Contacts of the strand formed by residues 137 - 142 (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 ARG 137 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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135C GLU* 3.7 21.6 + - - +
136C PRO* 1.3 79.8 - - - +
138C ASP* 1.3 74.1 + - + +
139C LEU* 3.5 2.5 - - - +
152C TRP* 3.6 4.1 - - - +
153C SER* 2.7 37.4 + - - +
155C ALA* 4.2 24.4 - - + +
230C SER* 5.0 1.3 - - - -
231C PRO* 4.3 17.7 - - + -
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Residues in contact with ASP 138 (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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137C ARG* 1.3 85.9 + - - +
139C LEU* 1.3 60.5 + - - +
140C GLN* 3.1 27.1 + - - +
151C THR 3.2 6.9 - - - +
152C TRP* 3.3 4.5 - - - -
153C SER* 3.4 19.5 + - - +
155C ALA* 6.0 0.3 - - - +
231C PRO* 5.1 4.2 - - - +
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Residues in contact with LEU 139 (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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137C ARG 4.9 2.2 - - - -
138C ASP* 1.3 74.2 - - - +
140C GLN* 1.3 62.7 + - - +
150C LEU* 4.2 15.7 - - + -
151C THR 3.3 15.3 - - - +
152C TRP* 3.8 26.9 - - + -
210C ALA 3.8 18.2 - - - +
211C ARG* 4.1 6.1 - - - -
212C VAL* 4.3 7.9 - - + +
230C SER* 3.2 27.1 - - - +
231C PRO* 3.3 25.3 - - + +
233C VAL* 3.8 24.7 - - + +
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Residues in contact with GLN 140 (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* 3.1 29.4 + - - +
139C LEU* 1.3 77.6 - - - +
141C ILE* 1.3 69.0 + - - +
150C LEU* 3.4 7.8 - - - +
151C THR* 2.9 56.9 + - - +
233C VAL* 4.9 2.2 - - - -
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Residues in contact with ILE 141 (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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140C GLN* 1.3 77.6 - - - +
142C SER* 1.3 69.5 + - - +
143C THR* 4.7 10.1 - - - +
148C PHE* 5.2 4.5 - - + -
149C LEU* 3.4 6.3 - - - +
150C LEU* 3.6 25.6 - - + -
233C VAL* 3.6 29.3 - - + +
234C CYS 4.5 1.8 - - - +
235C TRP* 3.6 48.0 - - + -
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Residues in contact with SER 142 (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* 1.3 81.6 - - - +
143C THR* 1.3 70.0 + - - +
144C ASP* 3.6 1.0 + - - -
148C PHE* 3.4 4.6 - - - +
149C LEU* 2.9 59.6 + - - +
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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