Contacts of the helix formed by residues 262 - 267 (chain A) in PDB entry 1EFP
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 ILE 262 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129A ALA* 4.0 17.4 - - + +
131A ASN* 3.9 24.2 - - - +
260A GLY 3.7 2.0 + - - -
261A ALA* 1.3 71.2 - - - +
263A GLN* 1.3 78.0 + - - +
264A HIS 3.1 0.2 + - - -
265A LEU* 3.2 13.5 + - + +
266A ALA* 3.0 21.8 + - - +
13B TYR 4.4 3.4 - - - +
14B ASN* 3.7 26.2 - - - +
15B VAL 3.9 16.6 - - - +
16B LYS* 4.0 17.7 - - + -
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Residues in contact with GLN 263 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129A ALA* 5.7 0.8 - - - +
242A GLY* 3.3 1.6 - - - -
243A GLN* 2.9 53.5 + - - +
261A ALA* 3.2 2.1 - - - +
262A ILE* 1.3 89.0 + - - +
264A HIS* 1.3 60.0 + - - +
266A ALA* 3.7 3.7 - - - +
399A FAD 2.8 68.6 + - + +
13B TYR* 2.7 49.9 + - - +
14B ASN* 4.9 3.5 + - - -
124B ILE* 6.0 0.4 - - - +
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Residues in contact with HIS 264 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198A SER* 4.8 0.2 - - - -
225A ALA 3.8 15.7 - - - -
226A SER* 4.0 2.2 - - - -
241A VAL* 3.1 19.3 + - + +
242A GLY* 3.8 4.3 - - - -
253A TYR* 2.9 29.9 + - - -
255A ALA* 5.8 0.2 - - + -
258A ILE* 3.7 40.4 - - + +
260A GLY* 5.1 0.4 - - - -
261A ALA* 2.8 22.0 + - - +
263A GLN* 1.3 72.7 - - - +
265A LEU* 1.3 70.5 + - + +
266A ALA 3.1 1.3 - - - -
267A GLY* 3.1 11.4 + - - -
268A MET* 3.7 21.6 - - + +
285A ILE* 5.7 0.4 - - + -
399A FAD 2.9 38.6 + - + +
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Residues in contact with LEU 265 (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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260A GLY* 3.9 21.8 - - - +
261A ALA 3.0 15.0 + - - +
262A ILE* 3.2 13.4 + - + +
264A HIS* 1.3 77.9 - - + +
266A ALA* 1.3 55.7 + - - +
268A MET* 2.8 39.4 + - - -
269A LYS* 2.9 24.9 + - + +
284A PRO* 5.6 4.5 - - + +
285A ILE* 4.0 27.4 - - + -
288A ILE* 4.2 26.5 - - + -
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Residues in contact with ALA 266 (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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129A ALA* 3.4 34.4 - - + +
130A GLY* 5.6 0.9 - - - -
148A ARG* 4.2 7.8 + - - -
243A GLN* 3.8 22.0 - - + -
247A VAL* 3.8 11.3 - - - +
262A ILE 3.0 10.2 + - - +
263A GLN 3.7 14.4 - - - +
264A HIS 3.1 0.2 - - - -
265A LEU* 1.3 75.0 - - - +
267A GLY* 1.3 57.3 + - - +
268A MET 3.8 0.5 + - - -
269A LYS* 4.8 12.2 - - - +
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Residues in contact with GLY 267 (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 VAL* 3.6 7.2 - - - +
242A GLY* 3.8 15.4 - - - -
247A VAL* 3.4 22.6 - - - -
248A VAL* 2.8 30.2 + - - +
264A HIS 3.1 7.6 + - - -
265A LEU 2.8 1.6 + - - -
266A ALA* 1.3 79.2 - - - +
268A MET* 1.3 62.9 + - - +
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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