Contacts of the strand formed by residues 196 - 198 (chain D) in PDB entry 4MNE
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 ILE 196 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150D SER* 3.5 0.5 - - - -
151D LEU* 2.8 57.8 + - + +
169D VAL* 4.1 7.6 - - + -
173D VAL* 3.8 21.3 - - + -
191D VAL* 4.8 10.1 - - + -
192D LYS 3.7 15.3 - - - +
193D PRO* 3.1 8.8 + - + +
195D ASN* 1.3 78.4 - - - +
197D LEU* 1.3 61.5 + - - +
204D ILE* 3.6 28.3 - - + -
205D LYS 3.5 7.6 - - - +
206D LEU* 4.0 14.4 - - + -
249D MET* 6.0 1.3 - - + -
252D SER* 5.2 2.7 - - - -
256D MET* 4.4 11.0 - - + -
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Residues in contact with LEU 197 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127D VAL* 3.8 9.9 - - + -
146D MET* 3.8 18.5 - - + +
149D GLY 3.4 4.9 - - - +
150D SER* 3.5 33.9 - - - +
194D SER 3.9 9.0 - - - +
196D ILE* 1.3 73.8 - - - +
198D VAL* 1.3 65.6 + - - +
204D ILE* 3.6 0.5 - - - +
205D LYS 2.9 35.7 + - - +
207D CYS* 3.8 27.4 - - + -
901D ACP 3.5 53.8 - - + +
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Residues in contact with VAL 198 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146D MET* 3.4 14.4 - - - +
148D GLY* 3.0 28.8 + - - +
149D GLY 2.9 16.0 + - - +
150D SER 5.1 0.2 - - - -
151D LEU* 4.0 21.3 - - + -
154D VAL* 4.1 15.0 - - + -
197D LEU* 1.3 78.7 - - - +
199D ASN* 1.3 61.1 + - - +
203D GLU 3.5 11.9 - - - +
204D ILE* 3.9 15.0 - - + -
371D PHE* 3.7 23.1 - - + -
375D LEU* 3.7 24.2 - - + -
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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
------------------------------------------------------------
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