Contacts of the helix formed by residues 214 - 223 (chain A) in PDB entry 2D2I
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 214 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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213A THR* 1.3 73.9 + - - +
215A ALA* 1.3 60.8 + - - +
216A ALA 3.3 2.7 - - - -
217A LYS* 3.2 20.2 + - - +
218A ALA* 2.8 30.7 + - - +
1339A SO4 3.2 12.6 + - - -
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Residues in contact with ALA 215 (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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156A THR* 3.4 30.1 - - + -
157A THR* 3.1 31.0 + - - +
160A LEU* 3.9 2.7 - - + +
178A MET* 4.2 3.4 - - + -
213A THR* 3.3 12.0 + - - +
214A GLY* 1.3 78.1 - - - +
216A ALA* 1.3 61.2 + - - +
218A ALA* 3.3 6.9 + - - -
219A VAL* 3.3 14.4 + - - +
1339A SO4 3.2 17.1 + - - +
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Residues in contact with ALA 216 (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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160A LEU* 3.7 17.6 - - + +
178A MET* 4.6 7.1 - - + +
213A THR* 5.0 4.4 + - + +
214A GLY 3.3 0.6 - - - -
215A ALA* 1.3 74.0 - - - +
217A LYS* 1.3 68.6 + - + +
219A VAL* 3.2 16.9 + - - +
226A LEU 5.7 0.7 - - - +
230A LEU* 3.7 17.4 - - + +
231A ASN* 3.2 44.6 - - - +
232A GLY* 3.9 3.6 - - - +
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Residues in contact with LYS 217 (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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213A THR 5.1 3.6 - - - +
214A GLY* 3.2 19.6 + - - +
216A ALA* 1.3 77.4 - - + +
218A ALA* 1.3 65.3 + - - +
219A VAL 3.0 1.6 + - - -
220A ALA* 3.0 22.9 + - - +
221A LEU* 4.4 0.3 + - - +
228A GLY 6.3 1.3 - - - +
230A LEU 4.2 13.0 - - - +
231A ASN* 4.9 9.0 - - + -
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Residues in contact with ALA 218 (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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124A PRO* 6.2 5.2 - - + -
132A THR* 5.9 0.2 - - - +
153A ALA* 5.7 3.1 - - + -
157A THR* 3.5 19.4 - - + +
214A GLY 2.8 18.1 + - - +
215A ALA* 3.4 7.9 - - - +
216A ALA 3.2 0.2 - - - -
217A LYS* 1.3 77.5 - - - +
219A VAL* 1.3 62.9 + - - +
220A ALA 2.9 0.9 - - - -
221A LEU* 2.8 40.1 + - + +
222A VAL* 3.9 2.4 + - - +
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Residues in contact with VAL 219 (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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157A THR* 4.6 4.7 - - + -
160A LEU* 3.6 28.5 - - + -
161A ALA* 4.5 15.9 - - + +
164A ALA* 4.9 1.3 - - + -
215A ALA 3.3 13.3 + - - +
216A ALA 3.2 15.5 - - - +
217A LYS 3.0 0.8 + - - -
218A ALA* 1.3 75.3 - - - +
220A ALA* 1.3 54.2 + - - +
222A VAL* 3.0 13.0 + - - +
223A ILE* 2.6 39.0 + - + -
226A LEU* 3.8 25.1 - - + +
230A LEU* 3.7 21.5 - - + -
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Residues in contact with ALA 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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217A LYS 3.0 14.6 + - - +
218A ALA 2.9 0.2 + - - -
219A VAL* 1.3 84.2 - - - +
221A LEU* 1.3 63.1 + - + +
223A ILE 3.5 11.0 - - - -
224A PRO* 3.1 25.5 - - - +
226A LEU 4.3 2.0 - - - +
227A LYS* 3.6 44.4 - - + +
228A GLY 4.9 1.3 - - - +
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Residues in contact with LEU 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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132A THR* 3.8 39.9 - - + +
138A ASN* 4.2 5.5 + - - -
141A GLU* 5.5 2.1 - - - +
217A LYS 5.3 0.2 - - - +
218A ALA* 2.8 30.7 + - + +
220A ALA* 1.3 80.3 - - + +
222A VAL* 1.3 61.7 + - + +
224A PRO* 4.6 5.9 - - - +
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Residues in contact with VAL 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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132A THR* 3.7 17.0 - - + +
133A TYR* 4.2 0.4 - - - -
134A VAL* 3.9 23.3 - - + +
137A VAL* 3.6 25.3 - - + +
138A ASN* 3.2 46.2 - - - +
141A GLU* 5.4 0.9 - - - +
157A THR* 5.0 2.0 - - + -
161A ALA* 4.1 15.0 - - + -
218A ALA 4.4 1.6 - - - +
219A VAL* 3.3 21.1 - - - +
221A LEU* 1.3 82.8 - - + +
223A ILE* 1.3 59.9 + - + +
224A PRO* 3.7 7.3 - - - +
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Residues in contact with ILE 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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137A VAL* 3.6 14.8 - - + -
161A ALA* 3.8 25.8 - - - +
164A ALA* 4.2 3.1 - - + -
165A LYS* 3.8 27.8 - - + +
168A HIS* 4.9 7.9 - - + -
219A VAL* 2.6 19.4 + - + +
220A ALA* 3.4 11.5 - - - -
222A VAL* 1.3 80.5 - - + +
224A PRO* 1.3 56.3 - - + +
225A GLU* 4.4 10.1 - - + +
226A LEU* 2.9 54.9 + - + +
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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
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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