Contacts of the strand formed by residues 232 - 238 (chain 6) in PDB entry 3J7Y
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 TYR 232 (chain 6).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2196 THR* 4.3 1.6 - - - -
2206 SER* 2.8 43.0 + - - +
2236 GLY* 5.2 1.8 - - - -
2246 HIS* 3.3 49.5 + - + -
2256 LEU* 4.3 3.6 - - + +
2266 LEU* 4.3 12.5 + - + +
2306 ALA* 5.7 2.0 - - + -
2316 GLU* 1.3 82.5 - - - +
2336 LEU* 1.3 59.7 + - - +
2346 HIS* 3.2 16.2 + - + -
2586 PHE* 3.5 24.0 - + + -
2936 LEU* 3.1 46.5 + - + +
2966 ARG* 3.9 5.6 - - + -
2976 THR* 3.7 32.7 - - - -
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Residues in contact with LEU 233 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2176 LEU* 5.8 0.4 - - + -
2186 LEU 3.5 7.2 - - - +
2196 THR* 3.5 11.3 - - + +
2316 GLU 4.0 1.0 + - - -
2326 TYR* 1.3 74.7 - - - +
2346 HIS* 1.3 57.9 + - - +
2356 TRP 3.8 9.4 - - - +
2366 LEU* 3.7 23.6 - - + -
2526 CYS* 3.8 25.4 - - + -
2556 LEU* 4.8 1.9 - - - +
2586 PHE* 5.9 0.2 - - - -
2956 GLN 5.3 0.4 - - - +
2966 ARG* 2.7 80.4 + - + +
2986 PHE* 3.5 35.4 - - + -
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Residues in contact with HIS 234 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2186 LEU* 2.8 24.1 + - + +
2206 SER* 3.9 22.0 + - - -
2246 HIS* 5.5 1.6 - + - -
2326 TYR* 3.2 21.8 + - + -
2336 LEU* 1.3 75.0 + - - +
2356 TRP* 1.3 52.2 + - - +
2536 PRO 2.7 24.9 - - - +
2546 TYR* 3.2 8.6 - + + -
2556 LEU* 3.0 34.7 + - + +
2566 PRO 3.3 31.1 + - - -
2576 PRO* 3.6 14.0 - - + +
2586 PHE* 3.5 24.7 + + - -
2686 LEU* 4.3 13.8 - - + +
2966 ARG* 3.5 7.1 + - - +
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Residues in contact with TRP 235 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2016 ALA* 3.4 19.3 - - + -
2026 PRO* 3.8 33.4 - - + -
2046 VAL* 4.7 7.2 - - + -
2166 LEU* 3.3 26.6 - - + +
2176 LEU* 4.3 2.0 - - - +
2186 LEU* 3.5 42.7 + - + +
2336 LEU* 3.8 8.8 - - - +
2346 HIS* 1.3 78.9 - - - +
2366 LEU* 1.3 68.5 + - - +
2376 LEU* 3.5 42.1 - - + +
2456 VAL* 4.7 8.3 - - + -
2506 VAL* 5.6 1.6 - - + -
2526 CYS* 3.2 20.6 - - - +
2536 PRO* 3.8 7.6 - - + -
2546 TYR* 3.8 22.7 - + + +
2706 PHE* 4.7 3.4 - + - -
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Residues in contact with LEU 236 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2156 THR* 6.0 1.8 - - - -
2166 LEU 4.0 4.5 - - - +
2176 LEU* 4.4 16.8 - - + +
2336 LEU* 3.7 23.1 - - + -
2356 TRP* 1.3 78.1 - - - +
2376 LEU* 1.3 69.2 + - - +
2386 THR* 3.3 32.9 + - + +
2506 VAL* 3.6 2.6 - - - +
2516 THR* 3.2 42.2 + - - +
2526 CYS* 2.8 14.0 + - + -
2816 PHE* 5.0 11.4 - - + -
2986 PHE* 4.5 4.7 - - + -
3036 PHE* 4.4 20.9 - - + -
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Residues in contact with LEU 237 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2156 THR* 3.5 4.3 - - - -
2166 LEU* 2.8 50.8 + - + +
2356 TRP* 3.5 45.5 - - + -
2366 LEU* 1.3 74.2 - - - +
2386 THR* 1.3 62.7 + - - +
2406 ILE* 3.8 15.5 - - + -
2456 VAL* 3.4 38.8 - - + +
2486 GLY 6.0 0.2 - - - -
2496 GLN 3.4 4.9 - - - +
2506 VAL* 3.5 35.0 - - + -
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Residues in contact with THR 238 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2156 THR* 4.2 5.4 - - + -
2366 LEU* 3.3 34.5 + - + +
2376 LEU* 1.3 73.6 - - - +
2396 ASN* 1.3 69.6 + - - +
2406 ILE* 3.2 5.5 + - - +
2486 GLY* 3.6 1.0 - - - -
2496 GLN* 2.8 60.3 + - - +
2506 VAL 4.1 0.9 + - - -
2516 THR* 4.3 10.2 - - + +
2816 PHE* 3.2 40.7 - - + -
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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