Contacts of the helix formed by residues 245 - 258 (chain A) in PDB entry 1F7U
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 ASN 245 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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194A LYS* 4.9 13.4 + - - +
198A LEU* 5.2 2.3 - - - +
231A ILE* 3.2 47.2 + - + +
234A GLU* 4.4 5.2 + - - +
240A LEU* 4.0 23.0 + - + +
244A THR* 1.3 78.3 - - - +
246A GLY* 1.3 61.7 + - - +
248A ALA* 3.3 20.8 + - - +
249A ARG* 3.6 8.1 + - - +
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Residues in contact with GLY 246 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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240A LEU* 3.0 13.7 + - - +
241A GLU* 3.2 30.1 - - - -
244A THR 3.0 1.4 - - - -
245A ASN* 1.3 75.7 + - - +
247A LYS* 1.3 56.6 + - - +
248A ALA 2.8 11.3 + - - -
249A ARG* 2.9 34.3 + - - +
250A GLU* 3.5 5.9 + - - +
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Residues in contact with LYS 247 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201A VAL* 4.3 15.9 - - + +
205A ARG* 3.0 45.3 - - - +
241A GLU* 3.6 14.0 - - + +
243A SER 3.0 24.5 + - - +
244A THR* 2.9 22.1 + - - +
246A GLY* 1.3 72.5 - - - +
248A ALA* 1.3 56.1 + - - +
250A GLU* 3.3 28.7 - - - +
251A TYR* 3.1 25.8 - - + -
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Residues in contact with ALA 248 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194A LYS* 5.1 3.8 - - + +
197A GLY* 3.7 30.6 - - - +
198A LEU* 4.2 15.7 - - + +
201A VAL* 4.0 12.8 - - + -
244A THR 3.9 5.8 - - - +
245A ASN* 3.3 14.6 - - - +
246A GLY 2.8 0.2 - - - -
247A LYS* 1.3 78.7 - - - +
249A ARG* 1.3 67.4 + - - +
250A GLU 3.1 1.3 - - - -
251A TYR* 3.4 7.0 + - - +
252A PHE* 3.4 15.4 + - - +
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Residues in contact with ARG 249 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194A LYS* 3.6 44.7 - - + +
240A LEU* 3.7 27.1 - - - +
241A GLU* 3.8 33.7 + - - +
245A ASN* 3.6 5.3 + - - +
246A GLY* 2.9 29.7 + - - +
248A ALA* 1.3 79.0 - - - +
250A GLU* 1.3 65.3 + - + +
252A PHE* 3.3 7.8 + - - +
253A LYS* 3.3 21.2 + - - +
340A LYS* 5.9 0.4 - - - +
342A ASP* 5.8 4.0 - - - +
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Residues in contact with GLU 250 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241A GLU* 3.1 42.1 - - - +
246A GLY 4.2 1.3 - - - +
247A LYS* 3.3 29.1 - - - +
249A ARG* 1.3 81.1 - - + +
251A TYR* 1.3 81.2 + - + +
252A PHE 3.0 1.8 - - - -
253A LYS* 3.0 27.2 - - - +
254A ARG* 2.7 37.0 + - - +
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Residues in contact with TYR 251 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197A GLY* 4.3 10.5 - - - +
200A ALA* 3.8 23.1 - - + -
201A VAL* 4.6 3.4 - - + -
204A GLU* 3.0 42.2 + - - -
247A LYS* 3.1 28.3 - - + -
248A ALA 3.4 9.6 + - - +
249A ARG 3.4 0.4 - - - -
250A GLU* 1.3 99.9 - - + +
252A PHE* 1.3 56.2 + - - +
254A ARG* 3.1 40.4 + - - +
255A MET* 2.9 35.0 + - + +
262A ALA* 4.5 6.6 - - + +
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Residues in contact with PHE 252 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192A TRP* 3.4 32.3 - + - -
193A GLY* 3.0 47.6 - - - +
194A LYS* 4.1 17.3 - - + +
197A GLY* 4.7 0.4 - - - -
248A ALA 3.4 9.1 + - - +
249A ARG* 3.3 13.4 + - - +
250A GLU 3.0 0.4 - - - -
251A TYR* 1.3 74.6 - - - +
253A LYS* 1.3 56.6 + - - +
254A ARG 2.9 4.7 - - - -
255A MET* 2.7 43.3 + - + +
256A GLU* 2.9 36.7 + - + +
344A THR* 4.4 18.4 - - + -
345A THR* 4.7 7.6 - - - -
350A ARG* 4.4 7.2 - - - -
976B A 5.7 0.4 - - - -
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Residues in contact with LYS 253 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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249A ARG 3.3 5.5 + - - +
250A GLU* 3.0 42.6 - - - +
252A PHE* 1.3 79.2 - - - +
254A ARG* 1.3 59.2 + - - +
256A GLU* 3.2 20.7 + - - +
257A ASP* 2.6 48.4 + - - +
344A THR* 4.6 12.6 - - + -
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Residues in contact with ARG 254 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204A GLU* 5.1 1.0 + - - -
250A GLU 2.7 18.5 + - - +
251A TYR* 3.1 50.5 + - - +
253A LYS* 1.3 88.4 - - + +
255A MET* 1.3 58.1 + - - +
257A ASP* 3.2 19.2 + - + +
259A ASP* 2.6 62.2 + - + +
261A GLU* 2.7 31.5 + - - +
262A ALA* 4.0 13.2 - - + +
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Residues in contact with MET 255 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192A TRP* 4.2 27.0 - - + -
196A PHE* 3.5 31.9 - - + +
197A GLY* 3.5 31.4 - - - +
200A ALA* 5.3 4.7 - - + -
251A TYR* 2.9 19.3 + - + +
252A PHE* 2.7 43.0 + - + +
254A ARG* 1.3 77.3 - - - +
256A GLU* 1.3 60.2 + - - +
258A GLY* 3.3 9.0 + - - -
262A ALA* 3.9 25.6 - - + +
263A LEU* 3.5 26.9 - - + +
265A ILE* 6.2 0.2 - - - -
266A TRP* 4.8 1.8 - - - -
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Residues in contact with GLU 256 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192A TRP* 4.2 14.7 + - + +
252A PHE* 2.9 56.0 + - + +
253A LYS* 3.4 13.5 - - - +
254A ARG 3.2 0.4 - - - -
255A MET* 1.3 80.2 - - - +
257A ASP* 1.3 60.2 + - - +
258A GLY 3.3 0.4 + - - -
344A THR* 3.5 19.2 - - - +
345A THR* 4.4 21.0 + - - +
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Residues in contact with ASP 257 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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253A LYS* 2.6 34.6 + - - +
254A ARG* 3.5 12.6 - - + +
255A MET 3.2 0.4 - - - -
256A GLU* 1.3 78.8 - - - +
258A GLY* 1.3 58.8 + - - +
259A ASP* 4.7 2.5 - - + +
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Residues in contact with GLY 258 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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255A MET 3.3 5.9 + - - -
256A GLU 3.3 4.0 - - - -
257A ASP* 1.3 80.5 - - - +
259A ASP* 1.3 54.5 + - - +
260A GLU* 2.7 20.1 + - - +
263A LEU* 3.6 14.7 - - - +
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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