Contacts of the helix formed by residues 263 - 274 (chain B) in PDB entry 1F0K
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 263 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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261B ARG* 3.8 3.6 - - - +
262B SER* 1.3 80.7 - - - +
264B ALA* 1.3 65.8 + - - -
265B LEU 3.4 2.7 - - - -
266B THR* 3.2 13.3 + - - -
267B VAL* 3.0 19.1 + - - +
289B GLN* 3.8 18.2 - - - +
292B ASN* 4.2 0.7 - - - -
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Residues in contact with ALA 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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127B GLN* 3.3 35.9 - - + +
128B ASN* 3.5 22.3 - - - +
149B PHE* 3.7 3.5 - - + -
161B ASN* 3.5 12.2 + - - +
263B GLY* 1.3 70.8 - - - -
265B LEU* 1.3 64.9 + - + +
267B VAL* 3.3 3.6 + - - +
268B SER* 3.2 18.4 + - - -
292B ASN* 3.3 17.7 - - - +
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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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18B GLY* 4.2 9.2 - - - +
21B PHE* 4.2 18.2 - - + -
22B PRO* 3.5 40.4 - - + -
127B GLN* 4.5 6.1 - - + -
161B ASN* 3.9 27.4 - - + +
162B PRO 4.7 11.5 - - - +
263B GLY 3.4 0.6 - - - -
264B ALA* 1.3 78.3 - - + +
266B THR* 1.3 57.2 + - - +
268B SER* 3.4 4.5 + - - -
269B GLU* 2.9 29.9 + - - +
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Residues in contact with THR 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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189B VAL* 6.4 1.8 - - + -
252B TYR* 4.8 7.2 - - - +
260B CYS* 4.2 15.9 - - + -
261B ARG 3.7 20.2 - - - +
263B GLY* 3.2 19.8 + - - -
264B ALA 3.2 0.4 - - - -
265B LEU* 1.3 76.6 - - - +
267B VAL* 1.3 61.4 + - - +
269B GLU* 3.2 10.9 + - - +
270B ILE* 2.9 39.1 + - + +
279B PHE* 4.8 1.3 - - + -
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Residues in contact with VAL 267 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149B PHE* 4.0 16.6 - - + -
262B SER* 3.6 29.2 - - - +
263B GLY 3.0 19.1 + - - +
264B ALA 3.3 6.9 + - - +
266B THR* 1.3 75.6 - - - +
268B SER* 1.3 63.5 + - - +
270B ILE* 3.3 3.5 + - - +
271B ALA* 3.0 22.8 + - + +
279B PHE* 4.1 14.6 - - + -
292B ASN* 3.4 29.8 - - + +
293B ALA* 4.2 1.8 - - - +
295B PRO* 6.0 0.2 - - + -
296B LEU* 3.7 26.7 - - + +
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Residues in contact with SER 268 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149B PHE* 3.6 13.4 - - - -
160B GLY* 4.9 0.5 - - - -
161B ASN* 3.1 46.3 + - - +
162B PRO 5.0 0.4 - - - -
163B VAL* 3.8 14.7 - - - +
264B ALA 3.2 5.6 + - - -
265B LEU 3.7 7.2 - - - -
266B THR 3.3 0.2 - - - -
267B VAL* 1.3 79.3 - - - +
269B GLU* 1.3 56.6 + - - +
271B ALA* 3.4 6.9 + - - +
272B ALA* 3.0 29.3 + - - +
338B SER* 4.7 1.0 + - - -
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Residues in contact with GLU 269 (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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163B VAL* 4.0 15.4 - - + +
164B ARG* 3.6 28.6 + - - +
167B VAL* 3.6 19.8 - - + +
248B MET* 4.5 8.3 - - - +
252B TYR* 2.6 40.1 + - + -
265B LEU 2.9 18.2 + - - +
266B THR* 3.5 10.3 - - - +
268B SER* 1.3 76.4 - - - +
270B ILE* 1.3 57.6 + - - +
272B ALA* 3.3 1.0 + - - +
273B ALA* 2.9 28.2 + - - +
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Residues in contact with ILE 270 (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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252B TYR* 3.4 36.6 - - + +
258B VAL* 4.1 23.1 - - + -
260B CYS* 4.5 4.0 - - - -
266B THR* 2.9 29.0 + - + +
267B VAL 3.3 5.8 + - - +
269B GLU* 1.3 73.2 - - - +
271B ALA* 1.3 65.9 + - - +
273B ALA* 3.2 4.8 + - - +
274B GLY 3.1 16.6 + - - -
275B LEU* 3.3 31.1 + - + +
277B ALA* 4.0 15.0 - - + -
279B PHE* 4.2 17.9 - - + -
296B LEU* 4.4 6.3 - - + -
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Residues in contact with ALA 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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149B PHE* 6.5 0.4 - - + -
267B VAL* 3.0 16.5 + - + +
268B SER* 3.6 8.3 - - - +
269B GLU 3.3 0.2 - - - -
270B ILE* 1.3 76.0 - - - +
272B ALA* 1.3 63.2 + - - +
274B GLY 3.1 9.5 + - - -
296B LEU* 4.3 16.6 - - + -
334B ALA* 3.2 34.8 - - - +
335B ARG* 3.2 10.0 - - - -
337B ALA 4.5 1.8 - - - +
338B SER* 3.4 17.6 - - - +
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Residues in contact with ALA 272 (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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163B VAL* 3.8 23.8 - - + -
167B VAL* 4.3 9.7 - - + +
168B LEU* 4.0 18.6 - - + -
268B SER 3.0 16.6 + - - +
269B GLU 3.6 4.5 - - - +
271B ALA* 1.3 77.3 - - - +
273B ALA* 1.3 61.3 + - - +
274B GLY 3.3 0.2 + - - -
335B ARG* 3.2 25.0 + - - +
338B SER* 3.3 18.4 + - - +
340B PRO* 5.8 0.2 - - + -
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Residues in contact with ALA 273 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167B VAL* 3.8 16.1 - - + +
170B LEU* 4.0 14.3 - - + +
176B ARG* 2.5 34.7 + - - -
252B TYR* 4.0 18.4 - - + -
269B GLU 2.9 16.0 + - - +
270B ILE* 3.2 7.6 + - - +
272B ALA* 1.3 76.7 - - - +
274B GLY* 1.3 51.8 + - - +
275B LEU* 4.1 14.5 - - + +
335B ARG* 3.7 5.6 + - - +
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Residues in contact with GLY 274 (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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173B PRO* 3.6 7.5 - - - +
176B ARG* 3.0 18.5 + - - -
270B ILE 3.1 4.2 + - - -
271B ALA 3.1 13.9 + - - -
272B ALA 3.1 0.8 - - - -
273B ALA* 1.3 79.9 - - - +
275B LEU* 1.3 58.8 + - - +
331B ALA* 3.1 38.6 - - - +
335B ARG* 3.9 7.6 - - - -
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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