Contacts of the helix formed by residues 78 - 90 (chain G) 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 G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11G GLY* 3.9 1.7 - - - -
12G ILE* 3.7 43.5 - - + +
45G THR 5.2 1.1 - - - +
46G GLY* 3.2 31.9 - - - +
47G THR* 4.6 2.5 - - - -
48G ASN* 4.1 18.6 - - - +
76G HIS 3.2 0.2 + - - -
77G SER* 1.3 81.7 + - - +
79G GLY* 1.3 62.7 + - - +
81G ALA* 3.0 31.2 + - + +
82G ASN* 3.0 14.1 + - - +
105G ALA* 4.2 7.1 - - + +
108G LEU* 3.3 35.9 - - + -
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Residues in contact with GLY 79 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9G VAL* 3.6 15.1 - - - +
10G HIS 3.2 22.2 + - - -
75G ALA* 3.5 6.5 - - - +
76G HIS 2.8 11.7 + - - -
78G MET* 1.3 79.1 - - - +
80G GLY* 1.3 55.7 + - - +
82G ASN* 3.4 6.3 + - - +
83G THR* 2.9 33.3 + - - -
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Residues in contact with GLY 80 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75G ALA* 3.6 16.0 - - - +
76G HIS 4.0 1.2 + - - -
77G SER 2.8 9.9 + - - -
79G GLY* 1.3 75.2 - - - +
81G ALA* 1.3 63.2 + - - +
83G THR* 3.3 2.9 + - - -
84G LEU* 3.0 29.3 + - - +
101G THR* 4.2 7.9 - - - -
104G GLY* 4.7 1.8 - - - -
106G ASN* 3.4 21.3 - - - -
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Residues in contact with ALA 81 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48G ASN* 3.4 3.0 - - - +
77G SER 3.9 2.0 + - - -
78G MET* 3.0 34.2 + - + +
80G GLY* 1.3 77.0 - - - +
82G ASN* 1.3 56.5 + - - +
84G LEU* 3.3 1.1 + - - -
85G TYR 2.9 19.6 + - - -
105G ALA 3.3 24.5 + - - +
106G ASN* 4.0 4.2 + - - +
108G LEU* 4.1 4.0 - - + -
109G THR* 2.8 32.4 + - - +
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Residues in contact with ASN 82 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9G VAL* 4.5 6.1 - - + -
10G HIS 4.3 1.6 + - - -
11G GLY* 5.7 0.6 - - - -
41G PHE* 3.7 14.2 - - + -
46G GLY* 3.2 18.3 + - - +
47G THR 3.8 5.2 - - - +
48G ASN* 3.0 20.9 - - - +
51G ASN* 3.0 38.7 - - + +
52G GLY* 4.8 4.9 - - - +
55G LEU* 4.0 5.8 - - + +
78G MET* 3.0 21.0 + - - +
79G GLY* 3.6 11.8 - - - +
81G ALA* 1.3 77.9 - - - +
83G THR* 1.3 55.9 + - - +
85G TYR* 3.4 4.7 + - - +
86G TYR* 3.0 28.2 + - - +
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Residues in contact with THR 83 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9G VAL* 3.8 9.2 - - - +
55G LEU* 4.0 8.6 - - - +
73G ILE* 3.6 38.5 - - + +
75G ALA* 3.5 14.4 - - - +
79G GLY 2.9 22.0 + - - -
80G GLY* 3.6 5.8 - - - -
82G ASN* 1.3 75.5 - - - +
84G LEU* 1.3 67.1 + - + +
86G TYR* 3.2 4.5 + - - +
87G ILE* 3.0 35.4 + - + +
99G VAL* 4.5 14.1 - - + -
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Residues in contact with LEU 84 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80G GLY 3.0 16.9 + - - +
81G ALA 3.8 1.1 - - - +
83G THR* 1.3 78.9 - - + +
85G TYR* 1.3 52.6 + - - +
87G ILE* 3.3 5.1 + - + +
88G LYS* 2.8 37.1 + - - +
106G ASN* 3.6 44.6 - - + +
109G THR* 3.7 15.7 - - + -
110G THR* 3.7 22.2 - - + -
112G LYS 4.3 7.2 - - - +
114G LEU* 3.8 6.9 - - + +
125G TYR* 3.7 38.4 - - + +
143G LEU* 3.8 10.5 - - + -
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Residues in contact with TYR 85 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48G ASN* 3.6 55.0 - - + +
49G TYR* 4.6 12.4 - - - +
52G GLY* 4.0 13.0 - - - -
53G PRO* 4.9 2.7 - - + -
81G ALA 2.9 16.7 + - - +
82G ASN 3.5 3.8 - - - +
84G LEU* 1.3 73.5 - - - +
86G TYR* 1.3 62.2 + - - +
88G LYS* 4.4 1.8 - - - -
89G ASN* 2.8 65.2 + - + +
90G LEU* 3.5 24.3 + - + +
109G THR* 3.6 10.9 - - + +
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Residues in contact with TYR 86 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52G GLY* 4.9 2.0 - - - +
55G LEU* 3.9 20.6 - - + -
56G SER* 3.5 25.3 + - - -
59G VAL* 3.2 41.1 - - + +
73G ILE* 4.5 5.4 - - + -
82G ASN 3.0 13.3 + - - +
83G THR 3.3 10.3 - - - +
85G TYR* 1.3 78.3 - - - +
87G ILE* 1.3 61.6 + - + +
90G LEU* 3.2 35.0 + - + +
91G ASP* 3.5 15.4 + - - -
92G GLY* 3.1 47.4 + - - -
95G LYS* 3.8 14.7 - - - +
96G VAL* 3.7 20.9 - - + -
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Residues in contact with ILE 87 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83G THR* 3.0 27.5 + - + +
84G LEU* 3.7 8.7 - - - +
86G TYR* 1.3 80.3 - - + +
88G LYS* 1.3 62.1 + - - +
90G LEU 4.3 4.0 - - - +
92G GLY* 4.2 10.1 - - - +
93G GLY* 3.7 24.4 + - - +
96G VAL* 4.4 10.5 - - + -
99G VAL* 4.3 13.0 - - + -
114G LEU* 4.1 20.4 - - + -
116G GLY* 4.5 4.7 - - - -
123G ILE* 3.7 31.2 - - + -
125G TYR* 3.5 21.1 - - + +
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Residues in contact with LYS 88 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84G LEU 2.8 21.0 + - - +
85G TYR* 4.0 1.6 - - - +
87G ILE* 1.3 76.5 - - - +
89G ASN* 1.3 84.5 + - - +
90G LEU 4.8 1.1 - - - +
109G THR* 4.4 24.2 - - + +
110G THR* 4.9 5.0 + - - -
114G LEU* 3.4 22.8 - - + +
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Residues in contact with ASN 89 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85G TYR* 2.8 59.3 + - + +
88G LYS* 1.3 106.2 - - - +
90G LEU* 1.3 68.9 + - + +
109G THR* 5.4 0.2 - - - +
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Residues in contact with LEU 90 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52G GLY* 3.3 41.7 - - - +
53G PRO* 3.7 10.3 - - + -
56G SER* 4.1 10.5 - - - -
85G TYR* 3.5 18.6 + - + +
86G TYR* 3.2 29.5 + - + +
87G ILE 4.3 5.7 - - - +
88G LYS 4.8 1.0 - - - +
89G ASN* 1.3 89.3 - - + +
91G ASP* 1.3 67.8 + - - +
92G GLY 3.7 0.7 + - - -
93G GLY 4.8 0.9 + - - -
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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