Contacts of the helix formed by residues 84 - 95 (chain G) in PDB entry 1DSX
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 84 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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81G ASN* 2.7 27.9 + - - -
82G ARG 3.2 0.6 - - - -
83G PRO* 1.3 76.6 - - - +
85G PHE* 1.3 62.8 + - - +
86G ASP 3.3 0.2 - - - -
87G ALA 3.3 10.9 + - - -
88G ILE* 3.4 10.2 + - - +
101G PRO* 4.7 0.7 - - - -
104G VAL* 3.6 20.0 - - - +
108G ILE* 4.2 2.3 - - - +
109G PHE* 3.5 25.9 - - - -
112G GLU* 3.6 31.2 - - - +
116G TYR* 6.1 0.7 - - - -
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Residues in contact with PHE 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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37G ILE* 3.9 20.0 - - + -
39G ILE* 3.6 18.4 - - + -
44G PHE* 3.6 46.2 - + + -
59G LEU* 3.8 19.3 - - + -
81G ASN 4.0 5.5 + - - +
82G ARG 3.1 13.6 + - - +
84G SER* 1.3 76.6 - - - +
86G ASP* 1.3 66.6 + - - +
88G ILE* 3.1 28.7 + - + -
89G LEU* 2.8 34.2 + - + +
92G TYR* 5.7 1.3 - + - -
116G TYR* 3.6 36.8 - + - -
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Residues in contact with ASP 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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82E ARG* 3.3 40.4 + - - +
83E PRO* 4.0 19.3 - - + +
42G LEU* 5.2 3.5 - - - +
44G PHE* 3.6 16.2 - - - -
82G ARG 4.3 3.2 + - - +
83G PRO* 3.8 12.4 + - - +
84G SER 3.3 1.2 - - - -
85G PHE* 1.3 75.7 - - - +
87G ALA* 1.3 58.4 + - - +
89G LEU* 3.4 5.2 + - - +
90G TYR* 3.0 27.0 + - - +
101G PRO* 6.0 2.0 - - + -
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Residues in contact with ALA 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 PRO 4.7 0.8 + - - -
84G SER 3.3 1.8 + - - -
85G PHE 3.2 0.4 - - - -
86G ASP* 1.3 76.4 - - - +
88G ILE* 1.3 59.6 + - - +
90G TYR* 3.2 9.6 + - - +
91G TYR* 3.0 26.2 + - - +
97G ARG 4.9 1.6 - - - +
98G LEU* 5.4 1.7 - - - +
99G ARG 3.2 30.2 + - - +
101G PRO* 3.6 14.7 - - + +
109G PHE* 3.4 25.2 - - + -
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Residues in contact with ILE 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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59G LEU* 4.7 0.4 - - + -
84G SER 3.6 14.6 - - - +
85G PHE* 3.1 36.9 + - + +
87G ALA* 1.3 76.0 - - - +
89G LEU* 1.3 62.4 + - - +
91G TYR* 3.2 14.9 + - - +
92G TYR* 3.3 34.8 - - + -
98G LEU* 5.5 0.4 - - + -
109G PHE* 4.4 17.5 - - + -
112G GLU* 4.7 2.9 - - + -
113G ILE* 4.5 11.0 - - + +
116G TYR* 4.0 33.7 - - + -
118G LEU* 3.6 26.2 - - + -
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Residues in contact with LEU 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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40E SER* 3.9 28.5 - - - +
82E ARG* 3.9 18.8 - - + +
37G ILE* 5.9 0.4 - - + -
44G PHE* 4.0 11.9 - - + -
45G GLU 5.0 1.1 - - - +
46G VAL* 3.9 36.6 - - + -
51G LEU* 5.9 0.2 - - + -
85G PHE* 2.8 32.2 + - + +
86G ASP* 3.6 10.1 - - - +
88G ILE* 1.3 71.6 - - - +
90G TYR* 1.3 57.9 + - - +
92G TYR* 3.1 9.5 + - + +
93G GLN* 3.0 46.5 + - + +
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Residues in contact with TYR 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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81E ASN* 3.9 22.2 - - + +
108E ILE* 3.5 33.6 - - + +
86G ASP 3.0 17.6 + - - +
87G ALA* 3.2 10.2 + - - +
89G LEU* 1.3 72.2 - - - +
91G TYR* 1.3 56.4 + - - +
93G GLN* 4.2 15.9 + - + +
94G SER* 2.7 53.7 + - - -
97G ARG* 2.5 70.9 + - + -
99G ARG* 4.6 14.4 - - + -
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Residues in contact with TYR 91 (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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54G PHE* 3.5 39.9 - + - -
56G GLU* 4.6 3.1 + - - -
57G THR* 4.7 1.1 - - + -
87G ALA 3.0 13.3 + - - +
88G ILE 3.3 9.6 - - - +
90G TYR* 1.3 76.3 - - - +
92G TYR* 1.3 70.9 + + - +
95G GLY 3.2 2.1 + - - -
96G GLY* 2.8 59.0 + - - -
97G ARG 3.3 13.1 + - - +
98G LEU* 3.8 25.6 - - + -
118G LEU* 3.7 55.5 + - + -
119G GLY 4.7 7.6 + - - -
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Residues in contact with TYR 92 (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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46G VAL* 4.9 4.3 - - + -
50G THR* 3.3 34.5 - - + +
51G LEU* 3.8 32.5 - - + -
53G GLN* 4.5 2.9 - - - +
54G PHE* 3.5 37.4 - + + -
57G THR* 2.7 35.2 + - - -
59G LEU* 3.7 20.5 + - + +
85G PHE* 5.9 0.9 - + - -
88G ILE* 3.3 39.7 + - + -
89G LEU* 3.1 11.2 + - + +
91G TYR* 1.3 84.8 - + - +
93G GLN* 1.3 62.1 + - - +
95G GLY* 3.3 11.1 + - - -
116G TYR* 4.6 1.4 + - - +
118G LEU* 3.7 14.5 - - + +
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Residues in contact with GLN 93 (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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40E SER* 3.0 26.5 + - - -
79E ASP* 2.8 33.1 + - - +
80E ARG 3.5 16.8 + - - +
81E ASN* 4.5 6.1 - - - +
82E ARG 5.3 0.5 + - - -
45G GLU 5.5 0.2 + - - -
46G VAL* 5.7 1.1 - - + +
50G THR* 4.3 9.4 - - + +
89G LEU* 3.0 41.2 + - + +
90G TYR* 3.9 18.9 + - + +
92G TYR* 1.3 75.8 - - - +
94G SER* 1.3 61.3 - - - +
95G GLY 3.6 0.3 + - - -
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Residues in contact with SER 94 (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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90G TYR* 2.7 42.0 + - - -
91G TYR 3.3 1.2 + - - -
93G GLN* 1.3 76.7 - - - +
95G GLY* 1.3 60.6 + - - +
96G GLY 3.7 0.2 + - - -
97G ARG* 2.8 58.7 + - - +
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Residues in contact with GLY 95 (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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53G GLN* 4.8 7.2 - - - -
54G PHE* 3.7 19.0 - - - -
91G TYR 3.2 4.8 + - - -
92G TYR 3.3 7.6 + - - -
93G GLN 3.3 3.8 - - - -
94G SER* 1.3 80.0 - - - +
96G GLY* 1.3 57.4 + - - +
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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