Contacts of the helix formed by residues 140 - 152 (chain G) in PDB entry 5XTD
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 CYS 140 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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101G ASN* 3.2 33.2 - - - +
103G HIS* 3.4 22.9 - - - -
138G LEU* 2.7 16.8 - - - +
139G MET* 1.3 80.7 - - - +
141G PRO* 1.3 60.8 - - - +
142G GLN* 3.0 21.1 - - + +
143G GLU* 2.7 26.7 + - + +
144G ILE* 3.2 4.8 + - - +
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Residues in contact with PRO 141 (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 GLN* 6.1 1.6 - - - +
83G VAL* 6.0 4.0 - - + -
84G LEU* 5.9 2.9 - - + -
87G LEU* 5.9 2.5 - - + -
99G SER 4.1 16.6 - - - +
100G VAL 3.8 7.0 - - - +
101G ASN 3.1 11.7 - - - +
102G SER 3.1 28.3 - - - +
103G HIS* 4.4 0.4 - - - -
104G PHE* 3.6 28.3 - - + -
138G LEU* 5.4 0.2 - - - -
139G MET 4.1 2.2 - - - +
140G CYS* 1.3 79.8 - - - +
142G GLN* 1.3 60.2 + - - +
144G ILE* 2.8 33.6 + - + +
145G VAL* 2.9 20.2 + - + +
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Residues in contact with GLN 142 (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 GLN* 4.5 8.9 + - - +
100G VAL* 3.2 29.0 + - - +
101G ASN* 3.2 26.5 + - - +
140G CYS* 3.8 5.6 - - + -
141G PRO* 1.3 80.8 - - - +
143G GLU* 1.3 58.6 + - + +
145G VAL* 3.7 14.4 + - - +
146G ASP* 2.9 31.8 + - + +
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Residues in contact with GLU 143 (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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137G LYS* 4.2 7.2 - - + +
138G LEU* 3.1 30.5 + - - +
139G MET* 3.1 31.2 - - + +
140G CYS* 2.7 16.0 + - + +
142G GLN* 1.3 73.4 - - + +
144G ILE* 1.3 62.1 + - - +
146G ASP* 3.5 16.7 - - + +
147G TYR* 2.9 26.7 + - - +
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Residues in contact with ILE 144 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83G VAL* 4.5 10.1 - - + -
104G PHE* 3.8 19.3 - - + -
122G MET* 3.6 43.5 - - + -
126G PHE* 5.5 0.9 - - + -
138G LEU* 3.6 31.4 - - + +
140G CYS 3.2 1.2 + - - -
141G PRO* 2.8 21.0 + - + +
143G GLU* 1.3 77.2 - - - +
145G VAL* 1.3 59.5 + - + +
147G TYR* 3.0 8.0 + - - +
148G ILE* 2.9 47.0 + - + +
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Residues in contact with VAL 145 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76G LEU* 4.0 30.4 - - + +
79G ILE* 4.7 5.8 - - + -
80G GLN* 3.7 44.6 - - + +
83G VAL* 4.8 6.3 - - + -
141G PRO* 2.9 17.6 + - + +
142G GLN* 4.2 13.5 - - - +
144G ILE* 1.3 77.6 - - + +
146G ASP* 1.3 56.9 + - - +
148G ILE* 3.3 15.8 + - + +
149G ALA* 2.9 26.5 + - - +
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Residues in contact with ASP 146 (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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142G GLN* 2.9 26.0 + - + +
143G GLU* 3.5 19.1 - - - +
144G ILE 3.1 0.2 - - - -
145G VAL* 1.3 74.6 - - - +
147G TYR* 1.3 64.9 + - - +
149G ALA* 3.0 12.0 + - - +
150G ASP* 2.9 20.4 + - - +
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Residues in contact with TYR 147 (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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128G PHE* 4.6 15.8 - + - -
130G ILE* 3.7 24.5 - - + +
131G PRO* 4.8 5.0 - - - +
134G ASP* 3.2 36.6 + - + -
143G GLU 2.9 20.0 + - - +
144G ILE* 3.5 6.1 - - - +
146G ASP* 1.3 76.9 - - - +
148G ILE* 1.3 56.2 + - + +
150G ASP* 2.8 16.7 + - + +
151G LYS* 2.4 58.5 + - + +
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Residues in contact with ILE 148 (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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76G LEU* 5.5 2.9 - - + -
79G ILE* 3.5 32.3 - - + -
83G VAL* 4.1 3.6 - - + -
126G PHE* 3.3 44.0 - - + -
144G ILE* 2.9 35.7 + - + +
145G VAL* 3.4 15.9 - - + +
146G ASP 3.1 0.2 - - - -
147G TYR* 1.3 80.7 - - + +
149G ALA* 1.3 57.4 + - - +
151G LYS* 3.8 8.1 - - + -
152G LYS* 2.6 45.9 + - + +
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Residues in contact with ALA 149 (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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76G LEU* 4.3 20.1 - - + +
145G VAL 2.9 13.3 + - - +
146G ASP* 3.0 17.9 + - - +
148G ILE* 1.3 76.9 - - - +
150G ASP* 1.3 54.0 + - - +
153G ASP* 3.3 21.5 - - - +
155G TYR* 3.7 31.6 - - + +
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Residues in contact with ASP 150 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146G ASP* 2.9 12.1 + - - +
147G TYR* 2.8 22.9 + - + +
149G ALA* 1.3 75.7 - - - +
151G LYS* 1.3 59.5 + - - +
153G ASP* 4.1 7.5 + - - +
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Residues in contact with LYS 151 (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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128G PHE* 6.0 5.2 - - + -
130G ILE* 6.1 0.2 - - + -
147G TYR* 2.4 48.5 + - + +
148G ILE* 3.8 9.0 - - + +
150G ASP* 1.3 76.1 - - - +
152G LYS* 1.3 67.1 + - - +
153G ASP* 3.0 6.4 + - - +
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Residues in contact with LYS 152 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74G LEU* 3.4 31.3 - - + +
76G LEU* 6.1 0.7 - - + -
79G ILE* 6.0 1.1 - - + -
126G PHE* 6.3 1.3 - - + -
148G ILE* 2.6 31.6 + - + +
151G LYS* 1.3 75.5 - - - +
153G ASP* 1.3 62.8 - - - +
154G VAL* 2.9 24.2 + - + +
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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