Contacts of the helix formed by residues 231 - 245 (chain F) in PDB entry 1C9T
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 VAL 231 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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53F VAL* 5.6 0.7 - - + -
103F ILE* 5.0 3.6 - - + -
123F LEU* 4.2 6.3 - - + -
124F PRO* 4.2 9.9 - - + -
209F LEU* 3.4 33.7 - - + +
210F GLN 2.9 16.0 + - - +
211F GLY* 3.7 9.0 - - - +
212F ILE* 3.5 35.7 - - + -
229F THR* 2.9 5.9 + - - +
230F LYS* 1.3 71.2 - - - +
232F CYS* 1.3 61.7 + - - +
234F TYR* 3.0 19.3 + - - +
235F VAL* 3.3 9.4 + - - +
238F ILE* 4.1 20.9 - - + -
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Residues in contact with CYS 232 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124F PRO* 3.8 23.3 - - + +
125F THR 5.8 0.7 - - - -
127F SER* 4.4 2.9 - - - +
128F CYS* 2.0 60.8 - - - +
210F GLN* 4.1 8.0 + - - +
230F LYS* 3.0 18.2 + - - -
231F VAL* 1.3 76.9 - - - +
233F ASN* 1.3 71.5 + - - +
234F TYR 3.3 1.0 + - - -
235F VAL* 3.3 16.4 + - + +
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Residues in contact with ASN 233 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128F CYS* 4.1 4.5 - - - -
178F SER* 3.0 29.5 + - - -
179F ASN* 3.0 23.1 + - - +
230F LYS* 3.1 24.9 + - - +
232F CYS* 1.3 87.4 - - - +
234F TYR* 1.3 67.4 + - + +
235F VAL 3.6 0.4 + - - -
236F SER* 5.1 3.8 + - - -
237F TRP 5.6 0.2 + - - -
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Residues in contact with TYR 234 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91F HIS* 3.8 29.8 - + - -
101F ASN* 2.7 45.5 + - - -
103F ILE* 3.7 31.4 - - + -
179F ASN* 2.9 34.0 + - + +
229F THR* 3.8 17.4 - - + +
230F LYS 3.2 22.9 - - - -
231F VAL 3.0 6.9 + - - +
233F ASN* 1.3 84.8 - - + +
235F VAL* 1.3 65.2 + - - +
236F SER 3.2 2.5 - - - -
237F TRP* 2.9 14.5 + + + +
238F ILE* 2.8 25.1 + - + +
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Residues in contact with VAL 235 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123F LEU* 4.4 11.2 - - + -
124F PRO* 3.3 42.2 - - + +
125F THR* 5.4 2.0 - - - -
231F VAL* 3.3 11.1 + - + +
232F CYS* 3.3 19.3 + - + +
233F ASN 3.6 0.4 - - - -
234F TYR* 1.3 74.5 - - - +
236F SER* 1.3 66.5 + - - +
238F ILE* 3.3 10.5 + - - +
239F LYS* 2.9 52.2 + - + +
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Residues in contact with SER 236 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233F ASN 5.1 3.5 + - - -
234F TYR 3.2 0.8 - - - -
235F VAL* 1.3 79.0 - - - +
237F TRP* 1.3 64.9 + - - +
239F LYS* 2.9 10.7 + - - +
240F GLN* 2.8 25.3 + - - +
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Residues in contact with TRP 237 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89F ILE* 3.8 34.3 - - + -
91F HIS* 3.7 42.4 - + + +
92F PRO* 3.9 17.1 - - + +
103F ILE* 3.5 34.5 - - + -
105F LEU* 3.7 25.1 - - + -
234F TYR* 2.9 16.5 + - + +
236F SER* 1.3 76.8 - - - +
238F ILE* 1.3 84.9 + - + +
240F GLN* 3.2 6.6 + - + +
241F THR* 2.9 40.8 + - - -
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Residues in contact with ILE 238 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47F ILE* 3.9 14.6 - - + -
