Contacts of the helix formed by residues 253 - 266 (chain E) in PDB entry 5IJ7
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 SER 253 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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250E ARG* 4.1 14.6 + - - -
251E ILE 3.4 0.8 - - - +
252E ASN* 1.3 83.3 + - - +
254E LYS* 1.3 77.2 + - - +
255E ARG* 3.8 8.4 + - - +
256E MET* 3.1 28.8 + - - +
257E MET* 2.8 28.9 + - - +
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Residues in contact with LYS 254 (chain E).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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252E ASN 3.9 1.0 + - - -
253E SER* 1.3 88.5 - - - +
255E ARG* 1.4 63.8 + - + +
257E MET* 4.1 12.8 - - + +
258E ASN* 2.9 39.4 + - - +
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Residues in contact with ARG 255 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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253E SER* 3.8 8.0 + - - +
254E LYS* 1.4 83.3 - - + +
256E MET* 1.3 58.0 + - + +
258E ASN* 3.9 5.0 - - - +
259E ALA* 3.1 27.9 + - - +
278E GLN* 2.7 51.0 + - - +
279E LYS 3.6 26.5 + - - +
280E ILE* 3.6 27.2 - - - +
281E HIS 5.3 1.0 - - - +
590S GLU* 3.6 27.8 + - - -
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Residues in contact with MET 256 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203E LEU* 3.6 31.4 - - + -
212E VAL* 4.1 7.6 - - + -
213E ALA* 3.9 20.9 - - + -
215E PHE* 3.9 10.5 - - + -
250E ARG 3.7 14.4 - - - +
251E ILE* 3.6 26.0 - - + +
253E SER* 3.1 18.3 + - - +
255E ARG* 1.3 78.6 - - + +
257E MET* 1.3 63.6 + - - +
259E ALA* 3.3 2.5 + - - +
260E ILE* 3.0 30.4 + - + +
278E GLN* 4.5 9.0 - - - -
280E ILE* 3.9 30.1 - - + -
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Residues in contact with MET 257 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251E ILE 3.9 4.0 - - - +
252E ASN* 3.3 38.4 - - - +
253E SER 2.8 23.1 + - - +
254E LYS* 4.1 10.5 - - + +
256E MET* 1.3 70.0 - - - +
258E ASN* 1.4 59.1 + - - +
260E ILE* 3.4 9.6 + - + +
261E LYS* 3.0 28.5 + - - +
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Residues in contact with ASN 258 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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254E LYS* 2.9 30.6 + - - +
255E ARG* 3.9 5.2 - - - +
257E MET* 1.4 74.7 - - - +
259E ALA* 1.3 53.5 + - - +
261E LYS* 3.2 14.7 + - + +
262E GLU* 2.7 44.6 + - + +
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Residues in contact with ALA 259 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212E VAL* 3.8 17.6 - - + +
255E ARG 3.1 19.2 + - - +
256E MET* 3.3 8.0 + - - +
258E ASN* 1.3 74.7 - - - +
260E ILE* 1.4 56.0 + - - +
262E GLU* 3.5 7.2 + - - +
263E SER* 3.0 29.5 + - - -
275E PHE* 3.8 7.9 - - + -
278E GLN* 3.5 32.8 - - + +
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Residues in contact with ILE 260 (chain E).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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185E HIS* 5.6 1.3 - - + +
188E ASP* 4.6 1.8 - - - +
191E LEU* 3.9 37.5 - - + -
203E LEU* 4.5 11.9 - - + -
212E VAL* 4.0 15.0 - - + -
251E ILE* 4.2 23.8 - - + +
256E MET* 3.0 24.0 + - + +
257E MET* 3.7 10.1 - - + +
258E ASN 3.3 0.2 - - - -
259E ALA* 1.4 71.2 - - - +
261E LYS* 1.4 64.9 + - - +
263E SER* 2.6 24.1 + - - -
264E TYR* 3.3 25.9 + - + -
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Residues in contact with LYS 261 (chain E).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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257E MET 3.0 14.3 + - - +
258E ASN* 3.2 20.4 + - + +
260E ILE* 1.4 74.8 - - - +
262E GLU* 1.3 67.3 + - + +
264E TYR* 3.0 22.3 + - - +
265E ASP* 3.1 40.5 + - - +
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Residues in contact with GLU 262 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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258E ASN* 2.7 26.2 + - + +
259E ALA* 3.7 7.2 - - - +
261E LYS* 1.3 77.3 - - + +
263E SER* 1.4 56.7 + - - +
265E ASP* 3.4 14.2 + - + +
266E TYR* 3.1 21.8 + - - +
275E PHE* 3.4 23.0 - - + -
276E ILE* 5.6 2.8 - - - +
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Residues in contact with SER 263 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205E ASN* 2.8 22.7 + - - -
208E THR* 2.7 26.2 + - - +
210E THR* 3.4 18.2 - - - -
212E VAL* 3.6 18.3 - - - +
259E ALA 3.0 15.9 + - - -
260E ILE* 2.6 18.7 + - - +
262E GLU* 1.4 76.6 - - - +
264E TYR* 1.3 58.1 + - - +
266E TYR* 3.5 9.9 + - - +
275E PHE* 3.7 15.7 - - - -
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Residues in contact with TYR 264 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188E ASP* 2.7 42.2 + - - -
190E ASN* 2.9 23.2 + - - +
191E LEU* 4.8 0.6 - - + +
205E ASN* 3.5 27.6 - - - -
207E GLN* 4.0 15.5 - - + -
208E THR* 3.6 19.2 - - + +
260E ILE* 3.3 30.3 + - + -
261E LYS* 3.0 10.9 + - - +
263E SER* 1.3 80.7 + - - +
265E ASP* 1.4 62.3 + - - +
266E TYR 3.5 1.4 + - - +
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Residues in contact with ASP 265 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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261E LYS* 3.1 46.5 + - - +
262E GLU* 3.4 12.5 + - + +
264E TYR* 1.4 76.7 - - - +
266E TYR* 1.3 65.3 + - - +
267E ASN* 3.3 8.0 + - - +
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Residues in contact with TYR 266 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208E THR* 3.9 22.0 - - - +
210E THR* 3.6 19.1 - - + -
262E GLU 3.1 13.2 + - - +
263E SER 3.5 13.0 - - - +
264E TYR 3.3 2.1 - - - +
265E ASP* 1.3 76.9 - - - +
267E ASN* 1.3 59.2 + - - +
268E PRO* 3.6 34.0 - - + +
271E THR* 3.8 11.7 - - + -
273E ARG 3.0 24.6 + - - -
274E PRO* 3.7 2.5 - - - +
275E PHE* 3.5 47.4 + + + -
575S ARG* 3.2 20.1 + - - -
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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