Contacts of the helix formed by residues 229 - 244 (chain B) in PDB entry 3COG
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 229 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204B ASP* 5.3 4.9 + - - +
227B VAL* 3.8 3.0 - - - +
228B ASN* 1.3 76.7 - - - +
230B GLU* 1.3 63.2 + - - +
231B SER* 3.4 22.4 - - - -
232B LEU* 3.6 23.9 - - + +
233B HIS* 2.9 31.2 + - - +
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Residues in contact with GLU 230 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82B LYS* 3.1 18.2 + - - -
83B TYR* 2.7 34.0 + - - -
228B ASN 3.4 2.9 + - - +
229B CYS* 1.3 76.6 - - - +
231B SER* 1.3 58.4 + - - +
233B HIS* 3.4 5.3 + - - +
234B ASN* 3.0 48.5 + - - +
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Residues in contact with SER 231 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229B CYS* 3.4 14.3 - - - -
230B GLU* 1.3 75.3 - - - +
232B LEU* 1.3 65.7 + - - +
234B ASN* 3.2 10.3 + - - +
235B ARG* 2.8 43.2 + - - +
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Residues in contact with LEU 232 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100B LEU* 3.5 34.5 - - + -
183B ILE* 4.0 19.7 - - + -
204B ASP* 4.1 28.0 - - + +
205B ILE* 4.2 7.9 - - + -
227B VAL* 3.7 21.5 - - + -
229B CYS* 3.6 24.2 - - + +
231B SER* 1.3 83.0 + - - +
233B HIS* 1.3 57.1 + - - +
235B ARG* 3.2 15.3 + - - +
236B LEU* 2.9 38.8 + - + +
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Residues in contact with HIS 233 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83B TYR* 3.4 60.7 - + + -
85B LEU* 4.2 6.7 - - + -
227B VAL* 3.8 17.0 - - + +
229B CYS 2.9 18.7 + - - +
230B GLU* 3.5 5.4 + - - +
232B LEU* 1.3 75.8 - - - +
234B ASN* 1.3 70.7 + - - +
236B LEU* 3.1 4.3 + - - +
237B ARG* 2.8 72.5 + - + +
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Residues in contact with ASN 234 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230B GLU* 3.0 40.9 + - - +
231B SER* 3.6 8.8 - - - +
233B HIS* 1.3 87.4 + - - +
235B ARG* 1.3 62.1 + - + +
237B ARG* 3.8 5.7 - - - +
238B PHE* 3.1 24.6 + - - +
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Residues in contact with ARG 235 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100B LEU* 2.8 55.2 + - + +
101B LEU* 5.1 2.4 - - - +
181B ASP* 5.4 7.9 + - - -
183B ILE* 4.5 18.2 - - - +
231B SER* 2.8 29.6 + - - +
232B LEU* 3.5 13.0 - - - +
234B ASN* 1.3 78.5 - - + +
236B LEU* 1.3 62.7 + - - +
238B PHE* 3.6 5.9 + - - +
239B LEU* 3.3 27.1 + - + +
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Residues in contact with LEU 236 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85B LEU* 3.5 32.8 - - + +
87B PHE* 5.2 2.9 - - + -
96B THR* 4.3 13.3 - - + +
97B ILE* 4.0 25.8 - - + -
100B LEU* 4.0 26.0 - - + -
205B ILE* 4.2 13.7 - - + -
225B VAL* 4.0 16.2 - - + -
227B VAL* 4.3 9.2 - - + -
232B LEU* 2.9 30.4 + - + +
233B HIS 3.5 4.0 - - - +
235B ARG* 1.3 75.3 - - - +
237B ARG* 1.3 58.6 + - - +
239B LEU* 3.3 5.3 + - - +
240B GLN* 2.9 24.9 + - - +
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Residues in contact with ARG 237 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63B SER 5.3 5.4 - - - -
68B ARG* 4.9 1.8 - - - +
69B ASN* 5.7 0.2 + - - -
72B GLU* 3.0 28.8 + - - -
83B TYR* 4.7 2.4 - - - +
84B CYS 3.0 24.2 + - - +
85B LEU* 3.6 12.6 - - - +
