Contacts of the helix formed by residues 260 - 269 (chain B) in PDB entry 1NZL
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 THR 260 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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258B LYS 4.8 4.3 - - - +
259B ILE* 1.3 80.0 - - - +
261B ARG* 1.3 60.0 + - - +
262B ARG* 3.6 7.8 + - - +
263B GLU* 2.9 27.6 + - + +
264B SER* 3.0 27.4 + - - -
281B ARG* 4.2 1.5 - - - -
284B GLU* 3.5 24.2 - - - +
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Residues in contact with ARG 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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260B THR* 1.3 72.7 - - - +
262B ARG* 1.3 64.1 + - - +
264B SER* 2.7 22.9 + - - -
265B GLU* 3.1 24.3 + - - +
281B ARG* 3.8 13.2 - - - +
284B GLU* 2.6 21.0 + - - +
307B HIS* 3.5 36.8 + - - +
498C PRO* 4.0 13.2 - - - +
499C GLN 2.6 48.6 + - - +
500C PTR 2.9 37.9 + - - +
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Residues in contact with ARG 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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260B THR* 3.3 7.1 - - - +
261B ARG* 1.3 81.0 - - - +
263B GLU* 1.3 59.3 + - - +
265B GLU* 3.4 13.2 + - - +
266B ARG* 3.2 21.3 + - - +
284B GLU* 4.5 0.4 + - - -
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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 ILE* 3.4 23.1 - - + -
260B THR* 2.9 21.6 + - + +
262B ARG* 1.3 74.2 - - - +
264B SER* 1.3 64.3 + - - +
266B ARG* 3.3 19.7 + - - +
267B LEU* 3.2 26.6 + - + +
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Residues in contact with SER 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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259B ILE* 3.5 15.4 - - - +
260B THR 3.0 12.4 + - - -
261B ARG 2.7 18.5 + - - -
263B GLU* 1.3 76.7 - - - +
265B GLU* 1.3 57.3 + - - +
267B LEU* 3.5 1.8 + - - +
268B LEU* 2.9 38.1 + - - +
279B LEU* 4.0 15.5 - - - -
281B ARG* 3.4 27.4 + - - -
293B SER* 4.3 2.2 - - - -
307B HIS* 3.4 12.3 - - - -
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Residues in contact with GLU 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 ARG* 3.1 27.9 + - - +
262B ARG* 3.8 10.7 - - - +
263B GLU 3.3 0.2 - - - -
264B SER* 1.3 74.1 - - - +
266B ARG* 1.3 59.3 + - - +
269B LEU* 2.8 51.8 + - + +
305B VAL* 4.2 21.4 - - + +
307B HIS* 2.9 32.4 + - + +
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Residues in contact with ARG 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 ARG 3.2 13.5 + - - +
263B GLU* 3.4 20.3 + - - +
264B SER 3.3 0.2 - - - -
265B GLU* 1.3 78.4 - - - +
267B LEU* 1.3 74.7 + - - +
269B LEU* 4.0 5.9 + - - +
270B ASN* 4.2 9.7 + - - +
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Residues in contact with LEU 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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256B PHE* 3.6 27.4 - - + -
259B ILE* 3.6 29.6 - - + -
263B GLU* 3.2 7.3 + - + +
264B SER* 3.8 4.9 - - - +
265B GLU 3.3 0.2 - - - -
266B ARG* 1.3 96.9 - - + +
268B LEU* 1.3 58.8 + - - +
270B ASN* 3.7 7.8 + - - +
273B ASN* 2.9 18.5 + - - -
279B LEU* 4.4 3.4 - - + -
351B CYS* 3.6 14.9 - - - -
352B PRO* 4.1 2.3 - - - +
353B THR* 3.4 29.4 - - - +
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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 SER 2.9 23.6 + - - +
267B LEU* 1.3 73.6 - - - +
269B LEU* 1.3 58.2 + - - +
270B ASN 3.1 6.7 + - - +
273B ASN* 3.1 22.0 + - - +
277B THR* 3.5 28.9 - - + +
278B PHE* 3.7 7.9 - - - -
279B LEU* 4.0 7.0 - - + -
293B SER* 3.4 38.6 - - - +
294B VAL* 4.4 0.9 - - - +
295B SER* 3.9 15.6 - - - -
305B VAL* 3.9 22.9 - - + -
351B CYS* 3.7 29.6 - - + -
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Residues in contact with LEU 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 GLU* 2.8 41.5 + - + +
266B ARG* 4.0 4.5 + - - +
267B LEU 3.4 0.6 - - - -
268B LEU* 1.3 71.7 - - - +
270B ASN* 1.3 63.5 + - - +
271B PRO* 3.4 5.4 - - - +
295B SER* 5.7 2.0 - - - -
303B LEU* 3.5 54.9 - - + +
304B ASN* 3.8 5.2 - - - +
305B VAL* 3.7 23.6 - - + +
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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