Contacts of the strand formed by residues 246 - 252 (chain B) 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 GLN 246 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121A THR* 5.2 1.3 - - - -
241B ASP 5.2 4.7 - - - +
242B GLU* 5.2 7.3 + - - +
244B GLN 4.2 10.4 - - - +
245B PRO* 1.3 74.6 - - - +
247B ASN* 1.3 69.9 + - + +
248B LEU* 3.5 2.7 - - - -
262B TRP* 3.9 3.0 - - - +
263B GLU* 3.0 44.7 + - + +
264B VAL* 6.2 0.4 - - - -
265B ARG* 5.6 1.0 - - - +
301B HIS* 3.2 35.6 + - - -
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Residues in contact with ASN 247 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246B GLN* 1.3 82.8 - - + +
248B LEU* 1.3 62.8 + - - +
249B GLU* 2.9 31.8 + - - +
261B SER* 3.2 16.3 + - - +
262B TRP* 3.5 3.9 - - - +
263B GLU* 2.7 35.2 + - - +
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Residues in contact with LEU 248 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121A THR* 4.3 29.2 - - - +
122A ARG 4.6 1.6 - - - +
123A LEU* 3.3 52.8 - - + +
246B GLN 3.5 1.8 - - - -
247B ASN* 1.3 72.9 - - - +
249B GLU* 1.3 70.0 + - - +
250B CYS* 4.1 15.5 - - - -
260B CYS* 4.6 3.6 - - + -
261B SER 3.5 14.6 - - - +
262B TRP* 3.9 21.1 - - + -
276B LEU* 5.3 9.6 - - + -
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Residues in contact with GLU 249 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123A LEU* 5.5 0.9 - - - -
225A ARG* 3.4 29.0 + - - -
247B ASN* 2.9 36.6 + - - +
248B LEU* 1.3 78.3 - - - +
250B CYS* 1.3 68.5 + - - +
251B PHE* 3.5 26.1 - - + -
260B CYS* 3.2 0.5 - - - -
261B SER* 2.9 41.0 + - - +
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Residues in contact with CYS 250 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123A LEU* 5.0 5.9 - - + +
125A VAL* 3.7 28.7 - - + -
130A HIS* 3.3 22.7 - - - +
248B LEU* 4.1 15.3 - - - -
249B GLU* 1.3 79.9 - - - +
251B PHE* 1.3 72.8 + - - +
258B LEU* 4.0 7.6 - - + -
259B SER 3.4 5.6 - - - -
260B CYS* 2.0 47.6 - - - -
276B LEU* 5.8 0.7 - - - -
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Residues in contact with PHE 251 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130A HIS* 3.2 28.0 - + - +
131A VAL 4.7 0.9 - - - -
132A GLN* 3.8 32.1 - - + -
224A GLY* 5.2 1.8 - - - -
225A ARG* 3.5 49.1 - - + -
249B GLU* 3.5 35.0 - - + -
250B CYS* 1.3 85.0 - - - +
252B PHE* 1.3 61.4 + - - +
253B ASP 3.9 1.2 + - - -
257B VAL 4.1 0.2 - - - +
258B LEU* 3.4 4.2 - - - +
259B SER* 2.9 40.0 + - - +
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Residues in contact with PHE 252 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127A LEU* 3.6 44.6 - - + +
130A HIS 2.5 15.7 + - - +
131A VAL* 3.2 7.7 - - - +
132A GLN* 3.0 21.5 + - - -
163A TRP* 3.4 44.4 - + + -
251B PHE* 1.3 72.3 - - - +
253B ASP* 1.3 65.2 + - - +
254B GLY* 3.2 6.8 + - - -
255B ALA* 3.3 19.1 - - - -
256B ALA* 3.2 27.6 - - - -
257B VAL 3.0 22.7 - - - -
258B LEU* 3.7 12.5 - - + +
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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