Contacts of the strand formed by residues 174 - 177 (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 HIS 174 (chain 6).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1366 ARG* 3.9 25.1 - - - -
1406 GLU* 3.6 23.2 + - + +
1726 PRO* 3.5 23.1 - - + +
1736 LEU* 1.3 75.7 + - - +
1756 VAL* 1.3 61.4 + - - +
1876 VAL 5.9 0.2 - - - -
1886 TYR* 5.4 8.1 - + - -
2036 GLU 4.0 0.7 - - - +
2046 VAL* 3.5 1.0 - - - -
2056 THR* 2.8 56.3 + - - +
2066 TYR* 4.8 4.7 - - - -
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Residues in contact with VAL 175 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1736 LEU* 3.4 26.3 + - + -
1746 HIS* 1.3 75.3 - - - +
1766 ALA* 1.3 68.0 + - - +
1866 PRO* 3.7 4.0 - - - +
1876 VAL* 3.0 38.2 + - + +
2026 PRO* 3.4 35.0 - - + -
2036 GLU 3.4 6.7 - - - +
2046 VAL* 4.0 8.5 - - + -
2706 PHE* 3.6 34.1 - - + -
3176 SER* 4.3 10.1 - - - +
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Residues in contact with ALA 176 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1756 VAL* 1.3 77.5 - - - +
1776 TYR* 1.3 59.3 + - - +
1786 ALA 3.8 1.0 + - - -
1846 LEU* 3.8 31.7 - - + +
1856 MET 3.4 9.6 - - - +
1866 PRO* 3.9 9.0 - - + -
1876 VAL 4.2 0.9 - - - +
2026 PRO* 3.7 4.5 - - - -
2036 GLU* 2.8 45.6 + - + +
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Residues in contact with TYR 177 (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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1766 ALA* 1.3 70.5 - - - +
1786 ALA* 1.3 64.5 + - - +
1796 VAL* 3.8 0.4 - - + +
1846 LEU* 4.6 1.1 - - - -
1856 MET* 2.8 48.1 + - + +
1876 VAL* 3.4 32.5 - - + -
1936 VAL* 5.9 4.9 - - + -
1976 GLU* 3.6 14.6 - - + +
1986 ALA* 3.5 24.4 - - + +
2006 GLN 3.2 24.7 - - - -
2026 PRO* 3.6 29.8 - - + +
2186 LEU* 3.8 14.7 - - - +
2546 TYR* 2.8 40.0 + - - -
2576 PRO* 5.3 0.3 - - - +
2686 LEU* 5.8 0.3 - - - +
2706 PHE* 4.0 7.4 - + - -
3196 PHE* 5.2 11.8 - + - -
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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