53F VAL* 4.6 2.9 - - + -
103F ILE* 4.3 13.0 - - + -
105F LEU* 3.7 25.8 - - + -
123F LEU* 3.8 30.7 - - + -
231F VAL* 4.1 14.1 - - + -
234F TYR* 2.8 27.9 + - + +
235F VAL* 3.5 8.7 - - - +
237F TRP* 1.3 89.5 - - + +
239F LYS* 1.3 64.5 + - - +
241F THR* 3.0 10.0 + - - -
242F ILE* 3.1 37.9 + - + +
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Residues in contact with LYS 239 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123F LEU* 4.7 14.6 - - + -
125F THR* 6.0 3.6 - - - +
235F VAL* 2.9 41.9 + - + +
236F SER* 3.4 10.3 - - - +
238F ILE* 1.3 74.7 - - - +
240F GLN* 1.3 65.0 + - - +
242F ILE* 3.5 7.8 + - + +
243F ALA* 3.3 19.4 + - - +
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Residues in contact with GLN 240 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114B LEU* 5.7 2.8 - - - +
236F SER 2.8 18.4 + - - +
237F TRP* 3.8 7.0 - - + +
239F LYS* 1.3 71.8 - - - +
241F THR* 1.3 64.8 + - - +
243F ALA* 3.0 18.6 + - - +
244F SER* 2.9 42.8 + - - +
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Residues in contact with THR 241 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51F TRP* 4.5 2.9 - - + -
89F ILE* 3.7 28.5 - - + -
105F LEU* 3.7 18.8 - - + -
237F TRP* 2.9 36.5 + - - -
238F ILE 3.5 6.3 - - - -
240F GLN* 1.3 76.3 - - - +
242F ILE* 1.3 58.0 + - - +
244F SER* 3.5 2.2 + - - -
245F ASN* 2.7 57.8 + - - +
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Residues in contact with ILE 242 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48B ASN* 4.9 2.4 + - - -
49B SER* 4.0 1.4 + - - -
47F ILE* 4.4 11.0 - - + -
48F ASN* 4.4 18.4 - - - +
51F TRP* 3.7 45.7 + - + +
105F LEU* 4.5 6.5 - - + -
123F LEU* 5.6 1.3 - - + -
238F ILE* 3.1 38.7 + - + +
239F LYS* 3.8 7.6 - - + +
241F THR* 1.3 79.4 - - - +
243F ALA* 1.3 61.6 + - - +
244F SER 3.3 0.7 + - - -
245F ASN* 3.5 14.9 + - - +
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Residues in contact with ALA 243 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48B ASN* 3.7 19.4 - - + +
49B SER* 2.5 33.0 + - - -
114B LEU* 3.5 6.7 - - + +
239F LYS 3.3 9.6 + - - +
240F GLN* 3.0 16.1 + - - +
242F ILE* 1.3 81.2 - - - +
244F SER* 1.3 55.8 + - - +
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Residues in contact with SER 244 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49B SER* 3.5 10.7 - - - -
111B ALA* 5.2 0.9 - - - +
112B ALA 4.5 4.7 - - - +
114B LEU* 3.7 21.7 + - - +
240F GLN* 2.9 37.4 + - - +
241F THR* 4.1 3.4 - - - -
243F ALA* 1.3 77.5 - - - +
245F ASN* 1.3 70.4 + - - +
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Residues in contact with ASN 245 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49B SER* 2.9 22.3 + - - -
50B GLN* 4.2 4.0 + - - -
111B ALA* 3.7 12.9 - - - +
51F TRP* 3.7 17.3 - - + -
87F LYS* 3.8 18.6 + - + +
89F ILE* 3.5 15.8 - - + +
107F LYS* 2.9 37.4 + - - +
241F THR* 2.7 47.5 + - - +
242F ILE 3.5 8.6 + - - +
244F SER* 1.3 88.2 - - - +
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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