Contacts of the helix formed by residues 219 - 228 (chain A) in PDB entry 6OE7
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 GLY 219 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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172A ARG* 3.3 15.3 - - - +
175A THR* 5.2 0.4 + - - -
217A LEU 3.7 2.6 + - - -
218A ASP* 1.3 78.1 + - - +
220A GLU* 1.3 61.5 + - - -
221A GLU* 3.4 3.6 - - - -
222A ALA* 3.3 4.1 + - - +
223A VAL* 3.1 31.0 + - - +
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Residues in contact with GLU 220 (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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19A ALA 4.2 7.7 - - - +
20A TYR* 4.2 9.8 - - + +
21A GLN 5.9 1.1 - - - +
68A ARG* 2.6 38.3 + - - -
219A GLY* 1.3 69.6 - - - -
221A GLU* 1.3 62.4 + - - +
223A VAL* 4.0 8.2 - - - +
224A SER* 2.7 34.4 + - - +
302A EDO 3.4 30.1 + - - -
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Residues in contact with GLU 221 (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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218A ASP 6.0 0.2 - - - +
219A GLY 5.1 0.7 - - - -
220A GLU* 1.3 78.2 - - - +
222A ALA* 1.3 56.2 + - - +
224A SER* 3.5 3.8 - - - -
225A LYS* 3.0 45.3 + - + +
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Residues in contact with ALA 222 (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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217A LEU* 4.1 15.2 - - + +
218A ASP 4.1 24.2 + - - +
219A GLY 3.3 9.2 + - - +
220A GLU 3.3 0.4 - - - -
221A GLU* 1.3 75.3 - - + +
223A VAL* 1.3 66.1 + - - +
225A LYS* 3.3 0.7 + - - -
226A TRP* 2.9 26.7 + - - +
240A LEU* 3.6 24.1 - - + +
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Residues in contact with VAL 223 (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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53A LEU* 4.5 6.7 - - + -
68A ARG* 3.7 25.6 - - - +
119A VAL* 4.1 10.0 - - + +
175A THR* 4.0 32.1 - - + +
217A LEU* 4.1 17.3 - - + -
219A GLY 3.1 20.1 + - - +
220A GLU* 3.9 13.7 - - - +
222A ALA* 1.3 76.7 - - - +
224A SER* 1.3 58.5 + - - +
226A TRP* 3.3 2.6 + - - +
227A LEU* 3.0 46.3 + - + +
302A EDO 4.8 1.6 - - - -
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Residues in contact with SER 224 (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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21A GLN 5.0 5.0 + - - -
66A SER* 6.1 2.9 - - - -
68A ARG* 2.9 22.9 + - - +
220A GLU* 2.7 24.6 + - - +
221A GLU* 3.5 4.7 - - - -
223A VAL* 1.3 76.9 - - - +
225A LYS* 1.3 57.6 + - - +
227A LEU* 3.2 7.6 + - - +
228A ASP* 3.0 33.3 + - - +
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Residues in contact with LYS 225 (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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117A ARG* 3.2 16.5 + - - -
221A GLU* 3.0 29.1 + - + +
222A ALA 3.3 0.2 + - - -
224A SER* 1.3 76.3 - - - +
226A TRP* 1.3 62.3 + - - +
228A ASP* 3.4 6.6 + - - -
232A VAL* 3.5 33.8 - - + +
240A LEU* 3.6 32.0 - - + +
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Residues in contact with TRP 226 (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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112A LEU* 4.3 9.4 - - + -
117A ARG* 2.8 57.4 + - + +
118A CYS 3.0 33.2 + - - -
119A VAL* 4.1 2.9 - - + -
177A ALA* 3.8 7.0 - - + -
178A GLY 3.1 15.8 + - - +
179A ILE* 4.4 4.0 - - + -
198A ILE* 3.6 32.1 - - + -
217A LEU* 3.7 27.1 - - + -
222A ALA 2.9 16.7 + - - +
223A VAL 3.8 2.0 - - - +
225A LYS* 1.3 77.6 - - - +
227A LEU* 1.3 59.4 + - - +
237A ALA* 3.5 44.9 - - + -
238A LEU* 4.3 7.4 - - + -
240A LEU* 3.6 5.7 - - + +
241A ILE* 3.5 18.6 - - + -
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Residues in contact with LEU 227 (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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53A LEU* 3.3 39.5 - - + +
54A LEU* 3.6 10.5 - - - -
55A SER* 3.5 25.2 + - - +
58A HIS* 4.8 0.2 + - - -
65A SER 4.8 2.5 - - - +
66A SER* 6.5 0.4 - - - -
68A ARG* 3.3 44.9 - - + +
117A ARG* 4.3 12.4 - - - +
118A CYS* 4.4 0.2 - - - -
119A VAL* 3.8 17.5 - - + +
223A VAL* 3.0 31.4 + - + +
224A SER* 3.7 4.7 - - - +
226A TRP* 1.3 76.5 - - - +
228A ASP* 1.3 58.4 + - - +
229A PHE* 3.0 13.9 + - - +
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Residues in contact with ASP 228 (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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23A ARG* 3.0 26.8 + - - -
65A SER* 2.6 40.8 + - - +
66A SER* 4.2 7.4 - - - -
117A ARG* 3.8 4.3 - - - -
224A SER 3.0 18.0 + - - +
225A LYS 3.4 3.8 + - - +
226A TRP 3.3 2.2 - - - -
227A LEU* 1.3 71.8 - - - +
229A PHE* 1.3 55.5 + - - +
230A GLY 3.0 4.7 + - - -
231A GLU* 3.3 13.8 + - - +
232A VAL* 3.0 35.0 + - + +
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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