Contacts of the helix formed by residues 78 - 90 (chain H) in PDB entry 2QXU
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 MET 78 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11H GLY* 4.0 1.7 - - - -
12H ILE* 3.3 55.0 - - + +
45H THR 4.5 3.4 - - - +
46H GLY* 3.3 28.3 - - - +
47H THR* 6.0 0.2 - - - -
48H ASN* 5.6 0.9 - - - +
76H HIS 3.2 0.4 + - - -
77H SER* 1.3 81.8 + - - +
79H GLY* 1.3 61.8 + - - +
80H GLY 3.0 0.2 - - - -
81H ALA* 3.0 24.1 + - - +
82H ASN* 3.1 13.0 + - - +
105H ALA* 4.2 8.4 - - + +
108H LEU* 3.4 35.2 - - + -
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Residues in contact with GLY 79 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9H VAL* 3.8 15.1 - - - +
10H HIS 3.3 22.5 + - - -
75H ALA* 3.6 7.1 - - - +
76H HIS 2.7 17.6 + - - -
78H MET* 1.3 73.3 - - - +
80H GLY* 1.3 56.2 + - - +
82H ASN* 3.4 6.2 + - - +
83H THR* 2.9 33.1 + - - -
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Residues in contact with GLY 80 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75H ALA* 3.7 15.3 - - - +
76H HIS 3.9 0.8 + - - -
77H SER 2.8 10.5 + - - -
79H GLY* 1.3 76.2 - - - +
81H ALA* 1.3 64.4 + - - +
83H THR* 3.3 3.3 + - - -
84H LEU* 3.0 28.4 + - - +
101H THR* 4.1 7.7 - - - +
104H GLY* 4.7 1.6 - - - -
106H ASN* 3.2 23.4 - - - +
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Residues in contact with ALA 81 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48H ASN* 3.2 11.7 - - - +
77H SER 4.0 1.6 + - - -
78H MET* 3.0 25.7 + - - +
80H GLY* 1.3 77.6 - - - +
82H ASN* 1.3 57.1 + - - +
84H LEU 3.4 0.5 + - - -
85H TYR 3.0 18.4 + - - -
105H ALA 3.4 24.1 + - - +
106H ASN* 3.9 4.3 + - - +
108H LEU* 4.1 7.2 - - + -
109H THR* 2.7 32.1 + - - +
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Residues in contact with ASN 82 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9H VAL* 4.6 6.7 - - + -
10H HIS 4.4 1.4 + - - -
11H GLY* 5.7 0.6 - - - -
41H PHE* 3.8 11.8 - - + -
46H GLY* 3.0 20.4 + - - +
48H ASN* 2.9 24.6 - - - +
51H ASN* 3.1 42.8 - - + +
52H GLY* 4.8 2.9 - - - +
55H LEU* 4.0 7.1 - - + +
78H MET* 3.1 16.2 + - - +
79H GLY* 3.7 11.7 - - - +
81H ALA* 1.3 76.8 - - - +
83H THR* 1.3 63.0 + - - +
85H TYR* 3.3 4.1 + - - +
86H TYR* 3.0 24.1 + - - +
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Residues in contact with THR 83 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9H VAL* 3.9 8.5 - - - +
55H LEU* 3.9 9.6 - - - +
73H ILE* 3.7 35.2 - - + +
75H ALA* 3.6 12.6 - - - +
79H GLY 2.9 23.1 + - - -
80H GLY* 3.6 7.4 - - - -
81H ALA 3.3 0.2 - - - -
82H ASN* 1.3 76.6 - - - +
84H LEU* 1.3 64.1 + - + +
86H TYR* 3.2 5.9 + - - +
87H ILE* 3.1 35.5 + - + +
99H VAL* 4.3 16.8 - - + -
125H TYR* 5.9 0.4 - - + -
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Residues in contact with LEU 84 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80H GLY 3.0 16.3 + - - +
