Contacts of the helix formed by residues 262 - 267 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129C ALA* 4.1 16.8 - - + +
131C ASN* 3.6 28.7 - - - +
260C GLY 3.7 2.0 + - - -
261C ALA* 1.3 72.2 - - - +
263C GLN* 1.3 73.7 + - - +
264C HIS 3.1 0.2 + - - -
265C LEU* 3.2 10.1 + - - +
266C ALA* 3.0 23.0 + - - +
13D TYR 4.6 8.5 - - - +
14D ASN* 4.3 11.7 - - - +
15D VAL 4.3 4.9 - - - +
16D LYS* 4.0 36.3 - - + +
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Residues in contact with GLN 263 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129C ALA* 5.2 1.8 - - + +
242C GLY* 3.2 2.8 - - - -
243C GLN* 2.9 55.8 + - - +
261C ALA* 3.1 1.6 + - - +
262C ILE* 1.3 93.7 + - - +
264C HIS* 1.3 57.5 + - - +
266C ALA* 3.8 2.6 - - - +
399C FAD 2.7 72.3 + - + +
13D TYR* 2.9 44.7 + - - +
14D ASN* 5.1 2.5 + - - +
124D ILE* 5.9 0.4 - - - +
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Residues in contact with HIS 264 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225C ALA 3.8 15.5 - - - -
226C SER* 4.0 3.2 - - - -
241C VAL* 3.2 18.2 + - + +
242C GLY* 3.8 2.6 - - - -
253C TYR* 2.7 31.4 + - - -
255C ALA* 5.9 0.2 - - + -
258C ILE* 3.9 36.3 - - + +
260C GLY 5.0 0.2 - - - -
261C ALA* 2.7 22.9 + - - +
263C GLN* 1.3 72.2 - - - +
265C LEU* 1.3 69.4 + - + +
266C ALA 3.0 1.8 - - - -
267C GLY* 3.0 14.2 + - - -
268C MET* 3.7 23.5 - - + +
285C ILE* 5.6 0.7 - - + -
399C FAD 2.8 37.7 + - + +
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Residues in contact with LEU 265 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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260C GLY* 3.5 30.3 - - - +
261C ALA 3.1 4.8 + - - +
262C ILE* 3.2 9.6 + - - +
264C HIS* 1.3 78.9 - - + +
266C ALA* 1.3 61.8 + - - +
267C GLY 3.0 0.6 + - - -
268C MET* 3.6 18.4 - - + -
269C LYS* 3.0 34.2 + - + +
284C PRO* 5.5 5.8 - - + +
285C ILE* 3.7 29.6 - - + -
288C ILE* 4.2 27.8 - - + -
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Residues in contact with ALA 266 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129C ALA* 3.3 30.5 - - + +
130C GLY* 5.4 0.8 - - - -
148C ARG* 3.9 19.1 + - - -
242C GLY* 4.7 0.4 - - - -
243C GLN* 4.0 20.0 - - + +
247C VAL* 4.0 3.1 - - - +
262C ILE 3.0 13.7 + - - +
263C GLN 3.8 11.4 - - - +
264C HIS 3.0 0.6 - - - -
265C LEU* 1.3 76.1 - - - +
267C GLY* 1.3 56.3 + - - +
268C MET 3.6 0.4 + - - -
269C LYS* 5.1 10.6 - - - +
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Residues in contact with GLY 267 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148C ARG* 5.8 0.2 - - - -
241C VAL* 3.5 7.1 - - - +
242C GLY* 3.8 15.8 - - - -
247C VAL* 3.5 21.0 - - - -
248C VAL* 2.8 29.9 + - - +
264C HIS 3.0 9.3 + - - -
266C ALA* 1.3 80.6 - - - +
268C MET* 1.3 62.3 + - - +
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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