Contacts of the strand formed by residues 148 - 153 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141A ILE* 5.1 3.6 - - + -
142A SER 3.4 8.3 - - - +
143A THR* 3.6 37.5 - - + -
144A ASP* 4.6 2.7 - - - +
147A HIS* 1.3 83.7 - - - +
149A LEU* 1.3 64.0 + - - +
196A THR* 3.3 7.4 - - - +
197A LEU* 2.9 46.1 + - + +
198A GLY 5.3 1.3 - - - -
199A PRO* 5.6 3.1 - - + -
202A LEU* 4.0 18.2 - - + -
235A TRP* 3.7 33.4 - + + +
236A ASP 3.8 13.5 - - - -
237A SER* 4.2 0.7 - - - -
238A GLN* 3.8 32.8 - - + -
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Residues in contact with LEU 149 (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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141A ILE* 3.4 6.2 - - - +
142A SER* 2.9 54.0 + - - +
144A ASP* 5.2 7.0 - - - +
147A HIS* 5.1 4.5 - - + +
148A PHE* 1.3 76.3 - - - +
150A LEU* 1.3 70.0 + - - +
151A THR* 3.5 24.2 - - - +
194A GLN* 3.5 25.6 - - + +
195A ALA 3.7 5.4 - - - +
196A THR* 3.8 15.5 - - + -
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Residues in contact with LEU 150 (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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139A LEU* 4.1 14.6 - - + -
140A GLN 3.5 6.3 - - - +
141A ILE* 3.6 28.7 - - + -
148A PHE* 6.6 0.2 - - + -
149A LEU* 1.3 78.4 - - - +
151A THR* 1.3 63.1 + - - +
152A TRP* 3.9 18.6 - - + -
173A VAL* 3.8 29.2 - - + -
188A LEU* 6.0 0.2 - - + -
194A GLN* 3.2 27.9 - - - +
195A ALA* 2.9 21.6 + - + +
197A LEU* 4.7 16.8 - - + -
210A ALA* 4.5 13.0 - - + -
233A VAL* 4.4 6.3 - - + -
235A TRP* 5.2 3.4 - - + -
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Residues in contact with THR 151 (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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138A ASP* 3.1 6.2 - - - +
139A LEU* 3.2 4.0 - - - +
140A GLN* 2.9 57.3 + - + +
142A SER* 5.6 0.9 - - - -
149A LEU* 3.5 16.6 - - - +
150A LEU* 1.3 76.3 + - - +
152A TRP* 1.3 71.2 + - - +
193A SER 4.4 4.3 - - - +
194A GLN* 5.0 2.0 - - + +
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Residues in contact with TRP 152 (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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136A PRO* 4.0 9.4 - - + -
137A ARG 3.8 6.3 - - - +
138A ASP* 3.1 10.1 - - - +
139A LEU* 3.8 21.5 - - + -
150A LEU* 3.9 14.1 - - + -
151A THR* 1.3 84.1 - - - +
153A SER* 1.3 68.8 + - - +
171A PHE* 3.1 45.2 - + + -
173A VAL* 3.8 28.0 - - + -
190A SER* 4.5 1.3 - - - -
192A THR 3.5 20.6 - - - -
193A SER* 2.7 43.5 + - - +
194A GLN* 3.6 26.5 - - - -
195A ALA* 3.9 7.2 - - + -
212A VAL* 3.9 20.4 - - + -
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Residues in contact with SER 153 (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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136A PRO* 3.4 11.3 - - - +
137A ARG* 2.6 40.0 + - - +
138A ASP* 3.8 14.5 + - - -
152A TRP* 1.3 78.9 - - - +
154A VAL* 1.3 81.6 + - - +
193A SER* 4.6 0.7 - - - -
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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