Contacts of the strand formed by residues 224 - 229 (chain B) in PDB entry 7CN9
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 224 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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560A LEU* 6.0 2.0 - - + -
561A PRO* 4.8 10.9 - - + +
562A PHE* 3.5 37.8 + - + +
204B TYR* 3.5 3.8 - - - -
205B SER* 3.0 28.9 + - - +
223B LEU* 1.3 74.6 - - - +
225B PRO* 1.3 86.6 - - - +
226B LEU* 3.0 40.9 + - - +
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Residues in contact with PRO 225 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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562A PHE* 3.6 19.1 - - + -
40B ASP 5.6 5.6 - - - +
202B LYS* 4.9 7.0 - - + -
203B ILE 3.1 16.8 - - - +
204B TYR* 3.6 31.1 - - + +
224B GLU* 1.3 95.3 - - + +
226B LEU* 1.3 66.6 + - - +
227B VAL 3.3 5.6 - - - +
228B ASP* 5.7 2.9 - - + -
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Residues in contact with LEU 226 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172B SER* 5.6 4.3 - - - +
174B PRO* 4.9 11.0 - - + -
177B MET* 4.6 18.8 - - + -
178B ASP* 3.1 38.4 - - - +
203B ILE* 2.9 7.1 + - + +
205B SER* 4.1 17.5 - - - +
224B GLU* 3.0 23.6 + - - +
225B PRO* 1.3 76.0 - - - +
227B VAL* 1.3 74.3 + - + +
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Residues in contact with VAL 227 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128B ILE* 5.9 3.8 - - + -
170B TYR* 3.6 35.0 - - + +
172B SER* 4.6 6.7 - - - +
201B PHE 3.6 1.9 - - - +
202B LYS* 3.7 0.4 - - - -
203B ILE* 2.9 35.4 + - + +
225B PRO* 3.3 3.5 - - - -
226B LEU* 1.3 94.5 - - + +
228B ASP* 1.3 62.9 + - - +
229B LEU* 3.6 36.6 - - + +
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Residues in contact with ASP 228 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200B TYR* 2.6 48.7 - - - +
201B PHE 3.1 2.4 + - - -
202B LYS* 2.9 21.5 + - + +
225B PRO* 5.7 3.8 - - + -
227B VAL* 1.3 75.7 - - - +
229B LEU* 1.3 58.8 + - - +
230B PRO* 3.0 19.8 - - - +
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Residues in contact with LEU 229 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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360A ASN* 5.7 5.2 - - - +
117B LEU* 6.3 2.2 - - + -
128B ILE* 4.0 28.5 - - + -
168B PHE* 5.5 11.0 - - + -
170B TYR* 3.9 32.3 - - + -
201B PHE* 2.6 46.0 + - + +
227B VAL* 3.6 21.2 - - + +
228B ASP* 1.3 70.0 - - - +
230B PRO* 1.3 61.3 - - + +
231B ILE* 2.5 25.8 + - + -
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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