Contacts of the helix formed by residues 257 - 267 (chain H) in PDB entry 2FRV
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 TYR 257 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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108H HIS 3.7 16.4 + - - -
109H LEU* 4.2 12.1 - - + -
112H PHE* 3.1 49.5 - + + +
113H TYR* 3.4 19.2 + + + -
252H PHE* 3.0 11.1 + - - +
253H ILE* 3.7 33.7 - - + +
256H VAL* 1.3 71.3 - - - +
258H ILE* 1.3 59.5 + - + +
260H ASP* 3.9 0.9 - - - +
261H LEU* 2.9 36.8 + - + +
411H THR 4.8 1.7 + - - -
414H ARG* 3.8 16.3 - - - +
415H GLY* 3.7 26.3 + - - -
418H CYS* 4.0 22.2 - - + -
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Residues in contact with ILE 258 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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253H ILE* 2.8 41.1 + - + +
254H GLU* 4.1 11.4 - - - +
256H VAL 3.4 0.4 - - - +
257H TYR* 1.3 80.6 - - + +
259H THR* 1.3 60.2 + - + +
261H LEU* 3.2 11.1 + - + +
262H LEU* 3.0 44.9 + - + +
392H LEU* 4.8 13.5 - - + -
393H VAL* 5.5 4.9 - - + -
415H GLY* 3.2 41.5 - - - +
419H LEU* 4.6 17.0 - - + -
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Residues in contact with THR 259 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141H LEU* 3.9 34.1 - - - +
142H SER* 3.9 8.0 + - - -
143H PRO* 5.3 1.3 - - + -
195H HIS* 5.5 0.7 - - - -
254H GLU 3.6 15.9 - - - +
255H GLN* 2.9 29.3 + - - +
256H VAL* 3.1 6.6 + - - -
258H ILE* 1.3 76.4 - - + +
260H ASP* 1.3 67.9 + - - +
262H LEU* 3.4 7.9 + - - +
263H ALA* 3.1 24.3 + - - +
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Residues in contact with ASP 260 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112H PHE* 4.2 10.5 - - + -
113H TYR* 2.9 19.6 + - + +
141H LEU* 5.4 4.4 - - - +
191H ILE* 3.9 14.1 - - - +
192H ALA* 4.6 6.5 - - + -
195H HIS* 2.2 48.4 + - - +
256H VAL 3.0 16.7 + - - +
257H TYR 3.9 0.7 - - - +
259H THR* 1.3 77.4 + - - +
261H LEU* 1.3 68.4 + - - +
263H ALA* 4.3 4.9 - - - -
264H VAL* 3.0 32.5 + - + +
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Residues in contact with LEU 261 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112H PHE* 3.9 25.1 - - + -
257H TYR* 2.9 27.8 + - + +
258H ILE* 3.4 17.5 - - + +
259H THR 3.2 0.2 - - - -
260H ASP* 1.3 80.6 - - - +
262H LEU* 1.3 68.2 + - + +
264H VAL* 3.9 1.6 - - - +
265H ALA* 3.0 29.5 + - + +
393H VAL* 6.4 2.0 - - + -
411H THR* 3.6 34.3 - - + +
412H ALA* 4.2 16.6 - - + +
415H GLY* 3.6 31.9 - - - +
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Residues in contact with LEU 262 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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258H ILE* 3.0 33.0 + - + +
259H THR* 4.2 5.2 - - - +
261H LEU* 1.3 83.0 - - + +
263H ALA* 1.3 54.0 - - - +
265H ALA* 4.4 2.0 - - + -
266H GLY* 2.9 28.6 + - - -
392H LEU* 4.7 9.0 - - + -
393H VAL* 3.7 44.2 - - + +
396H THR* 3.5 38.2 - - + +
397H LEU* 3.4 24.4 - - + +
412H ALA* 5.4 2.7 - - + -
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Residues in contact with ALA 263 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141H LEU* 3.7 28.9 - - + -
188H VAL* 5.5 6.3 - - + -
259H THR 3.1 17.8 + - - +
260H ASP* 3.8 6.3 - - - +
262H LEU* 1.3 74.8 - - - +
264H VAL* 1.3 67.9 + - + +
266H GLY* 3.2 9.3 + - - -
267H PHE* 3.0 28.8 - - + -
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Residues in contact with VAL 264 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112H PHE* 5.3 12.6 - - + -
120H TRP* 3.9 31.9 - - + -
121H VAL* 4.8 9.0 - - + -
184H LEU* 4.1 18.8 - - + -
188H VAL* 4.3 10.8 - - + -
192H ALA* 5.2 6.1 - - + -
260H ASP* 3.0 19.5 + - + +
261H LEU* 4.2 2.5 - - - +
263H ALA* 1.3 75.6 - - + +
265H ALA* 1.3 64.1 + - - +
267H PHE* 2.9 20.2 + - - +
268H TYR* 3.4 20.9 - - + -
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Residues in contact with ALA 265 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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261H LEU* 3.0 23.9 + - + +
262H LEU* 3.8 6.1 - - + +
264H VAL* 1.3 77.2 - - - +
266H GLY* 1.3 63.3 + - - +
268H TYR* 2.9 16.6 + - - +
269H LYS* 3.4 13.2 + - - +
397H LEU* 3.9 17.7 - - + -
408H LEU* 4.0 32.4 - - + +
411H THR* 6.5 0.4 - - + -
412H ALA* 6.1 3.6 - - + -
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Residues in contact with GLY 266 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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262H LEU 2.9 16.1 + - - -
263H ALA* 3.6 7.4 - - - -
264H VAL 3.0 1.2 - - - -
265H ALA* 1.3 77.6 - - - +
267H PHE* 1.3 59.5 + - - +
268H TYR 3.3 0.6 + - - -
269H LYS* 3.8 22.2 - - - +
397H LEU* 3.9 10.1 - - - +
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Residues in contact with PHE 267 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183H VAL* 3.5 21.5 - - + +
184H LEU* 3.2 33.9 - - + -
185H PRO* 3.7 29.8 - - + -
188H VAL* 3.9 25.1 - - + -
263H ALA* 3.0 32.8 - - + -
264H VAL 2.9 9.5 + - - +
266H GLY* 1.3 71.9 - - - -
268H TYR* 1.3 64.2 + - + +
269H LYS 3.7 1.6 - - - -
270H ASN* 5.4 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