Contacts of the helix formed by residues 216 - 224 (chain A) in PDB entry 2XTM
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 ASN 216 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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99A TYR* 2.9 30.2 + - - -
133A PHE* 3.0 20.8 + - - +
134A GLY* 5.7 0.9 - - - -
214A TYR* 4.0 13.2 - - - +
215A THR* 1.3 81.3 + - - +
217A GLY* 1.3 64.3 + - - +
218A LEU 3.0 4.0 + - - -
219A TYR* 3.0 28.6 + - - +
220A SER* 3.0 22.0 + - - -
1230A GOL 3.4 16.0 + - - +
1231A GOL 5.5 0.2 - - - +
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Residues in contact with GLY 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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216A ASN* 1.3 75.7 - - - +
218A LEU* 1.3 60.0 + - - +
220A SER* 3.3 8.4 + - - -
221A LEU* 3.1 25.6 + - - +
1230A GOL 3.4 5.6 + - - -
1231A GOL 3.6 30.9 + - - -
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Residues in contact with LEU 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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92A TYR* 5.8 1.1 - - - +
95A VAL* 5.2 1.3 - - + -
96A GLN* 3.6 39.3 - - - +
99A TYR* 3.7 43.1 - - + -
216A ASN* 3.0 2.0 + - - -
217A GLY* 1.3 72.6 - - - +
219A TYR* 1.3 66.8 + - - +
221A LEU* 3.2 33.1 + - + +
222A ILE* 3.2 19.9 + - + +
1230A GOL 3.1 19.7 + - - +
1231A GOL 4.6 3.0 - - - -
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Residues in contact with TYR 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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26A ILE* 3.7 9.2 - - - +
99A TYR* 3.4 43.4 - + + -
102A SER* 2.7 29.2 + - - -
103A ALA* 4.0 8.1 - - + -
104A PRO* 3.5 29.3 - - - +
105A GLY* 3.7 11.4 - - - -
106A PRO* 3.5 26.5 - - + +
133A PHE* 3.8 11.8 - + - -
214A TYR* 4.5 5.8 - + - -
215A THR* 3.9 11.0 - - - +
216A ASN* 3.0 38.3 + - - +
218A LEU* 1.3 75.8 - - - +
220A SER* 1.3 62.9 + - - +
222A ILE* 3.2 7.6 + - + +
223A GLN* 3.0 24.5 + - - +
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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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215A THR* 4.3 6.2 + - - -
216A ASN 3.0 13.5 + - - -
217A GLY* 3.4 12.8 - - - -
218A LEU 3.2 0.2 - - - -
219A TYR* 1.3 76.8 - - - +
221A LEU* 1.3 61.6 + - - +
223A GLN* 3.3 7.8 + - - +
224A ARG* 3.0 48.0 + - - +
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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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217A GLY 3.1 20.9 + - - +
218A LEU* 3.2 28.2 + - + +
220A SER* 1.3 76.4 - - - +
222A ILE* 1.3 61.9 + - + +
224A ARG* 3.5 7.8 + - - +
225A SER* 2.9 28.4 + - - -
1231A GOL 5.4 7.6 - - - -
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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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96A GLN* 5.0 3.6 - - - +
99A TYR* 3.7 38.4 - - + +
100A LEU* 3.9 31.9 - - + -
103A ALA* 3.7 17.0 - - + -
218A LEU* 3.2 23.1 + - + +
219A TYR* 3.6 9.6 - - + +
221A LEU* 1.3 77.4 - - + +
223A GLN* 1.3 63.3 + - - +
225A SER* 3.1 17.3 + - - -
226A LYS* 3.5 33.4 - - - +
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Residues in contact with GLN 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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104A PRO* 3.7 31.4 - - + +
213A HIS* 5.3 5.2 - - - -
219A TYR 3.0 16.5 + - - +
220A SER* 3.7 8.1 - - - +
222A ILE* 1.3 77.7 - - - +
224A ARG* 1.3 65.2 + - + +
225A SER 3.3 1.0 + - - -
226A LYS* 3.4 27.4 + - - +
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Residues in contact with ARG 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 36.8 + - - +
221A LEU* 3.5 6.5 + - - +
222A ILE 3.2 0.2 - - - -
223A GLN* 1.3 81.4 - - + +
225A SER* 1.3 60.5 + - - +
226A LYS 3.4 4.1 - - - +
157B MET* 4.9 7.1 - - - +
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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