Contacts of the helix formed by residues 90 - 99 (chain G) in PDB entry 5DPW
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 THR 90 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52G GLN 3.6 12.0 + - - -
53G GLU* 3.3 22.4 - - - +
54G LEU 3.2 4.9 - - - -
55G THR* 4.8 5.4 - - + -
56G MET 5.5 0.4 - - - -
88G SER 4.7 5.4 - - - +
89G ALA* 1.3 76.0 - - - +
91G MET* 1.3 66.6 + - - +
92G ALA* 3.8 5.4 + - - +
93G GLU* 3.0 30.3 + - - +
94G ILE* 3.2 14.6 + - - +
96G ARG* 4.7 3.6 + - - -
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Residues in contact with MET 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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27G ILE* 3.8 16.6 - - + +
29G VAL* 3.4 33.7 - - + -
50G VAL* 3.6 20.0 - - + -
51G PRO 3.4 24.0 - - - +
52G GLN 3.4 0.4 + - - -
54G LEU* 2.7 24.0 + - + +
55G THR 4.8 1.8 - - - +
56G MET* 4.2 15.0 - - - +
59G PHE* 4.0 26.7 - - + -
90G THR* 1.3 72.0 - - - +
92G ALA* 1.3 57.5 + - - +
94G ILE* 3.2 8.0 + - + +
95G TYR* 2.8 28.9 + - - +
105G VAL* 5.0 1.8 - - + -
107G MET* 3.7 15.9 - - + -
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Residues in contact with ALA 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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27G ILE* 4.0 11.6 - - + +
52G GLN* 2.9 38.6 + - + +
90G THR* 3.1 5.4 - - - +
91G MET* 1.3 77.9 - - - +
93G GLU* 1.3 56.6 + - - +
95G TYR* 3.2 3.7 + - - +
96G ARG* 2.8 52.3 + - - +
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Residues in contact with GLU 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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89G ALA* 3.1 31.4 - - + +
90G THR* 3.0 19.0 + - - +
92G ALA* 1.3 75.7 - - - +
94G ILE* 1.3 62.7 - - + +
96G ARG* 3.2 19.9 + - - +
97G ASP* 2.8 46.8 + - + +
98G TYR* 5.9 0.7 - - + -
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Residues in contact with ILE 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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56G MET* 4.0 15.3 - - + -
79G VAL* 4.0 27.1 - - + -
85G VAL* 4.0 26.9 - - + -
89G ALA* 3.9 21.1 - - + -
90G THR 3.2 17.2 + - - +
91G MET* 3.4 13.5 - - + +
93G GLU* 1.3 79.3 - - + +
95G TYR* 1.3 55.6 + - - +
98G TYR* 2.7 56.0 + - + +
105G VAL* 4.6 9.0 - - + -
107G MET* 4.4 11.4 - - + -
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Residues in contact with TYR 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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16G VAL* 4.6 2.1 - - - +
20G ARG* 3.4 33.5 + - - -
27G ILE* 3.5 26.9 - - + -
28G PRO* 3.7 16.6 - - + +
91G MET 2.8 13.4 + - - +
92G ALA 3.2 8.9 + - - +
94G ILE* 1.3 76.9 - - - +
96G ARG* 1.3 64.7 + - + +
99G LYS* 2.9 53.4 + - + +
103G GLY* 3.0 32.6 + - - -
105G VAL* 3.3 24.7 - - + +
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Residues in contact with ARG 96 (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 THR* 4.7 3.8 + - - -
92G ALA* 2.8 37.1 + - - +
93G GLU* 3.2 27.8 + - - +
95G TYR* 1.3 79.4 - - + +
97G ASP* 1.3 66.4 - - - +
99G LYS* 4.7 2.3 + - - +
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Residues in contact with ASP 97 (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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93G GLU* 2.8 40.9 + - - +
96G ARG* 1.3 82.4 - - - +
98G TYR* 1.3 84.9 + - + +
99G LYS 3.8 0.7 - - - -
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Residues in contact with TYR 98 (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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112C GLN* 3.9 27.7 + - - +
114C THR* 4.2 6.9 + - + -
79G VAL* 3.6 21.9 - - + +
80G ASN* 3.7 33.1 + - - +
83G SER* 3.5 25.5 - - - -
85G VAL* 3.9 21.9 - - + +
93G GLU* 6.4 0.2 - - + -
94G ILE* 2.7 39.2 + - + +
97G ASP* 1.3 97.0 - - + +
99G LYS* 1.3 65.8 + - - +
100G ASP 3.6 1.2 + - - -
105G VAL* 4.3 10.2 - - + +
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Residues in contact with LYS 99 (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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94G ILE 3.8 0.2 + - - -
95G TYR* 2.9 52.3 + - + +
96G ARG 4.7 2.4 + - - +
97G ASP 3.8 0.4 - - - -
98G TYR* 1.3 81.1 - - - +
100G ASP* 1.3 79.6 + - - +
101G GLU* 4.2 10.4 + - - +
103G GLY* 4.2 13.7 - - - +
104G PHE 3.9 6.7 - - - +
105G VAL* 4.4 4.9 - - - -
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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