Contacts of the strand formed by residues 225 - 232 (chain A) in PDB entry 6ABP
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 ASP 225 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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130A TRP* 3.4 11.2 + - - -
197A LYS 3.6 15.5 - - - +
198A HIS* 2.8 32.0 + - - -
199A TRP 3.0 24.4 + - - -
221A PHE* 4.3 11.1 - - + -
222A LYS* 2.9 49.3 + - - +
224A ALA* 1.4 81.8 - - - +
226A ILE* 1.3 60.5 + - - +
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Residues in contact with ILE 226 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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128A ARG* 3.1 10.2 + - - -
199A TRP* 3.3 20.9 - - + +
201A ILE* 3.5 28.3 - - + -
213A VAL* 4.3 4.0 - - + -
216A THR* 3.7 32.5 - - + +
217A GLU* 6.3 0.4 - - + -
221A PHE* 3.7 22.9 - - + +
222A LYS 3.7 14.4 - - - +
223A ALA* 3.0 15.7 + - - +
224A ALA 3.4 0.8 - - - -
225A ASP* 1.3 87.1 - - - +
227A ILE* 1.3 66.1 - - - +
247A GLY* 3.4 33.0 - - - +
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Residues in contact with ILE 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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121A LEU* 3.5 21.3 - - + +
124A GLU* 3.5 35.0 - - + +
125A MET* 3.6 25.8 - - - +
128A ARG* 3.3 29.8 - - - +
130A TRP* 3.7 20.9 - - + -
199A TRP 2.9 10.5 + - - -
200A LEU* 3.4 15.1 - - + -
201A ILE 2.8 25.1 + - - -
226A ILE* 1.3 74.2 - - - +
228A GLY* 1.3 61.8 + - - +
229A ILE* 4.3 5.8 - - + -
247A GLY 3.6 1.8 - - - -
249A TYR* 4.0 14.6 - - + -
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Residues in contact with GLY 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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201A ILE* 3.9 10.3 - - - -
209A VAL* 3.6 22.7 - - - -
213A VAL* 4.6 3.6 - - - -
226A ILE* 4.7 0.2 - - - +
227A ILE* 1.3 75.5 - - - +
229A ILE* 1.3 64.6 + - - +
247A GLY 2.9 12.6 + - - -
248A PHE* 3.6 3.5 - - - -
249A TYR* 2.8 25.6 + - - +
250A GLY 3.7 1.7 + - - +
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Residues in contact with ILE 229 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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117A GLN* 2.8 37.3 + - + +
120A GLU* 3.7 18.4 - - + +
121A LEU* 3.7 44.9 - - + +
201A ILE 4.2 1.7 + - - +
209A VAL* 3.7 7.4 - - - +
227A ILE* 4.3 3.6 - - + -
228A GLY* 1.3 77.5 - - - +
230A GLY* 1.3 70.9 - - - +
249A TYR* 3.9 28.7 - - + -
250A GLY* 3.2 11.9 - - - +
252A LEU* 4.1 10.8 - - + -
288A LEU* 3.9 22.7 - - + -
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Residues in contact with GLY 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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117A GLN* 4.3 0.2 - - - -
206A ASP* 3.1 19.5 - - - -
209A VAL* 4.0 12.6 - - - -
229A ILE* 1.3 81.3 - - - +
231A ILE* 1.4 62.7 + - - +
248A PHE* 3.7 13.7 - - - -
250A GLY 2.9 13.5 + - - -
251A SER* 3.5 2.0 - - - -
252A LEU* 2.8 25.6 + - - +
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Residues in contact with ILE 231 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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108A LEU* 4.5 3.1 - - + -
113A ILE* 3.9 37.5 - - + +
114A GLY* 4.7 0.4 - - - -
117A GLN* 3.8 23.8 - - + +
151A ARG* 3.6 38.4 - - + +
203A GLY 4.5 0.4 - - - +
204A MET 3.4 16.8 - - - +
205A ASN* 3.1 3.8 - - - +
206A ASP* 2.8 27.3 + - - +
230A GLY* 1.4 81.2 - - - +
232A ASN* 1.3 76.9 + - - +
252A LEU* 3.7 15.3 - - + +
254A PRO* 4.3 9.2 - - + -
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Residues in contact with ASN 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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14A GLU* 3.7 1.8 + - - -
16A TRP* 3.6 24.0 - - + +
108A LEU* 4.9 0.2 - - - +
205A ASN* 3.8 6.3 - - - +
206A ASP* 3.3 9.6 - - - +
231A ILE* 1.3 85.6 + - - +
233A GLY* 1.3 58.4 + - - +
234A VAL* 2.9 16.0 + - + +
235A ASP* 3.0 29.3 + - - +
252A LEU 3.0 6.1 + - - -
253A LEU* 3.8 4.3 - - - +
254A PRO* 3.3 25.8 - - - +
256A PRO* 4.8 0.3 - - - +
307A ARA 2.6 48.1 + - - -
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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