Contacts of the helix formed by residues 86 - 91 (chain F) in PDB entry 6RQT
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 THR 86 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1180A ASN* 3.1 31.5 + - + +
1181A PRO* 5.3 0.7 - - + -
82F THR* 5.1 13.5 - - + +
84F TYR* 3.2 30.7 + - + +
85F MET* 1.3 76.1 - - - +
87F LYS* 1.3 60.8 + - - +
88F TYR* 4.3 1.0 + - - +
89F GLU* 3.3 24.8 + - - +
90F ARG* 2.8 27.7 + - - +
136F ARG* 5.2 5.2 + - - +
154F ASP* 4.7 7.0 - - + -
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Residues in contact with LYS 87 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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649A ASN* 5.7 4.9 - - - +
650A LEU* 4.4 23.1 - - + +
655A SER* 5.0 13.1 + - - -
1059A LYS* 6.4 0.4 - - - +
1180A ASN* 3.1 23.6 - - + +
86F THR* 1.3 75.3 - - - +
88F TYR* 1.3 66.8 + - + +
90F ARG* 3.1 14.1 + - + +
91F ALA* 2.4 36.3 + - - +
154F ASP* 4.8 9.6 + - - +
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Residues in contact with TYR 88 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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650A LEU* 4.2 16.5 - - + +
1180A ASN* 3.3 31.4 - - + +
1181A PRO 3.9 10.3 - - - +
1182A GLY* 4.2 2.5 - - - -
1183A GLU* 3.3 49.9 - - + +
1184A ALA 4.3 2.3 + - - -
1650A GLY* 4.2 9.0 - - - +
1651A THR* 2.9 57.9 + - - +
1654A PHE* 4.8 6.0 - - + -
1081B GLY 5.4 0.2 + - - -
1082B HIS 3.8 23.2 + - - -
1083B GLY* 4.8 3.4 - - - -
86F THR* 3.5 1.8 - - - +
87F LYS* 1.3 83.4 - - + +
89F GLU* 1.3 67.7 + - + +
91F ALA* 3.2 2.0 + - - -
92F ARG* 3.0 13.0 + - - +
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Residues in contact with GLU 89 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1034A TYR* 4.7 2.4 + - - -
1654A PHE* 3.2 37.0 - - - -
84F TYR 4.9 1.3 - - - +
85F MET* 3.6 18.8 - - + -
86F THR* 3.3 31.2 - - - +
87F LYS 3.2 0.2 - - - -
88F TYR* 1.3 79.0 - - + +
90F ARG* 1.3 56.4 + - - +
92F ARG* 2.9 18.3 + - - +
93F ILE* 2.9 22.7 + - + +
134F ILE* 3.2 26.9 - - - +
136F ARG* 3.4 30.8 + - - +
151F LEU* 5.5 2.6 - - + +
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Residues in contact with ARG 90 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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645A ALA* 5.6 1.4 - - - +
649A ASN* 2.5 43.0 + - - +
85F MET* 3.5 12.5 - - + +
86F THR 2.8 17.4 + - - +
87F LYS* 3.2 13.0 - - - +
89F GLU* 1.3 73.2 - - - +
91F ALA* 1.3 56.4 + - - +
92F ARG 3.1 4.5 + - - -
93F ILE* 4.9 1.6 - - - -
94F LEU* 3.3 34.5 - - + +
122F MET* 3.4 30.8 - - - +
125F LEU* 4.4 25.1 - - + +
153F VAL* 5.1 7.5 - - - +
154F ASP* 4.7 14.3 + - - -
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Residues in contact with ALA 91 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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642A ASN* 4.7 7.6 - - - +
645A ALA* 5.3 7.2 - - - +
646A GLU* 4.2 31.6 - - + +
649A ASN* 5.8 4.7 - - + +
650A LEU* 5.2 12.3 - - + -
1651A THR* 3.0 27.3 + - + +
87F LYS 2.4 25.2 + - - +
88F TYR* 3.2 7.4 - - - +
89F GLU 3.2 0.4 - - - -
90F ARG* 1.3 71.6 - - - +
92F ARG* 1.3 57.2 + - - +
95F GLY 5.6 0.2 - - - -
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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