Contacts of the helix formed by residues 268 - 273 (chain B) in PDB entry 1X1O
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 GLY 268 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138B THR* 3.6 23.6 + - - +
140B LYS* 4.2 16.6 - - - +
246B SER* 5.5 0.8 + - - -
249B MET* 5.5 1.8 - - - +
266B SER 4.1 1.2 + - - -
267B VAL* 1.3 73.8 - - - +
269B ALA* 1.3 58.9 + - - +
270B LEU 3.1 1.0 + - - -
271B THR* 3.2 7.3 + - - -
272B HIS* 2.9 31.4 + - - +
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Residues in contact with ALA 269 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120B LEU* 3.5 14.2 - - + +
124B TYR* 4.1 11.7 - - - +
249B MET 4.6 7.4 - - - +
267B VAL* 3.2 13.7 - - + +
268B GLY* 1.3 75.1 - - - +
270B LEU* 1.3 62.8 + - - +
271B THR 3.1 1.4 + - - -
272B HIS* 4.6 1.8 - - - -
273B SER* 3.1 36.8 + - - +
274B ALA 3.4 8.5 + - - -
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Residues in contact with LEU 270 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117B ILE* 3.4 18.2 - - - +
120B LEU* 4.0 6.3 - - + -
121B THR* 3.6 44.4 - - + +
124B TYR* 3.7 28.9 - - + -
135B ILE* 3.6 27.1 - - + -
136B LEU 3.8 17.7 - - - +
137B ASP* 4.5 2.5 - - + -
153B VAL* 4.5 12.3 - - + -
267B VAL* 3.5 17.5 - - + +
268B GLY 3.1 1.0 + - - -
269B ALA* 1.3 77.1 - - - +
271B THR* 1.3 64.9 + - + +
274B ALA* 3.3 17.5 - - - +
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Residues in contact with THR 271 (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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113B ARG* 2.7 29.2 + - - +
117B ILE* 4.2 11.9 - - + -
137B ASP* 5.2 4.4 - - + +
138B THR* 4.2 8.8 + - - -
140B LYS 2.7 28.7 + - - +
141B THR* 3.9 11.0 - - + +
142B THR* 4.8 0.7 + - - -
149B GLU* 4.0 33.1 - - + +
150B LYS* 6.0 0.2 - - - -
153B VAL* 4.3 12.8 - - + -
267B VAL 5.1 0.3 + - - -
268B GLY 3.2 5.6 + - - -
270B LEU* 1.3 84.1 - - + +
272B HIS* 1.3 64.0 + - - +
273B SER 3.6 0.7 - - - -
274B ALA* 4.7 1.8 - - - -
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Residues in contact with HIS 272 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105A ARG* 6.0 0.4 - - - -
109A ASN* 5.6 6.7 + - - -
112A GLN* 3.8 28.1 + - + -
276A ALA* 3.6 38.4 + - + +
277A LEU 6.2 0.2 - - - -
113B ARG* 5.8 0.9 - - - -
140B LYS* 3.9 32.5 + - + +
268B GLY 2.9 20.7 + - - +
269B ALA* 4.6 1.1 - - - -
271B THR* 1.3 80.2 + - - +
273B SER* 1.3 64.3 + - - +
274B ALA 3.9 0.4 - - - -
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Residues in contact with SER 273 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275A LYS* 5.8 10.1 - - - -
120B LEU* 4.2 5.7 - - - +
269B ALA* 3.1 28.8 + - - +
272B HIS* 1.3 88.2 - - - +
274B ALA* 1.3 60.0 + - - +
275B LYS 3.8 2.3 + - - -
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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