
202A VAL* 1.3 60.1 + - - +
203A HIS* 2.6 36.1 + - - -
229A VAL* 3.4 15.2 + - - +
231A ALA 5.9 0.2 + - - -
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Residues in contact with VAL 202 (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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148A VAL* 3.7 12.6 - - + +
200A ILE* 4.4 14.8 - - + -
201A SER* 1.3 70.8 - - - +
203A HIS* 1.3 75.8 + - - +
204A LEU* 4.8 3.8 - - + +
214A ILE* 4.5 13.0 - - + -
228A ILE* 5.0 1.3 - - + -
229A VAL 2.9 13.3 + - - +
230A ASN* 3.0 39.7 + - + +
231A ALA 4.5 2.4 + - - -
232A ALA* 3.3 14.8 + - + +
236A LEU* 4.0 17.0 - - + -
237A VAL* 4.1 21.8 - - + -
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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