81H ALA 3.8 3.4 - - - +
83H THR* 1.3 75.4 - - + +
85H TYR* 1.3 60.8 + - - +
87H ILE* 3.4 5.3 + - + +
88H LYS* 2.8 32.2 + - - +
106H ASN* 3.4 44.6 - - + +
109H THR* 3.8 12.6 - - + -
110H THR* 3.7 21.8 - - + -
112H LYS 4.0 9.2 - - - +
114H LEU* 3.7 8.5 - - + +
125H TYR* 3.9 35.0 - - + +
143H LEU* 3.8 12.1 - - + -
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Residues in contact with TYR 85 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48H ASN* 3.5 53.8 - - + +
49H TYR* 4.6 12.2 + - - -
52H GLY* 3.9 10.8 - - - -
53H PRO* 4.8 3.4 - - + -
81H ALA 3.0 17.3 + - - +
82H ASN* 3.5 4.9 - - - +
84H LEU* 1.3 73.6 - - - +
86H TYR* 1.3 62.6 + - - +
88H LYS* 4.5 1.8 - - - +
89H ASN* 2.7 61.2 + - + +
90H LEU* 3.5 29.0 + - + +
109H THR* 3.6 11.2 - - + +
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Residues in contact with TYR 86 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52H GLY* 4.7 2.7 - - - +
55H LEU* 3.9 20.2 - - + -
56H SER* 3.5 28.4 + - - -
59H VAL* 3.2 41.4 - - + +
73H ILE* 4.6 4.9 - - + -
82H ASN 3.0 13.7 + - - +
83H THR 3.3 10.8 - - - +
85H TYR* 1.3 78.5 - - - +
87H ILE* 1.3 60.8 + - + +
90H LEU* 3.1 35.3 + - + +
91H ASP* 3.4 15.1 + - - -
92H GLY* 3.1 49.5 + - - -
95H LYS* 3.7 13.3 - - - +
96H VAL* 3.9 17.0 - - + -
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Residues in contact with ILE 87 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83H THR* 3.1 30.3 + - + +
84H LEU* 3.7 8.7 - - - +
86H TYR* 1.3 86.1 - - + +
88H LYS* 1.3 63.6 + - - +
90H LEU 4.5 3.6 - - - +
92H GLY 4.0 9.6 - - - +
93H GLY* 3.8 24.5 + - - +
96H VAL* 4.5 5.8 - - + -
99H VAL* 4.4 11.4 - - + -
114H LEU* 4.1 21.1 - - + -
116H GLY* 4.4 5.2 - - - -
117H THR* 6.1 0.2 - - - +
123H ILE* 3.7 30.7 - - + -
125H TYR* 3.5 19.7 - - + +
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Residues in contact with LYS 88 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84H LEU 2.8 21.7 + - - +
85H TYR* 4.0 1.1 - - - +
87H ILE* 1.3 76.2 - - - +
89H ASN* 1.3 84.0 + - - +
90H LEU 5.0 0.6 - - - +
109H THR* 4.5 23.8 - - + +
110H THR* 4.8 6.8 + - - +
114H LEU* 3.2 27.1 - - + +
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Residues in contact with ASN 89 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85H TYR* 2.7 56.4 + - + +
88H LYS* 1.3 107.2 + - - +
90H LEU* 1.3 70.0 + - + +
109H THR* 5.5 0.2 - - - +
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Residues in contact with LEU 90 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52H GLY* 3.1 44.6 - - - +
53H PRO* 3.6 13.7 - - + -
56H SER* 4.1 7.2 - - - -
85H TYR* 3.5 20.2 + - + +
86H TYR* 3.1 26.1 + - + +
87H ILE 4.5 5.0 - - - +
88H LYS 5.0 0.5 - - - +
89H ASN* 1.3 88.6 - - + +
91H ASP* 1.3 68.7 + - - +
92H GLY 3.9 0.2 + - - -
93H GLY 5.0 0.3 + - - -
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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