Contacts of the helix formed by residues 218 - 228 (chain A) in PDB entry 2G5N
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 TYR 218 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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79A HIS* 3.5 39.0 - + - -
89A ASN* 2.6 41.2 + - - -
91A ILE* 4.0 28.9 - - + -
165A ASN* 3.0 26.8 - - + +
213A THR* 3.8 16.8 - - + -
214A LYS 3.3 25.1 - - - -
215A VAL* 2.8 10.8 + - - +
217A ASN* 1.3 87.6 - - + +
219A VAL* 1.3 59.8 + - - +
220A SER 3.3 2.7 - - - -
221A TRP* 3.1 13.2 + + + +
222A ILE* 2.8 31.6 + - + +
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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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111A LEU* 4.4 12.1 - - + -
112A PRO* 3.3 45.3 - - + +
215A VAL* 3.5 15.0 + - + +
216A CYS* 3.9 10.7 + - - +
217A ASN 3.7 1.6 - - - -
218A TYR* 1.3 76.3 - - - +
220A SER* 1.3 65.3 + - - +
222A ILE* 3.7 6.9 - - - +
223A LYS* 2.9 45.9 + - + +
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Residues in contact with SER 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 ASN 5.2 2.4 + - - -
218A TYR 3.3 0.8 - - - -
219A VAL* 1.3 79.2 - - - +
221A TRP* 1.3 63.2 + - - +
223A LYS* 4.0 3.9 - - - -
224A GLN* 3.0 45.5 + - - +
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Residues in contact with TRP 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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77A ILE* 3.9 29.5 - - + +
79A HIS* 3.7 46.0 - + + +
80A PRO* 3.5 21.9 - - + +
91A ILE* 4.0 23.3 - - + -
93A LEU* 3.7 32.3 - - + -
217A ASN 5.8 0.2 - - - +
218A TYR* 3.1 17.7 + - + +
220A SER* 1.3 76.4 - - - +
222A ILE* 1.3 81.7 + - + +
224A GLN* 3.9 7.3 - - - +
225A THR* 2.7 55.8 + - - +
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Residues in contact with ILE 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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36A ILE* 3.8 22.7 - - + -
42A VAL* 4.4 8.1 - - + -
91A ILE* 4.0 19.7 - - + -
93A LEU* 4.1 9.0 - - + -
111A LEU* 3.6 38.8 - - + -
215A VAL* 4.3 9.4 - - + -
218A TYR* 2.8 29.5 + - + +
219A VAL* 3.7 5.2 - - - +
221A TRP* 1.3 94.0 - - + +
223A LYS* 1.3 64.2 + - + +
226A ILE* 2.9 35.8 + - + +
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Residues in contact with LYS 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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111A LEU* 4.4 13.2 - - + -
219A VAL* 2.9 39.9 + - + +
220A SER* 4.0 4.7 - - - +
222A ILE* 1.3 75.6 - - - +
224A GLN* 1.3 65.3 + - + +
226A ILE* 3.6 4.9 + - - +
227A ALA* 3.1 24.6 + - - +
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Residues in contact with GLN 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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220A SER* 3.0 33.7 + - - +
221A TRP* 4.1 5.7 - - - +
223A LYS* 1.3 77.7 - - + +
225A THR* 1.3 64.1 + - - +
227A ALA* 3.4 5.8 + - - +
228A SER* 3.0 28.9 + - - +
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Residues in contact with THR 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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40A TRP* 5.1 0.2 - - + -
77A ILE* 3.6 37.7 - - + -
93A LEU* 3.8 19.5 - - + -
221A TRP* 2.7 45.0 + - + -
222A ILE 3.8 2.5 - - - -
224A GLN* 1.3 78.1 - - - +
226A ILE* 1.3 63.6 + - + +
228A SER* 3.2 2.2 + - - -
229A ASN* 2.8 36.8 + - - +
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Residues in contact with ILE 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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36A ILE* 4.5 7.4 - - + -
37A ASN* 4.0 11.7 - - - +
40A TRP* 3.3 54.7 + - + +
93A LEU* 3.2 39.0 - - + -
222A ILE* 2.9 26.9 + - + +
223A LYS* 4.1 4.7 - - - +
225A THR* 1.3 75.9 - - - +
227A ALA* 1.3 64.0 + - + +
229A ASN* 3.2 18.9 - - - +
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Residues in contact with ALA 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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223A LYS 3.1 19.6 + - - +
224A GLN* 3.8 6.7 - - - +
225A THR 3.2 0.2 - - - -
226A ILE* 1.3 81.0 - - - +
228A SER* 1.3 60.3 + - - +
229A ASN* 3.5 1.7 + - - +
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Residues in contact with SER 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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224A GLN* 3.0 18.1 + - - +
225A THR* 3.2 4.2 + - - -
226A ILE 3.2 0.2 - - - -
227A ALA* 1.3 79.6 - - - +
229A ASN* 1.3 69.4 + - - +
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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