Contacts of the helix formed by residues 227 - 232 (chain A) in PDB entry 1SER
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 227 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202A THR* 4.0 12.5 - - + +
204A HIS* 4.0 17.8 - - + -
225A THR* 3.2 23.8 + - + +
226A ALA* 1.4 75.0 - - - +
228A VAL* 1.4 57.3 + - - +
230A LEU* 4.0 10.5 - - - -
231A ASN* 2.7 36.8 + - + +
279A GLU* 4.2 13.9 - - + +
281A TYR* 4.4 15.9 - - + -
352A LEU* 5.5 0.9 - - - +
356A GLN* 3.8 21.3 + - - +
378A ASN* 3.5 34.3 + - + +
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Residues in contact with VAL 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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194A ALA* 4.6 2.2 - - + -
198A ALA* 3.8 34.3 - - + +
199A PHE* 4.1 25.4 - - + +
202A THR* 3.9 9.6 - - - +
204A HIS* 4.1 28.5 - - + +
223A THR* 3.9 22.7 - - + -
224A GLY 5.2 0.9 - - - +
225A THR* 3.0 19.0 + - + +
226A ALA 3.0 1.2 + - - -
227A GLU* 1.4 76.9 - - - +
229A VAL* 1.3 61.9 + - - +
231A ASN* 3.9 2.3 - - - +
232A ALA* 3.4 17.2 + - - +
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Residues in contact with VAL 229 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190A LEU* 3.7 26.9 - - + -
191A PRO* 4.0 21.3 - - + +
193A TYR 4.6 3.8 - - - +
194A ALA* 4.6 6.3 - - + -
223A THR* 4.3 19.1 - - + +
226A ALA* 3.0 10.4 + - - +
228A VAL* 1.3 73.9 - - - +
230A LEU* 1.3 69.8 + - - +
232A ALA* 2.8 15.9 + - - +
233A LEU* 3.2 14.9 + - + +
650B ILE* 3.6 30.5 - - + -
653B VAL* 4.1 16.8 - - + +
654B SER* 5.0 0.2 - - - +
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Residues in contact with LEU 230 (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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188A MET* 4.1 9.9 - - - -
190A LEU* 4.0 15.9 - - + -
226A ALA* 3.0 27.4 + - + +
227A GLU* 3.8 6.3 - - - +
229A VAL* 1.3 76.7 - - - +
231A ASN* 1.3 63.6 + - - +
233A LEU* 3.3 29.9 + - + +
234A HIS* 4.8 2.3 + - - -
248A TYR* 3.8 37.3 - - + -
250A GLY* 3.9 29.4 - - - +
279A GLU* 4.8 5.2 - - + +
281A TYR* 4.2 31.2 - - + -
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Residues in contact with ASN 231 (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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198A ALA 5.1 0.4 - - - +
201A GLY* 3.7 18.0 - - - +
202A THR* 3.6 26.2 - - + +
227A GLU* 2.7 24.6 + - + +
228A VAL 3.9 1.3 - - - +
230A LEU* 1.3 76.7 - - - +
232A ALA* 1.3 60.4 - - - +
233A LEU 3.3 0.5 + - - -
234A HIS* 4.1 0.9 + - - -
281A TYR* 2.7 39.7 + - + -
356A GLN* 4.0 17.4 - - - +
360A ALA* 3.7 12.5 - - - +
362A LEU* 3.5 37.3 - - - +
376A THR* 4.2 0.6 - - - +
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Residues in contact with ALA 232 (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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197A LYS* 4.7 9.9 - - - +
198A ALA* 4.0 15.7 - - + +
228A VAL 3.4 10.4 + - - +
229A VAL 2.8 9.7 + - - +
231A ASN* 1.3 78.9 - - - +
233A LEU* 1.3 64.2 + - - +
234A HIS 3.4 0.7 - - - -
235A SER* 3.2 22.6 - - - -
360A ALA* 5.3 4.3 - - - -
652B GLN* 3.4 7.6 - - - +
653B VAL* 3.8 22.9 - - + -
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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