Contacts of the helix formed by residues 251 - 257 (chain A) in PDB entry 3RN5
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 LYS 251 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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248A GLU* 6.0 2.0 - - - +
249A THR 3.6 5.7 + - - +
250A PRO* 1.3 75.0 - - - +
252A ILE* 1.3 67.5 + - - +
253A ASN* 3.5 17.0 - - - +
254A THR* 3.0 24.7 + - - +
255A LEU* 3.3 6.5 + - - +
286A ASP* 3.7 18.9 + - - +
287A ASN* 2.7 28.0 + - - +
288A THR* 3.7 10.3 - - + -
241D ASN* 3.7 24.7 - - + +
15L T 5.2 9.1 + - - -
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Residues in contact with ILE 252 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250A PRO 3.7 1.0 + - - -
251A LYS* 1.3 69.2 - - - +
253A ASN* 1.3 59.6 + - - +
255A LEU* 2.8 33.5 + - + +
256A GLN* 3.2 13.2 + - - +
268A PHE* 5.0 7.9 - - + -
284A LEU* 3.8 18.8 - - + +
285A SER* 3.9 7.9 - - - -
286A ASP* 3.2 16.2 + - - +
288A THR* 3.1 12.4 + - - +
289A GLY* 3.1 28.5 - - - +
290A LYS 3.6 9.6 - - - +
291A MET* 3.8 27.4 - - + -
324A LEU* 3.5 24.0 - - + -
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Residues in contact with ASN 253 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251A LYS* 3.5 8.5 - - - +
252A ILE* 1.3 76.8 - - - +
254A THR* 1.3 76.1 + - - +
256A GLN* 3.4 34.0 + - - +
257A THR* 3.7 11.8 + - - +
288A THR* 3.2 36.8 + - - +
184D GLU 5.0 1.6 + - - -
185D LYS* 4.4 5.2 + - - +
239D PRO* 3.6 25.0 - - + +
241D ASN* 3.5 24.6 + - - +
242D ILE* 4.4 7.9 - - - +
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Residues in contact with THR 254 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250A PRO* 4.9 5.2 - - + -
251A LYS* 3.0 21.1 + - - +
253A ASN* 1.3 82.8 + - - +
255A LEU* 1.3 64.5 + - + +
257A THR* 3.0 22.4 + - - -
258A GLN* 3.1 29.5 - - + +
241D ASN* 4.1 15.8 + - - -
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Residues in contact with LEU 255 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250A PRO* 3.7 29.2 - - + -
251A LYS 3.6 10.1 - - - +
252A ILE* 2.8 15.5 + - + +
254A THR* 1.3 78.0 - - + +
256A GLN* 1.3 63.2 + - - +
257A THR 3.0 2.2 - - - -
258A GLN* 3.0 21.9 + - + +
262A THR* 5.8 3.1 - - + -
264A VAL* 4.1 31.0 - - + -
268A PHE* 5.1 2.2 - - + -
291A MET* 3.7 22.9 - - + -
317A LEU* 3.6 22.4 - - + +
320A ASN* 3.9 1.0 - - - +
324A LEU* 3.3 26.2 - - + -
326A LEU* 4.4 2.2 - - + -
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Residues in contact with GLN 256 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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252A ILE* 3.2 16.4 + - - +
253A ASN* 3.5 18.8 - - - +
254A THR 3.3 0.4 - - - -
255A LEU* 1.3 77.1 - - - +
257A THR* 1.3 58.3 + - - +
288A THR 5.1 4.0 + - - -
289A GLY* 5.2 0.8 - - - -
290A LYS 4.3 7.3 + - - +
320A ASN* 3.4 9.5 + - - +
321A GLY* 3.0 53.2 + - - +
322A GLU* 4.1 11.1 + - - +
323A LYS 4.2 8.3 - - - +
324A LEU* 3.4 24.9 - - + +
185D LYS* 2.8 28.4 + - - +
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Residues in contact with THR 257 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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253A ASN 3.8 12.1 - - - +
254A THR* 3.0 17.6 + - - -
255A LEU 3.0 0.2 - - - -
256A GLN* 1.3 81.1 - - - +
258A GLN* 1.3 67.5 + - - +
259A PRO* 4.0 1.4 - - - +
320A ASN* 4.8 1.2 + - - -
185D LYS* 4.3 21.3 - - - +
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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