Contacts of the helix formed by residues 191 - 199 (chain 7) in PDB entry 5LN3
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 ALA 191 (chain 7).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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577 LEU* 4.6 13.7 - - + -
1837 ALA* 4.9 0.2 - - + -
1877 GLY* 3.2 20.7 + - - +
1907 LEU* 1.3 79.2 - - - +
1927 GLN* 1.4 61.9 + - - +
1947 LEU* 2.9 30.1 + - - +
1957 LEU* 3.2 17.9 + - + +
2177 CYS* 4.5 19.3 - - + +
2217 LEU* 5.1 5.8 - - + -
2247 ARG* 4.6 8.3 - - - +
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Residues in contact with GLN 192 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1817 SER* 3.1 25.8 + - - -
1827 LEU* 3.1 43.0 + - - +
1837 ALA* 3.2 8.3 + - + +
1877 GLY 3.2 8.3 + - - +
1887 ALA* 3.5 22.4 - - - +
1917 ALA* 1.4 74.8 - - - +
1937 PRO* 1.3 65.1 - - + +
1947 LEU 3.2 0.3 + - - -
1957 LEU* 3.3 13.9 + - - +
1967 ARG* 2.9 48.9 + - - +
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Residues in contact with PRO 193 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1887 ALA 4.5 0.4 - - - +
1897 TYR 3.1 27.1 - - - +
1907 LEU 3.4 9.4 - - - +
1927 GLN* 1.3 87.6 - - + +
1947 LEU* 1.4 57.1 + - + +
1967 ARG* 3.4 36.5 + - + +
1977 GLU* 2.7 30.7 - - - +
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Residues in contact with LEU 194 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1907 LEU 4.1 7.6 - - - +
1917 ALA* 2.9 19.3 + - - +
1937 PRO* 1.4 72.7 - - + +
1957 LEU* 1.3 66.2 + - + +
1967 ARG 3.3 0.5 + - - -
1977 GLU* 3.2 28.1 + - - +
1987 VAL* 4.4 7.1 - - - +
2177 CYS* 4.8 13.9 - - + -
2207 VAL* 4.6 19.7 - - + -
2247 ARG* 4.1 22.9 - - - +
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Residues in contact with LEU 195 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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577 LEU* 5.1 6.5 - - + -
587 GLY 4.8 6.1 - - - +
597 VAL* 4.9 11.9 - - + -
1817 SER* 4.6 5.4 - - - +
1827 LEU 4.3 11.4 - - - +
1837 ALA* 4.4 8.3 - - + -
1917 ALA* 3.2 17.5 + - + +
1927 GLN* 3.6 32.8 - - - +
1947 LEU* 1.3 79.7 - - - +
1967 ARG* 1.3 57.2 + - - +
1977 GLU 3.3 0.3 + - - -
1987 VAL* 3.4 6.5 + - - +
1997 LEU* 3.0 34.0 + - + +
2137 LEU* 4.4 20.2 - - + +
2147 VAL* 4.9 3.1 - - + -
2177 CYS* 3.7 31.4 - - + -
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Residues in contact with ARG 196 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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636 ILE* 5.6 8.2 - - - +
666 ARG* 4.2 36.2 - - - +
1817 SER* 6.3 0.4 - - - -
1927 GLN* 2.9 49.8 + - - +
1937 PRO* 3.5 39.0 - - - +
1947 LEU 3.2 0.8 - - - -
1957 LEU* 1.3 75.4 - - - +
1977 GLU* 1.3 58.3 - - - +
1997 LEU* 3.0 13.3 - - - +
2007 GLU* 2.9 57.7 + - + +
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Residues in contact with GLU 197 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1937 PRO* 2.7 27.0 - - - +
1947 LEU* 3.2 27.4 - - - +
1957 LEU 3.3 0.6 - - - -
1967 ARG* 1.3 78.7 - - - +
1987 VAL* 1.3 65.5 + - + +
2007 GLU* 4.1 7.5 - - - +
2017 LYS* 3.6 40.7 + - - +
2047 VAL* 4.6 0.2 - - - +
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Residues in contact with VAL 198 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1947 LEU 4.4 9.4 - - - +
1957 LEU* 3.6 9.6 - - - +
1977 GLU* 1.3 81.9 - - + +
1997 LEU* 1.4 70.9 + - + +
2007 GLU 3.4 0.4 - - - -
2017 LYS 3.1 23.0 - - - +
2047 VAL* 3.3 23.5 - - + +
2057 LEU* 4.1 14.5 + - + -
2087 THR* 6.0 2.2 - - + -
2137 LEU* 3.7 45.8 - - + -
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Residues in contact with LEU 199 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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597 VAL* 4.0 20.2 - - + -
607 LYS 3.9 20.0 - - - +
1807 PRO* 3.7 28.5 - - + +
1817 SER* 3.1 27.5 + - - +
1957 LEU* 3.0 30.6 + - + +
1967 ARG* 3.0 16.4 - - - +
1987 VAL* 1.4 90.7 - - + +
2007 GLU* 1.4 57.9 + - - +
2017 LYS 5.0 0.7 - - - -
2057 LEU* 4.0 20.4 - - + -
2107 ALA* 6.1 2.9 - - + -
2137 LEU* 5.6 4.7 - - + -
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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