Contacts of the helix formed by residues 85 - 93 (chain M) in PDB entry 6AH0
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 SER 85 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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57M ALA* 4.9 4.7 - - - -
59M ASP* 5.3 0.2 - - - +
83M VAL 3.4 2.1 - - - -
84M ARG* 1.3 77.2 - - - +
86M LYS* 1.3 61.1 + - - +
87M GLN 3.2 3.8 - - - +
88M ALA* 3.2 7.2 + - - +
89M LEU* 3.0 24.1 + - - -
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Residues in contact with LYS 86 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57M ALA* 4.7 11.3 - - - +
59M ASP* 4.8 9.1 - - - +
84M ARG 4.0 2.4 + - - -
85M SER* 1.3 70.0 - - - +
87M GLN* 1.3 59.8 + - - +
89M LEU* 4.9 0.2 - - - +
90M GLY 3.0 11.6 + - - -
98M PRO* 3.3 5.1 - - - +
99M VAL 2.9 41.5 + - - +
100M ILE* 5.2 1.3 - - - +
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Residues in contact with GLN 87 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85M SER* 3.2 1.2 - - - +
86M LYS* 1.3 74.2 - - - +
88M ALA* 1.3 63.5 + - - +
90M GLY* 3.3 1.9 + - - -
91M ARG* 3.1 19.6 + - - -
97M ARG 5.1 0.7 - - - +
98M PRO* 4.3 9.8 - - - +
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Residues in contact with ALA 88 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85M SER* 3.2 10.3 + - - +
87M GLN* 1.3 74.9 - - - +
89M LEU* 1.3 63.7 + - - +
91M ARG* 3.3 3.2 + - - +
92M ALA* 3.2 17.0 + - - -
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Residues in contact with LEU 89 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85M SER 3.0 14.9 + - - -
86M LYS 3.6 1.5 + - - -
87M GLN 3.3 0.2 - - - -
88M ALA* 1.3 71.7 - - - +
90M GLY* 1.3 68.1 + - - +
92M ALA* 2.9 12.8 + - - +
93M CYS* 3.0 9.4 + - - -
99M VAL* 4.4 10.1 - - - -
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Residues in contact with GLY 90 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86M LYS 3.0 13.3 + - - -
87M GLN 3.3 3.8 + - - -
88M ALA 3.2 0.4 - - - -
89M LEU* 1.3 73.7 - - - +
91M ARG* 1.3 56.4 + - - +
93M CYS* 2.9 19.0 + - - -
95M VAL* 3.0 23.6 + - - -
97M ARG 3.3 23.8 - - - -
99M VAL* 3.9 9.2 - - - +
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Residues in contact with ARG 91 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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437J GLY 5.3 1.8 - - - -
438J VAL* 5.6 1.3 - - - +
439J TYR* 3.9 23.9 + - - +
87M GLN 3.1 14.4 + - - -
88M ALA* 3.3 3.3 + - - +
89M LEU 3.2 0.4 - - - -
90M GLY* 1.3 73.8 - - - +
92M ALA* 1.3 61.1 + - - +
94M GLY* 3.2 13.0 + - - -
95M VAL 3.6 9.9 + - - +
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Residues in contact with ALA 92 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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437J GLY 4.8 10.1 - - - -
23M LEU* 4.7 14.4 - - - +
26M VAL* 3.9 4.6 - - - +
27M GLN* 3.3 28.6 + - - +
30M CYS* 5.4 2.3 - - - -
88M ALA 3.2 9.0 + - - -
89M LEU* 2.9 9.2 + - - +
91M ARG* 1.3 77.0 - - - +
93M CYS* 1.3 56.4 + - - +
94M GLY 3.2 3.1 + - - -
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Residues in contact with CYS 93 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26M VAL 5.6 0.7 - - - -
30M CYS* 6.0 6.1 - - - +
89M LEU 3.0 7.9 + - - -
90M GLY* 2.9 7.7 + - - -
92M ALA* 1.3 77.9 - - - +
94M GLY* 1.3 54.8 + - - +
95M VAL* 3.1 9.6 + - - -
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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