Contacts of the strand formed by residues 257 - 265 (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 VAL 257 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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252B PHE* 3.0 13.5 - - - -
253B ASP* 2.7 47.2 + - - +
255B ALA 3.9 5.2 - - - +
256B ALA* 1.3 86.4 - - + +
258B LEU* 1.3 64.4 + - - +
259B SER* 3.9 19.7 + - - +
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Residues in contact with LEU 258 (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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125A VAL* 4.3 24.7 - - + -
127A LEU* 4.7 12.6 - - + -
250B CYS* 4.0 7.9 - - + -
251B PHE 3.4 35.7 - - - +
252B PHE* 3.7 14.1 - - + +
256B ALA 4.3 0.2 - - - -
257B VAL* 1.3 74.5 - - - +
259B SER* 1.3 59.8 + - - +
260B CYS* 3.6 22.2 + - - +
278B TYR* 6.4 2.2 - - + -
289B CYS* 5.9 3.1 - - - -
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Residues in contact with SER 259 (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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249B GLU 4.1 0.3 - - - +
250B CYS* 3.4 1.2 - - - -
251B PHE* 2.9 39.4 + - - +
253B ASP* 6.1 0.5 - - - +
257B VAL* 3.9 16.6 + - - +
258B LEU* 1.3 70.3 - - - +
260B CYS* 1.3 61.2 + - - +
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Residues in contact with CYS 260 (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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248B LEU* 4.6 1.8 - - + -
249B GLU 3.2 3.6 - - - -
250B CYS* 2.0 46.4 - - - -
258B LEU* 3.6 21.0 + - - +
259B SER* 1.3 76.9 - - - +
261B SER* 1.3 64.1 + - - +
262B TRP* 4.9 1.8 - - - -
276B LEU* 3.5 36.6 - - + +
289B CYS* 6.4 0.4 - - - -
304B HIS 4.5 7.3 - - - -
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Residues in contact with SER 261 (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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247B ASN* 3.2 6.6 + - - +
248B LEU* 3.5 1.5 - - - +
249B GLU* 2.9 40.5 + - - +
259B SER 5.6 0.2 - - - -
260B CYS* 1.3 79.5 - - - +
262B TRP* 1.3 67.1 + - - +
263B GLU* 5.8 0.3 - - - +
303B ARG* 3.6 36.1 + - - +
304B HIS 4.1 10.5 - - - -
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Residues in contact with TRP 262 (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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245B PRO* 3.7 30.9 - - + +
246B GLN 3.9 3.8 - - - +
247B ASN 3.5 7.2 - - - -
248B LEU* 3.9 26.5 - - + -
260B CYS 5.1 1.6 - - - -
261B SER* 1.3 85.9 + - - +
263B GLU* 1.3 67.8 + - - +
264B VAL* 4.7 7.7 - - - +
274B PHE* 4.4 31.3 - - + +
275B GLY 4.6 5.2 - - - -
276B LEU* 3.7 42.0 - - + -
292B VAL* 3.7 29.2 - - + -
302B THR 4.0 0.5 - - - +
303B ARG* 3.6 1.0 - - - -
304B HIS* 2.9 43.9 + - - -
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Residues in contact with GLU 263 (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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245B PRO* 3.5 2.4 - - - +
246B GLN* 3.0 45.9 + - + +
247B ASN* 2.7 34.5 + - - +
261B SER* 5.8 0.4 - - - +
262B TRP* 1.3 77.4 - - - +
264B VAL* 1.3 62.9 + - - +
297B LEU* 3.8 34.7 - - + +
301B HIS* 4.6 17.5 - - + -
302B THR 3.4 7.9 - - - +
303B ARG* 4.3 18.6 + - + -
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Residues in contact with VAL 264 (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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243B ALA 4.2 9.6 - - - +
244B GLN 5.0 0.9 - - - -
245B PRO* 4.2 14.6 - - + -
246B GLN* 5.9 0.9 - - - +
262B TRP* 4.7 8.1 - - - +
263B GLU* 1.3 76.2 - - - +
265B ARG* 1.3 70.9 + - - +
268B VAL* 4.0 13.7 - - + -
269B ALA* 4.1 11.2 - - + -
274B PHE* 3.7 36.3 - - + -
294B ARG* 6.3 0.2 - - - +
301B HIS* 4.2 6.5 - - - -
302B THR* 2.9 47.1 + - - +
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Residues in contact with ARG 265 (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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56A LEU* 3.6 17.1 - - + +
242B GLU* 3.2 64.7 + - - +
244B GLN 5.6 0.6 + - - -
246B GLN* 5.6 0.9 - - - +
264B VAL* 1.3 78.8 - - - +
266B LYS* 1.3 58.8 + - - +
267B GLU* 3.1 31.6 + - - +
268B VAL* 3.9 20.2 - - + +
269B ALA* 3.0 26.7 + - - +
300B LEU* 3.2 43.9 + - - +
301B HIS* 3.5 25.9 - - + +
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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