Contacts of the helix formed by residues 231 - 235 (chain G) in PDB entry 3ECS
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 GLU 231 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21G ALA* 4.3 1.6 - - - +
107G SER* 3.8 15.7 - - - -
108G ARG* 2.9 30.7 + - - +
111G ILE* 3.9 7.2 - - + -
133G VAL* 3.3 21.1 - - + +
230G ALA* 1.3 76.6 - - - +
232G SER* 1.3 66.0 + - - +
233G PHE* 3.3 43.7 - - + -
234G LYS* 3.0 48.6 + - + +
235G PHE* 4.0 4.0 - - - -
287G ASP* 3.4 10.1 - - - +
507G SO4 3.9 1.9 + - - -
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Residues in contact with SER 232 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71G LEU* 4.2 5.1 - - - +
107G SER* 5.3 0.3 + - - -
231G GLU* 1.3 67.5 - - - +
233G PHE* 1.3 60.3 + - - +
234G LYS 2.8 10.0 + - - -
235G PHE* 2.9 34.8 + - - +
286G THR* 3.5 13.6 - - - +
287G ASP* 2.8 32.8 + - - -
288G LEU* 3.7 22.6 - - - +
303G LEU* 4.6 13.2 - - - +
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Residues in contact with PHE 233 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21G ALA* 4.4 5.2 - - + -
23G ALA* 3.4 31.9 - - + -
24G VAL* 4.0 23.6 - - + -
64G ALA 4.4 0.3 - - - +
67G SER* 2.7 24.8 + - - -
68G GLY* 3.6 16.2 + - - -
71G LEU* 4.0 16.2 - - + -
100G PHE* 5.1 7.4 - - + -
104G ILE* 3.9 41.5 - - + -
107G SER* 4.5 4.3 - - - -
108G ARG* 5.2 1.6 - - - -
231G GLU* 3.3 41.3 - - + -
232G SER* 1.3 80.6 + - - +
234G LYS* 1.3 70.0 + - + +
235G PHE 3.3 0.9 - - - -
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Residues in contact with LYS 234 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21G ALA* 5.5 3.6 - - - -
23G ALA* 5.8 0.2 - - - -
63G VAL* 5.1 0.2 - - - +
64G ALA* 4.1 11.4 - - + -
67G SER* 3.5 8.5 + - - -
133G VAL* 4.5 0.2 - - - +
197G ALA 3.0 31.1 + - - +
198G GLU* 3.6 17.0 - - - +
199G GLY* 3.5 9.1 - - - -
200G VAL* 3.1 22.6 + - + +
230G ALA* 4.2 7.9 - - + +
231G GLU* 3.0 42.3 + - - +
232G SER 2.8 1.2 - - - -
233G PHE* 1.3 96.4 - - + +
235G PHE* 1.3 64.8 + - - +
236G VAL* 3.0 5.4 + - - +
507G SO4 3.0 36.3 + - - -
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Residues in contact with PHE 235 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67G SER* 3.3 5.5 - - - -
71G LEU* 4.2 2.8 - - - +
200G VAL* 3.5 30.1 - - + -
231G GLU 4.0 2.7 - - - -
232G SER* 2.9 35.4 + - - +
234G LYS* 1.3 75.7 - - - +
236G VAL* 1.3 59.1 + - - +
284G LEU* 5.5 1.6 - - + -
286G THR* 3.9 19.1 - - - -
288G LEU* 4.3 20.9 - - + -
291G LEU* 4.2 15.7 - - + -
296G VAL* 4.0 22.0 - - + -
299G GLU* 4.3 5.6 - - + -
300G LEU* 3.8 43.1 - - + -
303G LEU* 4.9 5.4 - - + -
304G TYR* 2.9 26.9 + - + -
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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
------------------------------------------------------------
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