Contacts of the strand formed by residues 224 - 229 (chain A) in PDB entry 5KVI
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 GLY 224 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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151A ARG* 3.3 18.7 - - - +
157A ALA 3.0 9.5 + - - +
159A VAL* 3.0 25.3 + - - +
212A VAL* 4.3 11.4 - - - -
217A LEU* 3.3 10.2 - - - +
223A GLY* 1.3 74.7 - - - -
225A VAL* 1.3 66.4 + - - +
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Residues in contact with VAL 225 (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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144A PHE* 6.3 0.2 - - + -
147A ALA* 3.9 19.5 - - + +
151A ARG* 3.7 26.9 - - + +
159A VAL* 3.4 12.1 - - + +
161A ILE* 3.8 26.0 - - + -
210A PHE* 4.3 21.9 + - + +
211A TYR* 3.2 32.6 - - + +
212A VAL* 2.9 24.1 + - - +
224A GLY* 1.3 79.0 - - - +
226A ALA* 1.3 61.7 - - - +
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Residues in contact with ALA 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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159A VAL 2.9 6.9 + - - +
160A LEU* 3.5 4.8 - - + -
161A ILE* 2.8 28.4 + - - +
211A TYR* 4.7 0.2 - - - -
212A VAL* 3.0 26.0 - - + +
213A SER 3.7 3.6 - - - +
214A ALA* 3.6 26.7 - - - +
217A LEU* 4.1 14.1 - - + -
224A GLY 4.2 0.4 - - - -
225A VAL* 1.3 74.5 - - - +
227A VAL* 1.3 65.5 + - - +
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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
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160A LEU* 4.8 0.9 - - - -
161A ILE* 3.3 23.1 - - + +
163A SER* 4.0 16.6 - - - -
168A LEU* 3.7 22.2 - - + +
169A PRO* 4.1 13.0 - - + -
211A TYR* 3.7 32.6 - - + +
212A VAL 4.2 2.4 + - - -
214A ALA* 5.2 4.4 + - - +
226A ALA* 1.3 80.1 - - - +
228A LEU* 1.3 61.7 + - - +
229A THR* 3.4 30.1 + - + +
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Residues in contact with LEU 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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129A PRO* 4.7 10.1 - - + -
160A LEU* 4.2 14.7 - - + +
161A ILE 2.7 13.7 + - - +
162A VAL* 4.4 14.6 - - + -
163A SER 2.9 26.9 + - - +
214A ALA* 3.8 26.2 - - + -
226A ALA 4.2 0.6 - - - -
227A VAL* 1.3 68.8 - - - +
229A THR* 1.3 64.7 + - - +
231A LYS* 4.2 20.3 + - + +
245A LEU* 4.0 27.1 - - + -
251A ILE* 4.6 4.5 - - + -
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Residues in contact with THR 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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163A SER* 3.4 5.6 - - - -
165A ASP 3.5 6.5 - - - +
166A PRO* 3.6 23.4 + - - +
167A GLU 4.0 12.8 - - - +
168A LEU* 4.0 14.1 - - + -
227A VAL* 3.4 27.7 + - + +
228A LEU* 1.3 76.4 - - - +
230A GLY* 1.3 65.1 + - - +
231A LYS* 3.3 10.3 + - - +
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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