Contacts of the helix formed by residues 77 - 85 (chain A) in PDB entry 2QFI
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 LYS 77 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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75A HIS* 5.2 3.6 - - + -
76A GLY* 1.3 72.5 - - - +
78A ALA* 1.3 54.9 + - - +
80A SER* 2.5 35.7 + - - -
81A LEU* 3.0 10.8 + - - -
203A GLN 3.8 9.4 - - - +
204A SER* 3.2 46.3 + - - +
206A LEU* 3.0 40.4 - - + +
238A GLN* 3.2 39.7 - - + +
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Residues in contact with ALA 78 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59A VAL* 4.5 7.9 - - + +
62A TYR* 4.2 17.5 - - + +
63A SER* 3.5 14.4 - - - +
75A HIS* 5.4 1.5 - - + +
76A GLY* 3.2 23.9 - - - +
77A LYS* 1.3 71.5 - - - +
79A GLU* 1.3 70.2 + - - +
81A LEU* 3.0 22.1 - - - +
82A ALA* 2.7 18.3 + - - +
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Residues in contact with GLU 79 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11A ARG* 3.5 20.4 + - - -
15A ALA* 5.6 0.9 - - - +
59A VAL* 4.8 1.8 - - - -
60A VAL* 4.4 5.4 - - + +
63A SER* 3.3 25.0 + - - +
64A LEU* 5.6 1.4 - - - +
76A GLY 2.5 24.3 + - - +
78A ALA* 1.3 72.6 - - - +
80A SER* 1.3 63.4 + - - +
82A ALA* 2.4 42.7 + - - +
144A SER* 2.9 29.4 + - - +
145A GLN* 3.4 26.5 + - + +
147A VAL* 2.7 26.9 - - + +
238A GLN* 4.8 1.6 - - - +
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Residues in contact with SER 80 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77A LYS* 2.5 17.8 + - - -
79A GLU* 1.3 73.9 - - - +
81A LEU* 1.3 58.9 + - - +
83A ALA* 2.8 21.9 - - - +
84A LEU 3.1 4.3 + - - -
145A GLN* 4.7 4.2 - - - +
200A GLU* 3.1 49.3 + - - +
201A ALA* 3.5 9.0 - - - -
203A GLN 5.2 1.7 + - - -
204A SER* 4.0 11.4 - - - -
238A GLN* 4.1 17.0 + - - +
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Residues in contact with LEU 81 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59A VAL* 5.5 3.1 - - + -
77A LYS* 3.0 9.1 + - + +
78A ALA* 3.0 22.0 - - - +
80A SER* 1.3 70.5 - - - +
82A ALA* 1.3 70.1 + - + +
83A ALA 2.3 20.9 + - - -
84A LEU* 2.5 24.7 + - + +
85A ALA* 3.5 4.2 + - - +
86A GLN* 4.1 0.2 + - - -
204A SER* 3.4 17.5 + - - +
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Residues in contact with ALA 82 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55A THR* 5.5 3.8 - - + -
56A ASN* 4.1 10.4 - - - +
59A VAL* 3.5 29.4 - - + -
78A ALA 2.7 10.9 + - - +
79A GLU* 2.4 22.9 + - - +
81A LEU* 1.3 72.9 - - + +
83A ALA* 1.3 58.6 + - - +
85A ALA* 5.4 0.4 - - - -
86A GLN* 3.0 24.0 + - - +
147A VAL* 3.9 16.3 - - + +
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Residues in contact with ALA 83 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79A GLU 3.7 1.6 - - - +
80A SER* 2.8 24.7 - - - +
81A LEU 2.3 12.3 + - - -
82A ALA* 1.3 71.6 - - - +
84A LEU* 1.3 64.6 + - - +
85A ALA 2.8 1.6 + - - -
86A GLN* 3.2 11.8 - - - +
87A SER* 2.8 28.1 + - - -
147A VAL* 4.2 3.1 - - + -
197A MET* 3.9 22.7 - - + +
200A GLU* 4.0 17.5 - - + +
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Residues in contact with LEU 84 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80A SER 3.1 3.0 + - - +
81A LEU* 2.5 15.8 + - - +
83A ALA* 1.3 82.6 - - - +
85A ALA* 1.3 59.1 - - + +
87A SER* 2.2 21.5 + - - +
88A MET* 3.8 13.4 + - + +
89A PHE* 3.4 37.3 + - + -
201A ALA* 3.5 39.7 - - + +
202A VAL* 4.2 13.2 - - + +
204A SER* 5.2 4.9 - - - +
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Residues in contact with ALA 85 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81A LEU 3.5 3.2 + - - +
82A ALA* 5.4 0.4 - - - -
83A ALA 2.8 1.8 + - - -
84A LEU* 1.3 83.3 - - + +
86A GLN* 1.3 65.3 - - - +
87A SER 2.4 10.7 + - - -
89A PHE* 1.9 48.8 + - + +
90A ILE* 4.8 12.6 - - + -
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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