Contacts of the helix formed by residues 257 - 270 (chain B) in PDB entry 6N0M
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 ASP 257 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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256B ARG* 1.3 78.6 - - - +
258B VAL* 1.3 59.8 + - - +
259B GLU 3.2 0.9 - - - +
260B ALA* 3.2 28.7 - - + +
261B LEU* 3.7 5.5 + - - +
418B GLU* 5.6 1.4 - - - +
446B HIS* 4.0 12.1 + - - -
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Residues in contact with VAL 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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256B ARG 4.6 0.7 - - - +
257B ASP* 1.3 75.3 + - - +
259B GLU* 1.3 67.0 + - - +
260B ALA 3.1 0.8 + - - -
261B LEU* 3.4 8.8 + - - +
262B MET* 3.4 30.1 + - - +
378B ILE* 3.9 22.9 - - + -
379B ALA* 4.1 12.1 - - + -
380B MET* 4.2 17.3 - - + -
381B HIS* 4.5 4.5 - - - +
446B HIS* 3.7 32.1 - - + +
447B PHE* 4.0 24.2 - - + -
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Residues in contact with GLU 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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256B ARG* 2.9 38.7 + - - +
257B ASP 3.2 0.6 - - - -
258B VAL* 1.3 75.1 - - - +
260B ALA* 1.3 69.0 + - - +
262B MET* 3.5 15.1 + - - +
263B GLU* 3.5 18.6 + - - +
380B MET* 3.6 9.6 - - - +
381B HIS* 3.4 30.5 + - + +
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Residues in contact with ALA 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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256B ARG 4.3 0.2 + - - -
257B ASP* 3.2 24.6 + - + +
259B GLU* 1.3 77.8 - - - +
261B LEU* 1.3 65.7 + - - +
263B GLU* 2.9 22.8 + - - +
264B ARG* 3.4 30.1 + - - +
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Residues in contact with LEU 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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257B ASP 3.7 4.1 + - - +
258B VAL* 3.4 11.8 + - - +
260B ALA* 1.3 77.4 - - - +
262B MET* 1.3 56.8 + - - +
264B ARG* 2.8 35.4 + - + +
265B MET* 3.1 23.3 + - - +
378B ILE* 4.5 6.7 - - + -
389B LEU* 4.1 16.4 - - + -
415B GLN 5.0 1.8 - - - +
416B LEU* 3.3 50.9 - - + +
444B TRP* 4.7 6.3 - - + +
447B PHE* 3.7 33.9 - - + -
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Residues in contact with MET 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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258B VAL* 3.4 17.9 + - - +
259B GLU* 3.9 10.5 - - - +
260B ALA 3.1 0.8 + - - -
261B LEU* 1.3 77.2 - - - +
263B GLU* 1.3 58.1 + - + +
265B MET* 3.6 14.4 - - - +
266B GLN* 3.3 31.8 + - - +
378B ILE* 4.2 26.0 - - + -
381B HIS* 3.5 51.8 - - + -
384B VAL* 3.8 26.2 - - + -
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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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259B GLU* 3.5 14.4 + - - +
260B ALA* 2.9 11.4 + - - +
262B MET* 1.3 78.5 - - + +
264B ARG* 1.3 64.2 + - - +
266B GLN* 3.1 28.3 + - + +
267B GLN* 3.2 24.7 + - - +
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Residues in contact with ARG 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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260B ALA* 3.4 35.9 + - - +
261B LEU* 2.8 16.9 + - - +
263B GLU* 1.3 72.8 - - - +
265B MET* 1.3 60.3 + - - +
267B GLN* 3.4 18.4 + - - +
268B LEU* 3.0 34.5 + - + +
414B ASN 4.6 2.2 + - - -
415B GLN* 2.8 65.5 + - + +
416B LEU* 4.5 10.8 - - + -
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Residues in contact with MET 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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261B LEU* 3.1 21.1 + - - +
262B MET* 3.6 14.8 - - - +
264B ARG* 1.3 73.6 - - - +
266B GLN* 1.3 58.8 + - - +
268B LEU* 4.0 1.2 - - - +
269B GLN* 3.0 31.2 + - - +
378B ILE* 3.7 27.1 - - + -
384B VAL* 3.6 23.8 - - + -
385B ASP 3.4 26.0 - - - +
386B THR* 3.9 9.2 - - - -
388B VAL* 3.6 22.3 - - + +
389B LEU* 4.3 7.2 - - + -
416B LEU* 3.4 22.0 - - + -
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Residues in contact with GLN 266 (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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262B MET* 3.3 20.1 + - - +
263B GLU* 3.1 22.3 + - + +
265B MET* 1.3 74.3 - - - +
267B GLN* 1.3 58.7 + - + +
269B GLN* 3.1 6.4 + - - +
270B GLU* 2.8 36.6 + - - +
286E ARG* 4.7 12.3 + - - -
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Residues in contact with GLN 267 (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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263B GLU* 3.2 26.9 + - - +
264B ARG* 3.4 21.6 + - - +
266B GLN* 1.3 80.7 - - + +
268B LEU* 1.3 56.2 + - + +
270B GLU* 2.5 31.8 - - - +
271B SER* 4.9 0.2 - - - -
415B GLN* 5.2 2.1 - - - +
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Residues in contact with LEU 268 (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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264B ARG* 3.0 21.5 + - + +
265B MET* 4.0 4.7 - - - +
266B GLN 3.1 0.2 - - - -
267B GLN* 1.3 81.3 - - + +
269B GLN* 1.3 61.8 + - - +
270B GLU 3.4 1.6 + - - +
271B SER* 3.7 17.9 + - - -
388B VAL* 4.4 13.4 - - + +
409B ASP* 5.0 3.1 - - - +
412B GLU* 3.6 32.5 - - + +
415B GLN* 3.7 25.4 - - - +
416B LEU* 3.5 39.5 - - + -
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Residues in contact with GLN 269 (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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265B MET 3.0 22.4 + - - +
266B GLN* 3.1 6.3 + - - +
268B LEU* 1.3 75.0 - - - +
270B GLU* 1.3 56.2 + - - +
271B SER* 3.8 5.4 + - - -
385B ASP* 6.1 7.0 - - + +
388B VAL* 4.6 10.9 - - + +
286E ARG* 6.3 0.4 - - - -
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Residues in contact with GLU 270 (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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266B GLN 2.8 18.4 + - - +
267B GLN* 2.5 27.6 - - - +
269B GLN* 1.3 69.9 - - - +
271B SER* 1.3 62.0 + - - +
286E ARG* 5.9 5.4 - - - +
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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