Contacts of the helix formed by residues 251 - 260 (chain D) in PDB entry 5EIB
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 251 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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98C ASP* 4.2 14.8 - - - +
2D ARG 5.8 1.1 - - - +
48D ARG* 5.1 3.1 - - - +
133D GLN* 3.2 22.9 - - + +
242D LEU* 3.7 9.2 - - - -
249D ASN 3.2 1.1 - - - +
250D ALA* 1.3 83.7 - - - +
252D LEU* 1.3 59.4 + - - +
253D ARG* 3.2 12.0 + - - +
254D LYS* 2.9 50.3 + - - +
255D LEU* 3.0 28.4 + - - +
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Residues in contact with LEU 252 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4D ILE* 4.0 24.7 - - + -
133D GLN* 2.7 22.7 + - + +
134D GLY* 4.3 20.4 - - - +
135D PHE 4.4 8.1 - - - +
136D GLN* 5.5 1.1 - - + +
165D ILE* 3.7 32.4 - - + +
167D ASN* 3.9 21.3 - - + +
200D GLU* 3.1 18.6 - - - +
242D LEU* 3.6 32.7 - - + +
251D ASP* 1.3 72.5 - - - +
253D ARG* 1.3 57.7 + - - +
255D LEU* 3.7 5.9 - - + +
256D ALA* 3.0 23.2 + - - +
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Residues in contact with ARG 253 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97C GLU* 4.9 6.1 + - - -
100C ALA* 3.5 25.1 - - + -
105C ARG* 3.7 38.4 - - - +
407C TRP* 4.7 14.0 - - + -
411C GLU* 4.2 7.3 + - - -
133D GLN* 4.5 4.0 + - - -
163D ASP* 2.6 32.7 + - - +
164D ARG* 4.1 5.5 - - - +
165D ILE* 3.8 37.8 - - + +
251D ASP* 3.2 8.1 + - - +
252D LEU* 1.3 76.8 - - - +
254D LYS* 1.3 62.0 + - - +
256D ALA* 3.2 1.6 + - - +
257D VAL* 2.9 40.9 + - + +
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Residues in contact with LYS 254 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98C ASP* 3.6 22.3 + - - -
100C ALA* 3.6 23.3 - - - +
101C ASN* 3.6 29.2 + - - +
501C GTP 2.9 31.6 + - - -
502C MG 3.6 4.8 - - - -
247D GLN 5.3 8.6 + - - +
249D ASN* 3.7 15.6 - - - +
250D ALA* 5.0 8.0 - - + +
251D ASP* 2.9 29.7 + - - +
253D ARG* 1.3 77.0 - - - +
255D LEU* 1.3 63.1 + - - +
257D VAL* 3.4 6.3 + - - +
258D ASN* 3.2 26.2 + - - +
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Residues in contact with LEU 255 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167D ASN* 5.8 0.7 - - - +
200D GLU* 3.3 25.8 - - - +
202D TYR* 3.5 24.5 - - + +
238D VAL 5.4 3.1 - - - +
242D LEU* 5.3 6.7 - - + -
249D ASN* 3.5 36.9 + - + +
251D ASP 3.0 17.2 + - - +
252D LEU* 3.7 11.9 - - + +
254D LYS* 1.3 77.0 - - - +
256D ALA* 1.3 56.3 + - - +
258D ASN* 3.3 2.4 + - - +
259D MET* 3.0 50.9 + - + +
268D PHE* 5.0 2.5 - - + -
316D ALA* 4.8 1.1 - - + -
378D ILE* 4.8 15.5 - - + -
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Residues in contact with ALA 256 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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407C TRP* 3.6 24.5 + - + -
165D ILE* 4.7 5.6 - - + -
199D ASP* 5.0 1.8 - - + +
200D GLU* 3.3 24.8 + - + +
252D LEU 3.0 19.2 + - - +
253D ARG* 3.2 7.5 + - - +
255D LEU* 1.3 77.1 - - - +
257D VAL* 1.3 56.6 + - - +
260D VAL* 2.8 40.7 + - + +
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Residues in contact with VAL 257 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100C ALA* 3.7 24.9 - - + +
101C ASN* 4.5 5.6 - - + +
102C ASN* 5.2 7.0 - - + +
105C ARG* 6.4 0.2 - - - -
182C VAL* 4.1 29.2 - - + +
404C PHE* 3.1 26.2 - - - -
407C TRP* 3.8 42.8 - - + +
408C TYR* 5.9 1.3 - - + -
253D ARG* 2.9 27.8 + - + +
254D LYS 3.9 4.5 - - - +
255D LEU 3.4 0.2 - - - -
256D ALA* 1.3 76.0 - - - +
258D ASN* 1.3 60.5 + - - +
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Residues in contact with ASN 258 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101C ASN* 4.8 3.2 + - - +
179C THR 2.9 24.6 + - - -
180C ALA* 3.2 26.9 - - - +
181C VAL* 3.2 25.2 + - + +
182C VAL 4.8 0.5 + - - -
404C PHE* 4.1 1.8 - - - -
248D LEU* 3.8 7.7 - - - +
249D ASN* 2.9 29.2 + - - +
254D LYS* 3.2 15.0 + - - +
255D LEU 3.6 2.7 - - - +
256D ALA 3.1 0.4 - - - -
257D VAL* 1.3 84.5 - - - +
259D MET* 1.3 61.6 + - + +
314D THR* 3.3 21.3 - - - +
350D ASN 5.4 0.2 - - - +
352D LYS* 4.3 6.1 - - + +
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Residues in contact with MET 259 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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249D ASN* 5.4 0.7 - - - +
255D LEU* 3.0 37.5 + - + +
256D ALA 4.2 0.9 - - - +
258D ASN* 1.3 85.1 - - + +
260D VAL* 1.3 60.5 + - + +
261D PRO* 3.2 5.0 - - - +
268D PHE* 3.5 26.2 - - + -
314D THR* 2.8 40.0 + - - +
315D VAL 4.0 2.5 - - - +
316D ALA* 3.9 23.3 - - - -
378D ILE* 3.6 37.5 - - + +
379D GLY 4.2 0.4 - - - -
380D ASN* 2.8 30.8 + - - +
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Residues in contact with VAL 260 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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404C PHE* 3.8 3.3 - - - -
406C HIS* 3.3 4.6 - - - +
407C TRP* 2.9 31.0 + - + -
199D ASP 3.8 18.6 - - - +
256D ALA* 2.8 22.6 + - + +
258D ASN 3.7 0.8 - - - -
259D MET* 1.3 81.2 - - + +
261D PRO* 1.3 61.6 - - - +
262D PHE 3.2 26.5 - - - +
263D PRO* 4.1 7.4 - - + +
265D LEU 3.7 7.4 - - - +
266D HIS* 3.9 13.2 - - + -
268D PHE* 3.8 22.2 - - + -
380D ASN* 4.3 0.9 - - - +
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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