Contacts of the strand formed by residues 214 - 220 (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 TRP 214 (chain 6).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1716 VAL* 4.3 19.1 - - + -
2066 TYR* 3.2 34.0 - + + +
2086 ALA* 3.3 47.5 + - + -
2096 GLU 4.4 8.4 - - - -
2136 LEU* 1.3 95.7 - - - +
2156 THR* 1.3 67.7 + - - +
2406 ILE* 3.0 40.3 + - + +
2426 GLY* 3.4 17.2 + - - -
2726 LEU* 3.5 26.0 - - + -
2736 PHE 3.2 26.9 - - - -
2746 LYS* 3.9 26.9 - - + -
2756 GLN* 3.5 2.5 - - - +
3146 ALA* 4.8 0.4 - - + -
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Residues in contact with THR 215 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2146 TRP* 1.3 76.5 - - - +
2166 LEU* 1.3 62.3 + - - +
2176 LEU* 3.8 1.1 + - - +
2366 LEU* 6.0 1.6 - - - -
2376 LEU 3.5 10.5 - - - -
2386 THR* 4.2 1.8 - - - -
2396 ASN 3.9 7.9 - - - +
2406 ILE* 4.2 0.4 - - - -
2716 LEU 3.5 5.4 - - - +
2726 LEU* 4.3 2.2 - - - -
2736 PHE* 3.2 49.1 + - - +
2756 GLN* 3.1 35.4 - - + +
2816 PHE* 3.9 20.9 - - + -
3086 GLN* 4.8 2.5 + - - -
3116 MET* 3.9 5.0 - - + +
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Residues in contact with LEU 216 (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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1736 LEU* 4.4 8.3 - - + -
2046 VAL* 3.6 39.5 - - + -
2066 TYR* 4.8 2.5 - - + -
2156 THR* 1.3 71.8 - - - +
2176 LEU* 1.3 68.4 + - - +
2356 TRP* 3.3 34.9 + - + +
2366 LEU* 3.8 0.7 - - - +
2376 LEU* 2.8 54.5 + - + +
2406 ILE* 3.7 9.1 - - + +
2456 VAL* 5.3 1.8 - - + -
2706 PHE* 3.8 13.7 - - + -
2716 LEU 3.3 6.5 - - - +
2726 LEU* 3.7 22.0 - - + -
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Residues in contact with LEU 217 (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 4.8 0.7 - - - +
2166 LEU* 1.3 82.3 - - - +
2186 LEU* 1.3 75.7 + - - +
2196 THR* 3.4 38.6 - - + +
2356 TRP* 4.3 6.7 - - - +
2366 LEU* 4.4 17.7 - - + +
2706 PHE* 3.2 5.4 - - - -
2716 LEU* 2.8 57.4 + - + +
2736 PHE* 4.6 9.4 - - + -
2986 PHE* 4.2 8.7 - - + -
3006 THR* 4.6 2.7 - - + -
3036 PHE* 3.6 38.1 - - + -
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Residues in contact with LEU 218 (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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1776 TYR* 3.8 14.6 - - - +
2176 LEU* 1.3 77.0 - - - +
2196 THR* 1.3 63.0 + - - +
2336 LEU* 3.5 3.8 - - - -
2346 HIS* 2.8 36.4 + - + -
2356 TRP* 3.5 30.5 + - + +
2546 TYR* 4.2 13.7 - - + -
2686 LEU* 3.8 35.2 - - + -
2696 ALA 3.2 12.1 - - - +
2706 PHE* 3.4 46.0 - - + +
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Residues in contact with THR 219 (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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1616 LEU* 3.8 18.9 - - - +
2176 LEU* 3.4 28.3 - - + +
2186 LEU* 1.3 77.1 - - - +
2206 SER* 1.3 60.8 + - - +
2216 LEU* 3.5 4.5 - - - +
2316 GLU* 4.0 14.6 - - + +
2326 TYR 3.6 4.0 - - - -
2336 LEU* 3.5 24.7 - - + +
2346 HIS* 4.6 0.7 - - - +
2686 LEU* 3.4 4.5 - - - -
2696 ALA* 2.8 40.8 + - - +
2716 LEU* 4.4 1.6 - - - +
2986 PHE* 4.3 6.5 - - + +
3006 THR* 4.2 10.3 - - + -
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Residues in contact with SER 220 (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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2196 THR* 1.3 71.0 - - - +
2216 LEU* 1.3 62.6 + - - +
2226 ASP* 3.7 1.4 + - - -
2236 GLY 4.5 0.9 + - - -
2246 HIS* 3.3 33.3 + - - -
2316 GLU* 3.2 23.7 - - - +
2326 TYR* 2.8 29.8 + - - +
2346 HIS* 3.9 6.2 + - - -
2666 HIS* 5.8 0.7 - - - -
2676 ARG 4.1 0.7 - - - -
2686 LEU* 3.2 29.9 - - - +
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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