233B HIS* 2.8 49.9 + - + +
234B ASN* 3.8 7.6 - - - +
236B LEU* 1.3 74.7 - - - +
238B PHE* 1.3 64.6 + - - +
240B GLN* 2.9 32.0 + - - +
241B ASN* 3.2 22.7 + - - +
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Residues in contact with PHE 238 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119A ARG* 4.1 17.0 - - + -
123A GLN* 3.6 33.7 - - + -
124A VAL* 4.0 20.4 - - + -
234B ASN 3.1 18.8 + - - +
235B ARG* 3.6 6.7 - - - +
237B ARG* 1.3 77.6 - - - +
239B LEU* 1.3 69.4 + - + +
241B ASN* 3.5 5.2 + - + +
242B SER* 2.9 51.5 + - - -
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Residues in contact with LEU 239 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124A VAL* 4.2 23.1 - - + -
96B THR* 3.5 27.1 + - + +
99B HIS* 3.4 45.3 - - + +
100B LEU* 3.5 15.0 - - + +
235B ARG 3.3 14.1 + - - +
236B LEU* 3.3 8.6 + - - +
237B ARG 3.2 0.6 - - - -
238B PHE* 1.3 87.5 - - + +
240B GLN* 1.3 66.2 + - - +
241B ASN 3.3 0.4 - - - -
242B SER* 4.2 2.2 - - - +
243B LEU* 2.9 37.5 + - + +
245B ALA 5.5 0.2 + - - -
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Residues in contact with GLN 240 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63B SER 4.5 1.2 - - - +
68B ARG* 3.3 23.0 + - - +
72B GLU* 2.9 28.5 + - - -
85B LEU* 3.8 7.5 - - + +
86B ALA 3.0 23.8 + - - +
87B PHE* 4.0 24.0 - - + -
96B THR* 4.2 0.8 - - - +
236B LEU 2.9 17.0 + - - +
237B ARG* 2.9 39.1 + - - +
239B LEU* 1.3 72.0 - - - +
241B ASN* 1.3 61.9 + - - +
244B GLY* 3.2 22.3 + - - -
245B ALA 4.2 1.0 + - - +
246B VAL* 3.7 17.4 - - + +
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Residues in contact with ASN 241 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91A LEU* 3.3 4.9 - - - +
119A ARG* 3.7 24.9 - - - +
501A 2AG 3.9 7.5 + - - -
62B ARG* 3.0 48.8 + - - +
63B SER* 3.0 37.5 + - - +
237B ARG 3.2 10.0 + - - +
238B PHE* 3.7 8.5 - - - +
240B GLN* 1.3 82.2 + - - +
242B SER* 1.3 61.0 + - - +
243B LEU 3.6 0.3 + - - -
244B GLY 3.6 2.8 + - - -
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Residues in contact with SER 242 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91A LEU* 3.5 20.4 - - - +
95A VAL* 4.5 0.7 - - - +
116A GLY 4.9 0.5 - - - +
119A ARG* 3.1 31.3 + - - +
120A TYR* 4.3 12.3 - - - +
124A VAL* 4.5 12.8 - - - -
238B PHE* 2.9 47.4 + - - -
239B LEU* 3.5 3.6 + - - -
241B ASN* 1.3 78.1 + - - +
243B LEU* 1.3 62.8 + - - +
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Residues in contact with LEU 243 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91A LEU* 3.5 3.6 - - - -
92A ALA* 3.2 24.8 + - - +
95A VAL* 3.7 29.7 - - + +
120A TYR* 3.7 22.0 - - + -
124A VAL* 4.1 14.1 - - + -
95B VAL* 5.0 3.4 - - + -
96B THR* 4.0 24.2 - - - +
99B HIS* 3.6 38.8 - - + +
239B LEU* 2.9 28.0 + - + +
242B SER* 1.3 78.6 - - - +
244B GLY* 1.3 63.4 + - - +
245B ALA* 3.3 7.1 + - + +
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Residues in contact with GLY 244 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88A ALA* 4.0 1.7 - - - +
89A SER* 2.6 26.7 + - - -
91A LEU* 4.3 1.1 - - - -
92A ALA* 3.7 3.4 - - - +
62B ARG* 3.5 25.1 - - - -
240B GLN 3.2 17.8 + - - -
242B SER 3.5 1.2 - - - -
243B LEU* 1.3 77.8 - - - +
245B ALA* 1.3 57.3 + - - +
246B VAL* 2.9 15.0 + - - +
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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