Contacts of the helix formed by residues 304 - 312 (chain A) in PDB entry 5E2I
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 SER 304 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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296A ILE* 4.2 11.2 - - - -
303A THR* 1.3 79.1 + - - +
305A LEU* 1.3 65.6 + - - +
306A GLU* 3.8 7.4 + - - +
307A SER* 2.8 38.5 + - - -
308A MET* 3.1 8.7 + - - +
604A PEG 4.0 12.6 + - - -
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Residues in contact with LEU 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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208A MET* 5.1 2.9 - - + -
211A LEU* 4.1 14.1 - - + +
229A PRO* 3.2 36.3 - - + +
230A ASN* 4.0 14.4 - - + -
235A SER* 4.2 16.6 - - - +
296A ILE* 3.8 20.5 - - + +
301A PHE* 3.6 37.9 - - + -
303A THR 4.7 0.2 - - - +
304A SER* 1.3 71.9 - - - +
306A GLU* 1.3 62.2 + - - +
308A MET* 3.2 9.5 + - - +
309A LEU* 3.0 29.6 + - + +
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Residues in contact with GLU 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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230A ASN* 5.7 1.9 - - - +
304A SER* 3.2 7.0 - - - +
305A LEU* 1.3 79.6 - - - +
307A SER* 1.3 57.8 + - - +
309A LEU* 3.3 11.3 + - - +
310A ASN* 2.9 41.7 + - - +
406A HIS* 2.8 40.8 + - - -
410A LYS* 3.8 11.4 + - - -
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Residues in contact with SER 307 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303A THR* 3.0 25.2 + - - +
304A SER* 2.8 24.6 + - - -
306A GLU* 1.3 73.6 - - - +
308A MET* 1.3 62.6 + - - +
310A ASN* 3.9 8.9 - - - +
311A SER* 2.9 30.5 + - - -
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Residues in contact with MET 308 (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 LEU* 3.1 50.3 - - + +
216A ARG* 4.1 3.6 - - - +
301A PHE* 4.5 8.7 - - - -
302A PRO* 3.8 30.7 - - + -
303A THR* 3.2 34.8 - - - +
304A SER 3.1 5.3 + - - +
305A LEU* 3.5 9.9 - - - +
307A SER* 1.3 81.9 + - - +
309A LEU* 1.3 60.3 + - - +
311A SER* 3.4 5.3 + - - -
312A GLY 3.1 3.1 + - - -
313A ASN* 2.9 59.9 + - - +
314A PHE* 3.7 2.6 - - - -
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Residues in contact with LEU 309 (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 LEU* 4.0 21.3 - - + -
229A PRO* 5.7 1.1 - - + -
230A ASN* 4.6 17.7 - - + -
305A LEU* 3.0 22.5 + - + +
306A GLU* 3.6 21.5 - - - +
308A MET* 1.3 76.9 - - - +
310A ASN* 1.3 62.0 + - - +
312A GLY* 3.4 7.4 + - - -
314A PHE* 3.6 24.0 - - + -
406A HIS* 4.8 4.7 - - + -
407A PHE* 3.9 37.2 - - + -
410A LYS* 4.1 33.9 - - + +
411A TYR* 5.3 1.1 - - - +
414A PHE* 4.2 6.2 - - - -
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Residues in contact with ASN 310 (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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306A GLU* 2.9 37.3 + - - +
307A SER* 3.9 7.6 - - - +
309A LEU* 1.3 75.7 - - - +
311A SER* 1.3 60.4 + - - +
312A GLY 3.5 0.7 + - - -
410A LYS* 2.6 38.8 + - - +
414A PHE* 3.7 13.5 - - - -
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Residues in contact with SER 311 (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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307A SER 2.9 20.2 + - - -
308A MET* 3.4 7.1 + - - -
310A ASN* 1.3 76.5 - - - +
312A GLY* 1.3 59.7 + - - +
313A ASN* 3.4 15.8 + - - +
414A PHE* 4.2 9.7 - - - -
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Residues in contact with GLY 312 (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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308A MET 3.1 3.4 + - - -
309A LEU 3.4 1.4 + - - -
310A ASN 3.3 4.6 + - - -
311A SER* 1.3 78.0 - - - +
313A ASN* 1.3 58.6 + - - +
314A PHE* 2.9 25.5 + - - +
316A LYS* 2.7 30.7 + - - -
414A PHE* 3.6 22.6 - - - -
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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