Contacts of the strand formed by residues 226 - 232 (chain A) in PDB entry 3WOO
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 ALA 226 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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82A VAL* 3.6 5.0 - - - +
83A THR* 2.9 31.4 + - + +
84A ASN 4.1 2.0 - - - +
85A HIS* 4.0 8.5 - - - -
88A ALA* 3.7 29.6 - - + -
92A ILE* 4.8 0.2 - - + -
198A LEU* 5.1 0.7 - - + -
200A TYR 3.5 12.6 - - - +
201A ALA* 4.4 9.4 - - + -
202A PRO* 4.5 1.6 - - - -
225A PHE* 1.3 79.8 - - - +
227A PHE* 1.3 69.9 + - - +
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Residues in contact with PHE 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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75A VAL* 4.2 0.7 - - + -
80A LEU* 3.9 28.5 - - + -
81A VAL 3.2 14.4 - - - +
82A VAL* 3.6 26.5 - - + -
198A LEU* 3.6 7.2 - - - +
199A ALA* 2.8 32.5 + - + -
200A TYR* 2.8 37.7 + + + +
225A PHE* 3.7 17.5 - + - -
226A ALA* 1.3 75.9 - - - +
228A TYR* 1.3 59.2 + - - +
256A PHE* 5.6 1.3 - + - -
701A LEU* 4.6 6.5 - - + -
705A MET* 3.5 37.9 - - + -
714A LEU* 4.3 4.9 - - + -
718A MET* 3.7 29.4 - - + -
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Residues in contact with TYR 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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67A LEU* 4.0 30.2 - - + +
80A LEU* 3.6 7.6 - - - +
81A VAL* 2.8 53.6 + - + +
83A THR* 4.3 10.1 - - + +
87A CYS 3.7 3.1 + - - -
88A ALA* 3.4 27.9 - - + -
91A ALA* 3.9 8.3 - - + +
118A ALA* 4.1 15.5 - - + -
122A ALA* 5.5 1.8 - - + -
123A ARG 5.4 1.1 - - - -
124A VAL* 5.0 1.6 - - + -
196A VAL* 3.6 25.6 - - + -
197A ARG 3.0 20.2 - - - +
198A LEU* 4.2 5.4 - - + -
199A ALA* 4.3 4.3 - - - -
227A PHE* 1.3 81.1 - - - +
229A ARG* 1.3 57.4 + - - +
805A GOL 3.4 30.5 + - - -
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Residues in contact with ARG 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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78A ASN* 2.9 39.0 + - - +
79A GLY 3.5 8.5 - - - +
80A LEU* 3.8 19.3 - - - +
112A THR* 3.6 16.6 - - - +
115A GLU* 2.7 45.2 + - - +
196A VAL* 3.7 2.4 - - - -
197A ARG 2.7 33.0 + - - +
199A ALA* 4.4 1.7 - - + +
228A TYR* 1.3 75.5 - - - +
230A ALA* 1.3 67.2 + - - +
231A TYR* 3.5 22.1 - - + -
247A PRO* 3.8 12.3 - - - -
714A LEU* 3.9 9.3 - - - +
717A GLU* 2.7 43.4 + - - -
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Residues in contact with ALA 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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74A PHE* 4.2 13.2 - - + -
79A GLY 2.9 14.7 + - - +
81A VAL* 4.6 6.7 - - + +
124A VAL* 4.8 8.1 - - + -
193A ILE* 3.9 31.2 - - + -
195A ASP 4.1 3.1 - - - -
196A VAL* 4.9 2.2 - - - +
228A TYR 4.3 0.4 - - - -
229A ARG* 1.3 75.0 - - - +
231A TYR* 1.3 55.7 + - - +
247A PRO* 3.3 6.8 - - - +
248A TYR* 2.8 33.7 + - + +
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Residues in contact with TYR 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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112A THR* 3.2 27.6 + - - -
115A GLU* 2.6 29.8 + - - -
193A ILE* 3.6 13.4 - - - +
194A LYS 4.8 0.7 + - - -
195A ASP* 3.0 38.8 + - - +
197A ARG* 3.5 44.0 + - + -
229A ARG* 3.5 29.5 - - + -
230A ALA* 1.3 73.8 - - - +
232A VAL* 1.3 69.1 + - - +
239A ALA 4.7 2.3 + - - +
245A ASN* 3.7 16.6 - - + -
246A VAL* 3.3 19.7 - - - -
247A PRO* 3.7 15.7 - - + -
248A TYR 4.4 0.2 - - - -
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Residues in contact with VAL 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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191A LEU* 5.5 0.9 - - + -
193A ILE* 4.1 12.8 - - + -
231A TYR* 1.3 79.8 - - - +
233A GLY* 1.3 70.2 + - - +
236A GLY* 3.8 20.0 - - - +
237A LYS 3.6 11.4 - - - +
238A PRO* 4.2 14.6 - - + -
239A ALA 4.8 1.8 - - - +
245A ASN* 3.2 10.0 - - - +
246A VAL* 2.9 39.8 + - + +
247A PRO 4.7 1.8 - - - +
248A TYR* 3.8 39.7 - - + -
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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