Contacts of the strand formed by residues 199 - 202 (chain A) in PDB entry 3URF
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 MET 199 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164A PRO* 3.7 10.5 - - + -
165A PHE* 3.5 28.9 - - - +
166A ALA* 3.9 10.3 - - - -
196A ILE* 3.4 19.4 - - + +
197A SER 2.9 13.6 + - - +
198A ASN* 1.3 82.4 + - - +
200A THR* 1.3 62.5 + - - +
206A LEU* 3.8 30.5 - - + -
207A ILE 3.2 13.0 - - - +
208A VAL* 4.2 16.4 - - + -
209A ASN* 3.1 13.5 + - - +
214A TYR* 4.1 21.3 - - + +
283A LEU* 5.8 0.4 - - + -
289A ILE* 5.9 0.9 - - + -
310A ALA* 4.4 9.9 - - + -
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Residues in contact with THR 200 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196A ILE* 4.0 4.0 - - - -
199A MET* 1.3 75.8 + - - +
201A PHE* 1.3 67.4 + - - +
202A SER* 5.2 4.5 - - - -
206A LEU* 4.1 0.4 - - - -
207A ILE* 2.5 56.1 + - - +
209A ASN* 2.9 23.5 + - - +
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Residues in contact with PHE 201 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168A LEU* 3.6 30.7 - - + -
185A SER 3.7 10.8 - - - -
187A TRP* 3.6 44.4 - + + -
189A HIS* 4.4 29.9 + - + +
196A ILE* 3.8 16.4 - - + +
200A THR* 1.3 78.5 - - - +
202A SER* 1.3 61.2 + - - +
203A ASN 5.7 0.2 - - - -
204A GLY* 3.5 38.8 - - - -
205A LYS 3.4 13.0 - - - -
206A LEU* 4.0 2.9 - - - +
308A PHE* 4.7 2.0 - + - -
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Residues in contact with SER 202 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200A THR* 3.7 6.4 + - - -
201A PHE* 1.3 78.0 - - - +
203A ASN* 1.3 68.5 + - - +
204A GLY 3.0 2.9 - - - -
205A LYS* 2.7 40.2 + - - +
207A ILE* 4.2 20.3 - - - +
288A GLU* 5.2 0.3 - - - +
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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
------------------------------------------------------------
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