Contacts of the helix formed by residues 255 - 267 (chain B) in PDB entry 1XUD
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 PRO 255 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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235B ASP* 5.9 0.9 - - - +
237B GLY 3.3 27.1 - - - +
238B ALA* 3.9 4.0 - - + -
239B LEU* 3.9 7.6 - - + +
252B PHE* 4.4 1.1 - - + -
253B MET 3.2 10.5 - - - +
254B LEU* 1.3 90.6 - - + +
256B ASP* 1.3 67.2 + - - +
257B ASP* 4.4 4.3 - - + +
258B ASP* 3.1 36.5 + - - +
259B VAL* 3.1 9.7 + - - +
3001B PB4 4.0 13.2 - - + -
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Residues in contact with ASP 256 (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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254B LEU 3.6 1.4 + - - -
255B PRO* 1.3 71.6 - - - +
257B ASP* 1.3 59.1 + - - +
259B VAL* 3.2 13.3 + - - +
260B GLN* 2.5 59.9 + - - +
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Residues in contact with ASP 257 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104A TYR* 2.8 39.6 + - - +
233B SER* 2.6 34.8 + - - -
235B ASP* 3.8 24.3 - - - +
238B ALA* 3.6 12.2 - - + +
255B PRO* 3.2 2.1 - - + +
256B ASP* 1.3 82.2 + - - +
258B ASP* 1.3 59.4 + - - +
260B GLN* 3.4 6.4 + - - +
261B GLY 3.0 22.2 + - - -
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Residues in contact with ASP 258 (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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104A TYR* 5.3 1.3 - - - -
145B TRP* 4.0 12.0 - - + -
230B LEU* 4.5 3.6 - - - +
238B ALA* 3.5 6.6 - - - +
239B LEU* 2.7 29.9 + - - -
240B MET* 3.0 36.1 + - - +
254B LEU* 3.5 15.9 - - + -
255B PRO* 3.1 29.2 + - - +
257B ASP* 1.3 75.4 - - - +
259B VAL* 1.3 65.7 + - - +
261B GLY* 3.7 1.3 - - - -
262B ILE* 2.9 28.2 + - - +
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Residues in contact with VAL 259 (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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148B VAL* 4.5 14.4 - - + -
254B LEU* 3.8 30.1 - - + +
255B PRO 3.1 14.8 + - - +
256B ASP* 3.2 16.1 + - - +
258B ASP* 1.3 76.6 - - - +
260B GLN* 1.3 64.8 + - + +
262B ILE* 3.3 6.4 - - - +
263B GLN* 3.0 57.6 + - + +
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Residues in contact with GLN 260 (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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104A TYR* 3.7 23.3 + - + -
256B ASP* 2.5 45.7 + - - +
257B ASP* 3.7 7.3 + - - +
259B VAL* 1.3 77.8 - - + +
261B GLY* 1.3 62.6 + - - +
263B GLN* 3.8 7.5 - - - +
264B SER* 3.0 25.3 + - - -
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Residues in contact with GLY 261 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104A TYR* 3.4 32.0 - - - -
106A VAL* 4.2 0.2 - - - +
230B LEU* 3.5 18.1 - - - +
257B ASP 3.0 12.4 + - - -
258B ASP* 3.7 2.9 - - - -
259B VAL 3.2 0.4 - - - -
260B GLN* 1.3 77.4 - - - +
262B ILE* 1.3 59.5 + - - +
264B SER* 2.6 22.5 + - - -
265B LEU* 3.7 3.3 + - - +
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Residues in contact with ILE 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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145B TRP* 3.7 19.7 - - + -
148B VAL* 3.9 17.3 - - + -
149B THR* 3.7 27.6 - - + -
151B LEU* 5.0 0.4 - - + -
228B LEU* 3.9 26.5 - - + +
230B LEU* 3.7 23.1 - - + +
258B ASP 2.9 15.3 + - - +
259B VAL* 3.3 11.9 - - - +
261B GLY* 1.3 75.4 - - - +
263B GLN* 1.3 63.0 + - + +
265B LEU* 3.1 7.8 + - + +
266B TYR* 3.0 51.1 + - + +
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Residues in contact with GLN 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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148B VAL* 2.9 33.2 - - - +
259B VAL* 3.0 37.0 + - + +
260B GLN* 3.8 6.1 - - - +
262B ILE* 1.3 79.9 - - + +
264B SER* 1.3 59.4 + - - +
265B LEU 3.0 5.6 - - - -
267B GLY* 2.7 39.2 + - - +
268B PRO* 3.6 23.1 - - + +
269B GLY 4.7 0.3 + - - -
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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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104A TYR* 3.8 19.9 - - - -
106A VAL* 3.8 16.5 - - - +
260B GLN 3.0 17.1 + - - -
261B GLY 2.6 18.2 + - - -
263B GLN* 1.3 77.3 - - - +
265B LEU* 1.3 61.3 + - - +
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Residues in contact with LEU 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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106A VAL* 3.8 33.4 - - + -
111B LEU* 4.1 21.1 - - + +
112B LYS* 3.1 35.2 - - + +
228B LEU 4.0 12.8 - - - +
229B GLY* 3.6 32.1 - - - +
230B LEU* 4.0 10.5 - - + -
261B GLY 4.0 2.5 - - - +
262B ILE* 3.1 6.9 + - + +
263B GLN 3.0 0.4 - - - -
264B SER* 1.3 86.6 - - - +
266B TYR* 1.3 69.4 + - + +
267B GLY 3.7 0.2 - - - -
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Residues in contact with TYR 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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112B LYS* 3.4 21.6 - - + -
113B TRP* 3.0 43.1 + + + -
116B MET* 3.7 19.6 - - + +
149B THR* 4.1 7.6 - - - -
150B PRO* 3.2 29.2 - - + +
151B LEU* 3.9 35.0 - - + -
228B LEU* 2.6 31.5 + - + -
262B ILE* 3.0 37.0 + - + +
265B LEU* 1.3 84.3 - - + +
267B GLY* 1.3 63.0 + - - +
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Residues in contact with GLY 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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148B VAL 3.6 2.3 - - - +
149B THR* 3.4 9.7 - - - +
150B PRO* 3.3 7.7 - - - +
263B GLN* 2.7 33.4 + - - +
265B LEU 3.7 0.4 - - - -
266B TYR* 1.3 77.6 - - - +
268B PRO* 1.3 74.3 - - - +
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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