Contacts of the helix formed by residues 297 - 306 (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 LEU 297 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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202A GLY 3.8 25.1 - - - -
203A LEU* 4.1 13.0 - - + +
211A ILE* 3.9 10.3 - - + +
256A VAL* 3.7 32.8 - - + -
257A GLY* 3.9 13.7 - - - -
277A ILE* 3.6 16.8 - - + -
295A GLY 3.3 2.0 + - - -
296A ASP* 1.3 70.5 + - - +
298A PHE* 1.3 90.1 + - + +
299A SER 3.1 0.9 - - - -
300A VAL 4.0 0.7 - - - -
301A VAL* 3.2 29.8 + - - +
302A PRO* 3.6 1.0 - - - +
399A FAD 2.9 33.3 + - + +
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Residues in contact with PHE 298 (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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202A GLY 3.5 18.6 - - - -
203A LEU* 3.1 27.1 - - + -
204A GLY* 5.3 0.7 - - - -
208A SER* 3.2 28.0 - - - -
211A ILE* 3.8 16.3 - - + +
296A ASP* 3.0 26.7 + - - +
297A LEU* 1.3 92.5 - - + +
299A SER* 1.3 60.5 + - - +
302A PRO* 3.5 15.1 - - - +
399A FAD 3.9 6.3 - - - -
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Residues in contact with SER 299 (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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296A ASP* 2.9 21.1 + - - +
298A PHE* 1.3 84.2 + - - +
300A VAL* 1.3 64.4 + - - +
301A VAL 3.7 0.2 - - - -
302A PRO* 3.8 5.9 - - - +
303A GLU* 3.5 22.2 + - - +
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Residues in contact with VAL 300 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277A ILE* 3.4 27.6 - - + -
293A LEU* 3.4 34.1 - - + -
295A GLY* 4.4 8.7 - - - -
296A ASP 2.9 24.9 + - - +
299A SER* 1.3 78.8 - - - +
301A VAL* 1.3 54.6 + - - +
303A GLU* 3.0 4.0 + - - +
304A LEU* 2.7 40.9 + - + +
239B VAL* 3.8 15.2 - - + +
242B LEU* 5.5 0.9 - - + -
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Residues in contact with VAL 301 (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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211A ILE* 3.5 36.1 - - + +
212A ILE* 4.7 3.4 - - + -
215A LEU* 4.0 20.4 - - + -
256A VAL* 3.9 26.0 - - + -
277A ILE* 3.6 22.2 - - + -
297A LEU* 3.2 18.0 + - + +
300A VAL* 1.3 76.0 - - - +
302A PRO* 1.3 62.7 - - + +
304A LEU* 3.0 9.6 + - + +
305A THR* 2.8 34.9 + - - +
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Residues in contact with PRO 302 (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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211A ILE* 4.6 12.8 - - + -
214A GLU* 6.1 0.4 - - - +
297A LEU 3.6 9.4 - - - +
298A PHE* 3.5 22.2 - - - +
299A SER* 3.8 8.1 - - - +
300A VAL 3.7 1.3 - - - -
301A VAL* 1.3 95.5 - - + +
303A GLU* 1.3 55.9 + - - +
305A THR* 3.9 8.7 - - - +
306A GLY* 3.2 19.8 + - - -
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Residues in contact with GLU 303 (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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299A SER 3.5 13.9 - - - +
300A VAL* 3.0 8.8 + - - +
302A PRO* 1.3 78.1 - - - +
304A LEU* 1.3 66.0 + - - +
306A GLY* 3.2 2.8 + - - -
307A LYS* 3.1 51.3 + - - +
238B SER* 4.6 2.9 + - - -
239B VAL* 3.2 30.6 + - + +
240B ASP* 4.5 1.6 - - - +
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Residues in contact with LEU 304 (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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215A LEU* 4.0 26.0 - - + -
219A LEU* 6.2 0.7 - - + -
254A VAL* 5.2 11.0 - - + -
275A VAL* 6.1 1.3 - - + -
277A ILE* 5.8 4.7 - - + -
300A VAL* 2.7 17.1 + - + +
301A VAL* 3.4 13.2 - - + +
303A GLU* 1.3 76.9 - - - +
305A THR* 1.3 61.5 + - - +
307A LYS 3.2 9.0 + - - -
308A LEU* 3.1 32.6 - - + +
239B VAL* 3.7 16.1 - - + +
242B LEU* 4.1 24.9 - - + -
243B VAL* 3.5 30.3 - - + -
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Residues in contact with THR 305 (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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211A ILE 4.6 0.9 + - - -
214A GLU* 4.6 14.8 - - + +
215A LEU* 3.3 46.6 + - - +
218A LYS* 3.9 23.4 - - + -
301A VAL* 2.8 25.0 + - - +
302A PRO* 3.9 8.7 - - - +
304A LEU* 1.3 73.0 - - - +
306A GLY* 1.3 61.1 + - - +
307A LYS 3.5 0.2 + - - -
308A LEU* 3.5 14.6 + - - +
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Residues in contact with GLY 306 (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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302A PRO 3.2 11.9 + - - -
303A GLU* 3.2 7.7 + - - -
304A LEU 3.2 0.8 - - - -
305A THR* 1.3 78.9 - - - +
307A LYS* 1.3 59.3 + - - +
308A LEU 3.3 4.2 + - - +
157C GLU* 4.0 5.4 - - - +
158C GLY* 3.9 17.1 + - - -
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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