Contacts of the helix formed by residues 297 - 306 (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 LEU 297 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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202C GLY 3.6 25.8 - - - +
203C LEU* 3.9 15.9 - - + +
211C ILE* 3.6 22.5 - - + +
256C VAL* 3.6 32.5 - - + -
257C GLY* 3.9 13.9 - - - -
277C ILE* 3.5 17.7 - - + -
295C GLY 3.3 2.6 + - - -
296C ASP* 1.3 71.1 - - - +
298C PHE* 1.3 78.1 + - + +
299C SER 3.1 0.4 - - - -
300C VAL 4.0 0.2 - - - -
301C VAL* 3.1 30.5 + - - +
302C PRO* 3.5 0.9 - - - +
399C FAD 2.9 29.5 + - + +
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Residues in contact with PHE 298 (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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202C GLY 3.5 17.5 - - - -
203C LEU 3.1 26.9 - - - -
204C GLY* 5.2 0.4 - - - -
208C SER* 3.6 26.7 - - - -
211C ILE* 4.4 12.1 - - + -
296C ASP* 2.9 29.2 + - - +
297C LEU* 1.3 88.1 - - + +
299C SER* 1.3 59.3 + - - +
302C PRO* 3.2 17.7 - - - +
399C FAD 3.5 10.3 - - - -
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Residues in contact with SER 299 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296C ASP* 2.8 23.3 + - - +
298C PHE* 1.3 80.8 - - - +
300C VAL* 1.3 67.9 + - - +
301C VAL 3.6 0.2 - - - -
302C PRO* 3.2 13.6 - - - +
303C GLU* 3.5 13.0 + - - +
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Residues in contact with VAL 300 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277C ILE* 3.4 27.4 - - + -
293C LEU* 3.5 34.3 - - + -
295C GLY* 4.4 18.4 - - - -
296C ASP 2.9 14.7 + - - +
299C SER* 1.3 76.2 - - - +
301C VAL* 1.3 62.4 + - - +
303C GLU* 3.0 4.3 + - - +
304C LEU* 2.8 34.3 + - + +
239D VAL* 3.7 15.7 - - + +
242D LEU* 5.7 1.1 - - + -
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Residues in contact with VAL 301 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211C ILE* 3.6 36.3 - - + +
212C ILE* 4.5 4.5 - - + -
215C LEU* 4.1 20.9 - - + -
254C VAL* 6.6 0.2 - - + -
256C VAL* 3.9 24.0 - - + -
277C ILE* 3.7 20.4 - - + -
297C LEU* 3.1 18.0 + - + +
300C VAL* 1.3 74.1 - - - +
302C PRO* 1.3 62.8 - - + +
304C LEU* 3.1 8.9 + - + +
305C THR* 2.8 36.4 + - - +
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Residues in contact with PRO 302 (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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211C ILE* 4.8 11.0 - - + -
297C LEU 3.5 9.2 - - - +
298C PHE* 3.2 19.1 - - - +
299C SER* 3.2 17.9 - - - +
301C VAL* 1.3 96.5 - - + +
303C GLU* 1.3 54.7 + - - -
305C THR* 3.7 7.9 + - - +
306C GLY* 3.1 21.0 + - - -
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Residues in contact with GLU 303 (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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299C SER 3.5 12.7 + - - +
300C VAL* 3.0 9.0 + - - +
302C PRO* 1.3 76.1 - - - +
304C LEU* 1.3 65.4 + - - +
306C GLY* 3.0 3.4 + - - -
307C LYS* 3.0 53.7 + - - +
238D SER* 4.9 1.9 + - - -
239D VAL* 3.0 31.3 + - + +
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Residues in contact with LEU 304 (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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215C LEU* 3.7 30.3 - - + -
219C LEU* 6.0 1.1 - - + -
254C VAL* 5.3 10.8 - - + -
275C VAL* 6.2 0.4 - - + -
277C ILE* 6.0 5.2 - - + -
300C VAL* 2.8 17.5 + - + +
301C VAL* 3.4 11.9 - - + +
303C GLU* 1.3 76.7 - - - +
305C THR* 1.3 61.8 + - - +
307C LYS 3.2 11.3 + - - +
308C LEU* 3.4 29.6 - - + +
239D VAL* 3.6 16.8 - - + +
242D LEU* 3.5 33.9 - - + -
243D VAL* 3.8 24.5 - - + -
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Residues in contact with THR 305 (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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211C ILE 4.6 0.7 + - - -
214C GLU* 4.5 12.9 - - + +
215C LEU* 3.2 43.2 + - - +
218C LYS* 3.6 38.5 + - + +
301C VAL* 2.8 21.1 + - - +
302C PRO* 3.9 8.0 - - - +
304C LEU* 1.3 76.2 - - - +
306C GLY* 1.3 61.5 + - - +
308C LEU* 3.9 3.7 - - - +
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Residues in contact with GLY 306 (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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157A GLU 4.3 3.3 - - - +
158A GLY* 3.8 16.9 + - - -
218C LYS* 5.5 0.9 + - - -
302C PRO 3.1 12.3 + - - -
303C GLU* 3.0 8.5 + - - -
305C THR* 1.3 80.0 - - - +
307C LYS* 1.3 57.9 + - - +
308C LEU 3.3 6.9 + - - +
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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