Contacts of the helix formed by residues 291 - 300 (chain C) in PDB entry 3ER8
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 GLN 291 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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288C MET 2.8 12.8 + - - +
289C PHE 4.1 2.6 - - - +
290C SER* 1.3 77.4 - - - +
292C ILE* 1.3 93.8 + - - +
293C ASP* 2.7 42.7 + - + +
294C ARG* 2.9 19.9 + - + +
295C LEU 3.6 4.2 + - - -
402C ASN* 3.8 19.6 - - + +
403C THR* 3.5 23.5 + - - +
460C ARG* 3.1 38.8 + - - +
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Residues in contact with ILE 292 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149C VAL 5.2 0.2 - - - +
290C SER 3.5 3.8 + - - -
291C GLN* 1.3 81.9 - - - +
293C ASP* 1.3 78.8 + - - +
295C LEU* 2.9 21.4 + - + +
296C GLU* 3.0 37.0 + - + +
403C THR* 3.2 6.0 + - - +
405C LEU* 3.7 18.8 - - + +
454C ILE* 3.9 28.0 - - + -
457C HIS* 2.9 44.2 - - + +
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Residues in contact with ASP 293 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291C GLN* 2.7 34.1 + - + +
292C ILE* 1.3 81.3 - - - +
294C ARG* 1.3 55.5 + - + +
296C GLU* 2.5 39.6 + - - +
297C ASP* 2.8 19.1 + - - +
460C ARG* 5.7 3.1 + - - -
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Residues in contact with ARG 294 (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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288C MET* 2.9 70.3 - - + +
289C PHE* 4.1 8.4 - - + -
291C GLN* 2.9 17.5 + - + +
293C ASP* 1.3 74.8 - - + +
295C LEU* 1.3 57.1 + - - +
297C ASP* 3.0 25.8 + - - +
298C LEU* 2.9 29.1 + - - +
304C LYS* 5.6 3.0 - - - +
305C PHE* 4.6 10.5 - - - -
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Residues in contact with LEU 295 (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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145C MET* 3.9 21.1 - - + +
146C ASN* 5.5 0.8 - - - +
147C VAL* 4.3 8.3 - - + +
148C ALA* 3.2 12.4 - - + +
289C PHE* 3.5 34.5 - - + +
291C GLN 3.6 1.3 + - - +
292C ILE* 2.9 14.0 + - - +
293C ASP 2.8 0.6 + - - -
294C ARG* 1.3 78.3 - - - +
296C GLU* 1.3 48.6 + - - +
298C LEU* 3.0 10.1 + - + +
299C SER* 2.8 33.4 + - - -
405C LEU* 3.6 29.2 - - + -
415C ILE* 4.0 11.9 - - + -
454C ILE* 3.7 28.5 - - + -
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Residues in contact with GLU 296 (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 ALA* 3.8 5.6 - - + -
149C VAL* 4.0 25.4 + - + +
292C ILE* 3.3 44.4 - - + +
293C ASP* 2.5 21.0 + - - +
295C LEU* 1.3 71.2 - - - +
297C ASP* 1.3 56.1 + - - +
299C SER* 3.1 25.4 - - - -
300C LYS* 3.3 22.3 + - - +
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Residues in contact with ASP 297 (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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293C ASP* 2.8 12.9 + - - +
294C ARG* 3.0 50.4 + - - +
296C GLU* 1.3 75.1 - - - +
298C LEU* 1.3 61.1 + - - +
299C SER 3.0 5.3 + - - -
300C LYS* 3.5 26.0 + - - +
301C ASP* 4.0 5.2 + - - +
304C LYS* 5.0 8.5 - - + +
305C PHE* 5.1 10.1 - - + -
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Residues in contact with LEU 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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142C LEU* 3.5 39.9 - - + +
145C MET* 4.7 2.9 - - + -
146C ASN* 3.2 17.0 - - - +
289C PHE* 3.4 28.0 - - + -
294C ARG 2.9 15.8 + - - +
295C LEU* 3.4 8.1 - - + +
297C ASP* 1.3 73.1 - - - +
299C SER* 1.3 62.9 + - - +
300C LYS 3.5 0.2 - - - -
301C ASP 3.6 13.5 - - - +
302C PRO* 3.1 41.5 - - + +
304C LYS* 5.8 0.4 - - - -
305C PHE* 3.3 31.4 - - + +
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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
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146C ASN* 4.0 8.1 + - - +
148C ALA* 2.8 46.1 + - - +
149C VAL* 4.1 12.3 - - - -
295C LEU 2.8 4.6 + - - -
296C GLU* 3.1 14.5 - - - -
297C ASP 3.0 0.4 - - - -
298C LEU* 1.3 77.7 - - - +
300C LYS* 1.3 61.4 + - - +
301C ASP 3.2 5.6 + - - -
302C PRO* 3.3 15.1 - - - +
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Residues in contact with LYS 300 (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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149C VAL* 5.9 3.4 - - + -
296C GLU* 3.3 25.7 + - - +
297C ASP* 3.5 15.6 + - - +
299C SER* 1.3 77.4 - - - +
301C ASP* 1.3 69.5 + - - +
302C PRO* 4.0 0.4 - - - -
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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