Contacts of the strand formed by residues 225 - 230 (chain A) in PDB entry 6A08
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 VAL 225 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151A ILE* 3.4 10.5 - - + +
153A PHE* 4.4 12.3 - - + -
214A VAL* 4.9 9.0 - - + +
217A VAL* 3.9 29.2 - - + -
218A ARG* 4.2 18.6 - - + -
221A THR* 4.1 9.9 - - + -
223A LEU 3.4 10.3 + - - +
224A PRO* 1.3 75.0 - - - +
226A VAL* 1.3 61.5 + - - +
227A LEU* 3.9 22.4 - - + -
243A GLY 5.2 3.5 + - - +
244A ALA* 3.4 13.5 - - - +
245A GLY 2.8 31.6 + - - +
246A GLY 3.4 1.4 + - - -
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Residues in contact with VAL 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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65A PHE* 3.3 42.4 - - + -
124A TRP* 6.3 1.1 - - + -
150A ALA* 4.5 6.1 - - + -
151A ILE 2.8 15.5 + - - +
152A VAL* 3.4 15.4 - - + -
153A PHE 2.7 28.6 + - - -
224A PRO 4.4 6.7 - - - +
225A VAL* 1.3 78.3 - - - +
227A LEU* 1.3 65.3 + - - +
228A LYS 3.5 0.5 + - - -
246A GLY* 3.2 18.6 - - - +
247A ILE 4.0 2.0 - - - +
248A VAL* 3.9 26.7 - - + -
281A LEU* 4.8 3.6 - - + -
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Residues in contact with LEU 227 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153A PHE* 3.5 13.5 - - + -
155A VAL* 4.0 13.5 - - + -
211A TRP* 3.7 24.7 - - + -
214A VAL* 4.0 28.3 - - + -
225A VAL* 3.9 20.2 - - + -
226A VAL* 1.3 74.7 - - - +
228A LYS* 1.3 56.4 + - - +
230A ILE* 3.7 17.6 - - + +
239A ALA* 3.7 25.1 - - + +
244A ALA* 4.2 12.8 - - + -
246A GLY 3.0 7.3 + - - -
247A ILE* 3.2 9.3 - - + +
248A VAL 2.8 26.5 + - - -
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Residues in contact with LYS 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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77A PRO* 3.7 14.4 - - + -
152A VAL* 3.7 24.7 - - + -
153A PHE 2.9 12.2 + - - +
154A THR* 3.5 8.3 - - + +
155A VAL* 2.8 29.9 + - - +
156A ASP* 3.9 1.6 + - - +
226A VAL 3.5 0.8 + - - -
227A LEU* 1.3 72.5 - - - +
229A GLY* 1.3 62.5 + - - +
248A VAL* 3.8 17.0 - - + -
250A SER* 4.4 5.2 + - - +
252A HIS* 4.1 10.7 + - - -
283A ASP* 3.6 12.3 - - - -
304A LEU* 4.0 11.9 - - + -
402A FMN 2.9 72.4 + - - +
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Residues in contact with GLY 229 (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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155A VAL* 4.0 7.4 - - - +
156A ASP* 3.3 37.0 - - - +
228A LYS* 1.3 77.4 - - - +
230A ILE* 1.3 65.2 + - - +
231A LEU* 3.8 3.8 + - - +
248A VAL 2.9 9.0 + - - -
250A SER* 3.7 17.1 - - - +
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Residues in contact with ILE 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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155A VAL* 4.0 17.9 - - + -
211A TRP* 4.9 4.7 - - + -
227A LEU* 3.7 33.0 - - + +
229A GLY* 1.3 77.5 - - - +
231A LEU* 1.3 63.9 + - - +
232A ALA 3.8 7.6 - - - +
235A ASP* 4.0 26.7 - - + +
236A ALA* 3.7 33.2 - - + +
239A ALA* 4.8 0.2 - - + -
247A ILE* 4.1 21.8 - - + -
248A VAL 3.2 7.0 + - - +
249A VAL* 3.2 25.3 - - - +
250A SER 3.4 4.0 + - - -
270A ILE* 4.5 2.9 - - + -
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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