Contacts of the strand formed by residues 226 - 231 (chain A) in PDB entry 4QA7
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 SER 226 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186A GLU* 4.0 21.1 + - - +
190A SER* 4.6 4.7 - - - -
197A THR* 3.6 18.2 + - - -
216A ASP 3.3 6.5 - - - +
217A VAL* 3.2 41.6 + - - +
218A GLY* 3.7 13.3 - - - -
224A TYR 3.3 1.8 - - - -
225A TYR* 1.3 81.7 + - - +
227A VAL* 1.3 64.6 + - - +
403A K 3.7 8.0 - - - -
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Residues in contact with VAL 227 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186A GLU* 5.3 0.2 - - - +
196A MET* 4.5 7.6 - - - -
197A THR* 2.7 17.2 + - - +
198A VAL* 3.4 18.4 - - + -
199A SER 2.8 26.7 + - - -
224A TYR 4.8 2.9 - - - +
226A SER* 1.3 79.0 - - - +
228A ASN* 1.3 68.6 + - - +
229A VAL* 4.5 1.8 - - + -
247A VAL* 4.1 14.8 - - + -
251A VAL* 4.6 2.2 - - + -
369A ILE* 3.9 36.6 - - + -
372A ASN* 6.1 3.4 - - + -
373A LEU* 4.0 27.8 - - + -
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Residues in contact with ASN 228 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181A HIS* 2.9 32.1 + - - -
186A GLU* 3.0 19.7 + - - +
199A SER* 3.5 6.3 - - - -
201A HIS* 3.4 2.5 - - + -
212A GLY* 3.4 14.1 - - - +
213A ASP 3.3 16.2 - - - +
214A VAL* 3.6 19.9 + - - +
216A ASP* 2.9 38.2 + - - +
226A SER 4.2 0.4 + - - -
227A VAL* 1.3 82.0 - - - +
229A VAL* 1.3 64.3 + - - +
230A PRO* 3.2 9.3 - - - +
369A ILE* 4.1 3.7 - - - +
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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
----------------------------------------------------------
198A VAL* 5.2 0.2 - - + -
199A SER 2.8 16.7 + - - +
200A LEU* 3.9 22.2 - - + -
201A HIS* 3.3 17.6 + - - +
227A VAL* 4.5 5.8 - - + -
228A ASN* 1.3 76.9 - - - +
230A PRO* 1.3 64.4 - - - +
231A ILE* 3.2 22.0 - - + +
243A ILE* 3.7 26.9 - - + -
247A VAL* 4.1 10.8 - - + -
362A ILE* 6.1 1.6 - - + -
365A ILE* 4.1 17.7 - - + -
366A LEU* 5.6 0.2 - - + -
369A ILE* 3.7 19.5 - - + -
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Residues in contact with PRO 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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201A HIS* 3.7 5.8 - - - +
203A PHE* 3.6 25.4 - - + -
212A GLY 3.7 9.4 - - - +
213A ASP* 3.8 9.4 - - - +
214A VAL* 3.4 32.5 - - + +
228A ASN 3.2 13.0 - - - +
229A VAL* 1.3 83.5 - - - +
231A ILE* 1.3 61.5 + - - +
232A GLN* 4.5 7.9 + - - +
357A ASN* 5.1 0.2 - - - +
361A ARG* 5.7 4.0 - - - +
362A ILE* 4.9 3.6 - - - +
365A ILE* 3.3 32.4 - - + +
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Residues in contact with ILE 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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200A LEU* 4.2 19.1 - - + -
201A HIS 2.8 14.6 + - - +
202A LYS* 3.2 24.0 - - - +
203A PHE 3.2 7.0 + - - +
229A VAL* 3.2 26.0 - - + +
230A PRO* 1.3 74.4 - - - +
232A GLN* 1.3 78.6 + - - +
235A ILE* 3.7 24.7 - - + -
240A TYR* 4.1 28.5 - - + -
243A ILE* 4.7 7.4 - - + -
277A PHE* 3.7 7.6 - - + -
357A ASN* 3.4 19.3 - - - +
362A ILE* 5.1 3.8 - - + -
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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