Contacts of the strand formed by residues 148 - 153 (chain C) in PDB entry 6NMY
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 148 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141C ILE* 5.2 4.5 - - + -
142C SER 3.4 11.0 - - - +
143C THR* 4.0 36.3 - - + -
144C ASP 4.5 0.4 - - - +
146C ASP* 4.9 7.6 - - - -
147C HIS* 1.3 80.5 - - - +
149C LEU* 1.3 59.7 + - - +
150C LEU* 5.8 2.0 - - + -
196C THR* 3.2 4.9 - - - -
197C LEU* 2.9 47.7 + - + +
198C GLY 5.2 0.9 - - - -
199C PRO 5.4 2.7 - - - -
202C LEU* 3.9 19.7 - - + -
235C TRP* 3.4 36.8 - + + +
236C ASP 3.7 14.8 - - - -
237C SER* 4.1 9.2 - - - -
238C GLN* 3.8 22.7 - - - -
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Residues in contact with LEU 149 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141C ILE* 3.4 5.6 - - - +
142C SER* 2.9 58.0 + - - +
144C ASP* 3.4 35.4 - - + +
147C HIS 4.5 0.2 - - - +
148C PHE* 1.3 76.4 - - - +
150C LEU* 1.3 64.7 + - - +
151C THR* 3.7 21.3 - - - +
194C GLN* 5.6 6.3 - - + +
195C ALA 3.5 5.8 - - - +
196C THR* 3.7 18.6 - - + -
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Residues in contact with LEU 150 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139C LEU* 4.2 14.4 - - + -
140C GLN 3.4 4.9 - - - +
141C ILE* 3.6 28.7 - - + -
148C PHE* 5.8 1.3 - - + -
149C LEU* 1.3 78.7 - - - +
151C THR* 1.3 62.7 + - - +
152C TRP* 3.9 15.9 - - + -
173C VAL* 3.9 27.4 - - + -
188C LEU* 5.7 0.2 - - + -
194C GLN* 3.3 29.6 - - - +
195C ALA* 2.9 25.3 + - + +
197C LEU* 4.8 19.1 - - + +
210C ALA* 4.5 11.4 - - + -
212C VAL* 5.3 0.7 - - + -
233C VAL* 4.3 7.2 - - + -
235C TRP* 5.2 3.6 - - + -
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Residues in contact with THR 151 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138C ASP 3.2 2.7 - - - +
139C LEU* 3.3 2.4 - - - +
140C GLN* 2.9 60.0 + - - +
142C SER* 5.8 0.3 - - - -
149C LEU* 3.7 17.3 - - - +
150C LEU* 1.3 76.1 + - - +
152C TRP* 1.3 71.9 + - - +
193C SER 4.4 4.0 - - - +
194C GLN* 5.1 2.4 - - + +
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Residues in contact with TRP 152 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136C PRO* 3.8 20.0 - - + -
137C ARG 3.7 8.3 - - - +
138C ASP 3.3 7.9 - - - +
139C LEU* 3.8 18.2 - - + -
150C LEU* 3.9 12.6 - - + -
151C THR* 1.3 88.2 - - - +
153C SER* 1.3 60.4 + - - +
154C VAL* 4.9 0.7 - - + -
171C PHE* 3.1 41.9 - + + -
173C VAL* 4.0 19.1 - - + -
190C SER* 4.3 2.5 - - - -
192C THR 3.4 20.4 - - - -
193C SER* 2.3 48.3 + - - +
194C GLN* 3.5 28.0 - - - -
195C ALA* 3.8 8.3 - - + -
212C VAL* 4.0 28.0 - - + -
230C SER* 6.3 0.2 - - - -
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Residues in contact with SER 153 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136C PRO* 3.4 2.1 - - - +
137C ARG* 2.7 42.4 + - - +
138C ASP* 3.4 25.1 + - - +
152C TRP* 1.3 77.4 - - - +
154C VAL* 1.3 58.2 + - - +
155C ALA* 4.2 14.4 + - - +
193C SER* 4.4 1.6 - - - -
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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