Contacts of the strand formed by residues 274 - 278 (chain A) in PDB entry 3KJO
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 274 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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34A PRO* 4.1 8.1 - - - -
226A HIS* 4.1 15.1 - - - -
241A ILE* 3.7 2.6 - - - +
242A TYR* 2.9 34.0 + - - +
265A LEU* 4.2 3.1 - - - +
272A GLY 2.9 6.3 + - - -
273A ARG* 1.3 75.0 - - - +
275A ILE* 1.3 67.3 + - - +
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Residues in contact with ILE 275 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A PRO* 4.4 7.5 - - - +
35A PRO 5.1 3.8 - - - +
66A TYR* 4.2 8.7 + - - -
181A LEU* 4.0 26.2 - - + -
222A VAL* 4.5 4.0 - - + -
226A HIS* 5.1 5.2 - - + +
229A VAL* 4.5 24.5 - - + +
230A ALA* 4.8 5.6 - - + +
233A LEU* 4.3 26.7 - - + -
239A LEU* 4.4 14.6 - - + -
240A ARG 3.5 9.4 - - - +
241A ILE* 4.4 10.8 - - + -
242A TYR* 4.7 1.3 - - - -
265A LEU* 3.8 22.4 - - + -
274A GLY* 1.3 81.1 - - - +
276A ARG* 1.3 70.7 + - - +
277A VAL* 5.4 0.2 - - + -
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Residues in contact with ARG 276 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A PRO* 4.6 5.4 - - + -
35A PRO* 3.4 28.8 - - - +
66A TYR* 3.7 31.5 + - - +
67A GLU* 5.4 3.4 - - - +
69A LEU 5.0 2.0 + - - -
70A PRO 3.4 22.0 + - - -
71A ILE* 3.7 34.7 - - - +
72A ILE 3.8 19.2 + - - +
73A TYR* 3.9 20.5 + - + -
239A LEU* 3.6 1.2 - - - +
240A ARG* 2.9 34.2 + - + +
242A TYR* 3.8 21.5 - - + +
275A ILE* 1.3 79.2 - - - +
277A VAL* 1.3 73.7 + - - +
278A LEU* 3.5 0.6 + - + +
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Residues in contact with VAL 277 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A TYR* 4.8 2.6 + - - -
73A TYR* 4.2 2.3 - - - -
233A LEU* 4.0 19.1 - - + -
234A LYS 6.3 0.2 - - - +
237A SER* 4.5 16.8 - - - +
238A PHE 3.6 12.3 - - - +
239A LEU* 3.9 16.8 - - + -
275A ILE* 5.4 0.4 - - + -
276A ARG* 1.3 85.3 + - - +
278A LEU* 1.3 70.7 + - - +
279A PRO* 3.6 8.7 - - + +
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Residues in contact with LEU 278 (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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73A TYR* 3.6 31.2 - - + -
165A THR* 3.8 29.2 - - + -
238A PHE* 2.8 33.1 + - + +
239A LEU 3.9 21.5 - - - +
240A ARG* 3.9 30.3 - - + +
242A TYR* 5.2 0.2 - - - +
276A ARG* 4.5 2.5 - - + +
277A VAL* 1.3 79.0 - - - +
279A PRO* 1.3 67.1 - - + +
280A GLU 3.9 0.5 + - - -
282A ASN* 4.0 13.9 - - + +
284A ASP* 5.2 0.2 - - + -
285A VAL* 3.7 22.0 - - + -
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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