Contacts of the helix formed by residues 253 - 263 (chain D) in PDB entry 4UX9
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 GLN 253 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180D PHE* 4.6 15.9 - - + -
198D LEU 5.5 2.0 + - - +
199D GLY 4.4 16.8 - - - +
200D MET* 5.8 1.4 - - - +
251D LYS 4.0 5.3 + - - -
252D LEU* 1.3 72.8 - - - +
254D PRO* 1.4 70.6 - - + +
255D THR* 3.1 4.7 + - - +
256D VAL* 3.2 19.5 + - + +
257D ARG* 2.9 24.9 + - - +
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Residues in contact with PRO 254 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1366C SO4 4.7 0.6 + - - -
252D LEU 3.6 4.4 - - - +
253D GLN* 1.4 91.3 - - + +
255D THR* 1.3 61.5 + - - +
257D ARG* 3.6 11.7 - - + +
258D THR* 2.9 29.5 + - - -
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Residues in contact with THR 255 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185C TYR* 5.2 14.5 + - + +
192C ARG* 5.3 0.2 - - - +
229C ASP* 4.8 0.5 - - - +
230C TYR* 3.5 43.5 - - + -
1366C SO4 2.7 37.4 + - - +
253D GLN* 3.1 4.2 + - - +
254D PRO* 1.3 80.7 - - - +
256D VAL* 1.4 65.4 - - + +
258D THR* 3.5 10.6 + - - -
259D TYR 3.6 7.8 + - - -
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Residues in contact with VAL 256 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230C TYR* 4.1 24.5 - - + +
198D LEU* 3.6 54.5 - - + +
252D LEU* 4.4 7.9 - - + -
253D GLN* 3.2 19.4 + - + +
255D THR* 1.4 74.5 - - + +
257D ARG* 1.3 65.7 + - - +
259D TYR* 3.2 6.6 + - + +
260D VAL* 3.0 29.7 + - + +
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Residues in contact with ARG 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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246D PRO 5.3 0.2 + - - -
249D MET* 3.3 24.9 + - + +
250D LYS* 3.7 52.2 + - - +
252D LEU* 3.9 21.5 + - + +
253D GLN 2.9 17.0 + - - +
254D PRO* 3.6 11.4 - - + +
256D VAL* 1.3 78.4 - - - +
258D THR* 1.3 56.0 + - - +
260D VAL* 3.9 0.7 - - - +
261D GLU* 2.7 66.0 + - + +
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Residues in contact with THR 258 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189C ARG* 4.5 6.6 + - - +
228C ARG 3.3 26.2 - - - +
229C ASP* 3.9 7.0 - - + -
1366C SO4 4.5 6.6 + - - -
254D PRO 2.9 16.2 + - - -
255D THR 3.6 9.0 - - - -
256D VAL 3.3 0.2 - - - -
257D ARG* 1.3 76.4 - - - +
259D TYR* 1.3 63.1 + - - +
261D GLU* 3.9 7.2 - - - +
262D ASN* 3.1 34.8 + - - +
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Residues in contact with TYR 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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229C ASP* 3.2 35.6 - - + +
230C TYR* 3.9 18.6 - + + -
231C ILE* 3.7 40.1 - - + +
232C ASP* 5.3 0.9 - - + -
259C TYR* 5.4 0.2 + - - -
1364C SO4 5.3 0.7 + - - -
198D LEU* 6.1 1.1 - - + -
231D ILE* 3.3 24.0 + - + +
234D TRP* 4.8 11.9 - + + -
235D ASN* 4.5 3.1 + - - -
255D THR 3.6 1.6 + - - -
256D VAL* 3.2 9.0 + - + +
258D THR* 1.3 80.1 - - - +
260D VAL* 1.3 71.3 + - + +
262D ASN* 3.2 11.4 + - + +
263D ARG* 3.2 59.7 + - + -
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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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198D LEU* 3.8 29.4 - - + -
234D TRP* 4.1 27.5 + - + +
243D THR* 5.7 1.6 - - - +
244D PRO* 5.0 0.4 - - + -
249D MET* 3.5 35.7 - - + +
252D LEU* 3.8 17.9 - - + -
256D VAL* 3.0 20.5 + - + +
257D ARG 3.9 0.9 - - - +
259D TYR* 1.3 83.6 - - + +
261D GLU* 1.3 59.9 + - - +
263D ARG* 3.4 22.9 + - - +
265D LYS* 4.8 1.9 + - - -
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Residues in contact with GLU 261 (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 MET* 3.7 26.5 - - + +
257D ARG* 2.7 67.0 + - + +
258D THR* 3.9 6.9 - - - +
260D VAL* 1.3 76.6 - - - +
262D ASN* 1.3 62.2 + - - +
263D ARG 3.3 2.5 + - - +
265D LYS* 3.4 26.0 + - - +
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Residues in contact with ASN 262 (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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264B PRO* 3.5 20.8 - - - +
265B LYS 5.0 3.1 + - - +
228C ARG* 3.1 59.9 + - - +
229C ASP* 3.0 24.7 + - - +
258D THR* 3.1 25.2 + - - +
259D TYR* 3.2 6.5 + - + +
261D GLU* 1.3 76.2 - - - +
263D ARG* 1.3 69.4 + - - +
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Residues in contact with ARG 263 (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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264B PRO* 4.6 4.1 - - - +
265B LYS 5.3 1.0 + - - -
1364C SO4 3.1 43.8 + - - -
234D TRP* 4.2 14.4 - - + +
235D ASN* 3.3 28.5 + - - +
238D ILE* 4.2 19.7 - - + -
259D TYR* 3.2 53.9 + - + +
260D VAL* 3.5 14.2 - - - +
261D GLU 3.3 7.8 - - - +
262D ASN* 1.3 83.4 + - - +
264D PRO* 1.4 88.4 - - + +
265D LYS* 3.7 10.4 + - - +
266D TYR* 5.9 1.0 + - - -
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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