Contacts of the helix formed by residues 232 - 245 (chain A) in PDB entry 6DU2
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 232 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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133A PRO 5.4 0.2 - - - -
134A HIS* 3.8 25.1 - - - +
230A SER 3.3 14.1 + - - +
231A ASP* 1.3 79.8 + - - +
233A GLU* 1.3 62.6 + - - +
234A LEU 3.4 2.2 - - - -
235A HIS* 3.2 9.8 + - + -
236A ASP* 2.8 53.1 + - - -
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Residues in contact with GLU 233 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132A ARG* 3.4 28.5 - - - +
222A VAL* 4.1 13.0 - - + +
223A ALA* 5.1 11.2 - - + +
231A ASP* 2.8 14.9 + - - +
232A THR* 1.3 77.2 + - - +
234A LEU* 1.3 65.8 + - - +
236A ASP* 3.3 16.8 + - - +
237A LEU* 3.0 34.7 + - + +
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Residues in contact with LEU 234 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100A THR* 4.0 16.6 - - + +
101A LEU* 4.2 7.4 - - + -
132A ARG* 3.7 33.4 - - + +
133A PRO 4.1 9.8 + - - +
134A HIS* 4.4 1.1 - - - +
135A VAL* 3.9 36.6 - - + -
138A PHE* 3.4 55.3 - - + -
205A LEU* 4.7 6.7 - - + -
222A VAL* 4.7 9.4 - - + -
231A ASP* 4.4 0.8 + - - -
232A THR 3.4 0.2 - - - -
233A GLU* 1.3 78.4 - - - +
235A HIS* 1.3 64.9 + - - +
237A LEU* 3.4 9.3 + - + +
238A LEU* 3.5 6.1 + - - +
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Residues in contact with HIS 235 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134A HIS* 3.8 35.5 + + + +
137A GLU* 3.2 33.6 + - - -
232A THR* 3.2 12.9 + - + +
233A GLU 3.2 0.4 - - - -
234A LEU* 1.3 80.0 - - - +
236A ASP* 1.3 75.1 + - - +
237A LEU 3.3 1.0 + - - -
238A LEU* 3.3 21.1 + - + +
239A PRO* 3.8 5.0 - - - +
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Residues in contact with ASP 236 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232A THR* 2.8 39.8 + - - +
233A GLU* 3.3 19.7 + - - +
235A HIS* 1.3 89.9 - - - +
237A LEU* 1.3 61.3 + - + +
238A LEU 3.4 0.2 - - - -
239A PRO* 3.5 17.7 - - - +
240A PHE* 4.9 1.7 + - - +
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Residues in contact with LEU 237 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138A PHE* 4.7 2.2 - - + -
205A LEU* 4.1 26.0 - - + -
220A VAL* 4.0 18.8 - - + -
221A PRO 4.2 7.9 - - - +
222A VAL* 4.2 20.2 - - + -
233A GLU* 3.0 26.5 + - + +
234A LEU* 3.9 9.2 - - + +
235A HIS 3.2 0.6 - - - -
236A ASP* 1.3 78.4 - - + +
238A LEU* 1.3 65.0 + - - +
239A PRO 3.4 0.4 - - - -
240A PHE* 3.1 20.6 + - + +
241A PHE* 3.0 34.6 + - + -
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Residues in contact with LEU 238 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137A GLU* 3.7 43.7 - - + +
138A PHE* 4.1 22.9 - - + +
141A ARG* 3.7 33.0 - - + -
142A MET* 4.6 9.4 - - + -
145A LEU* 5.1 2.7 - - + -
234A LEU 3.5 13.3 + - - +
235A HIS* 3.3 10.5 + - + +
237A LEU* 1.3 77.3 - - - +
239A PRO* 1.3 71.0 - - + +
241A PHE* 3.1 6.3 + - + +
242A GLU* 2.8 29.4 + - + +
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Residues in contact with PRO 239 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235A HIS 3.8 6.5 - - - +
236A ASP* 3.5 17.7 - - - +
238A LEU* 1.3 94.1 - - + +
240A PHE* 1.3 60.2 + - - +
242A GLU* 3.4 12.8 - - + +
243A GLN* 3.4 18.2 + - - +
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Residues in contact with PHE 240 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220A VAL* 4.2 26.0 - - + -
236A ASP 5.3 1.1 - - - +
237A LEU* 3.1 23.1 + - + +
239A PRO* 1.3 78.4 - - + +
241A PHE* 1.3 66.4 + + - +
243A GLN* 3.3 18.8 + - - +
244A LEU* 3.1 43.4 + - + +
253A VAL* 4.0 27.1 - - + -
254A LEU* 4.2 9.9 - - + -
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Residues in contact with PHE 241 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93A VAL* 4.2 12.1 - - + -
138A PHE* 4.1 15.9 - + - -
142A MET* 3.7 28.3 - - + -
145A LEU* 4.4 5.2 - - + -
146A PHE* 3.6 29.8 - + + -
203A LEU* 4.3 6.3 - - + -
204A ILE 6.3 0.2 - - - -
205A LEU* 4.1 18.8 - - + -
220A VAL* 3.9 39.5 - - + -
237A LEU* 3.0 41.8 + - + -
238A LEU* 3.7 7.2 - - + +
240A PHE* 1.3 74.1 - + + +
242A GLU* 1.3 61.0 + - - +
244A LEU* 4.2 9.9 - - + -
245A SER* 2.8 33.6 + - - -
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Residues in contact with GLU 242 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141A ARG* 2.6 52.0 + - - +
145A LEU* 3.6 10.7 - - + +
238A LEU* 2.8 22.8 + - + +
239A PRO* 3.4 16.4 - - + +
241A PHE* 1.3 75.4 - - - +
243A GLN* 1.3 61.4 + - - +
245A SER* 2.8 14.1 + - - -
246A ARG* 2.8 43.0 + - - +
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Residues in contact with GLN 243 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239A PRO 3.4 7.8 + - - +
240A PHE* 3.3 23.7 + - - +
241A PHE 3.2 0.4 - - - -
242A GLU* 1.3 79.3 - - - +
244A LEU* 1.3 65.1 + - + +
246A ARG* 3.0 18.8 + - - +
247A VAL* 3.5 18.5 + - + +
253A VAL* 3.9 27.6 - - + +
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Residues in contact with LEU 244 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91A ILE* 3.0 23.0 - - - +
146A PHE* 4.3 1.3 - - + -
203A LEU* 3.8 36.1 - - + -
220A VAL* 3.9 15.0 - - + -
240A PHE* 3.1 45.6 + - + +
241A PHE* 3.1 14.3 + - + +
243A GLN* 1.3 76.1 - - + +
245A SER* 1.3 57.5 + - - +
246A ARG 3.0 5.5 + - - -
247A VAL* 3.3 11.9 + - + +
250A VAL* 4.7 11.4 - - + +
253A VAL* 3.9 35.9 - - + -
254A LEU* 4.6 7.0 - - + -
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Residues in contact with SER 245 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90A LYS* 5.9 0.2 - - - -
91A ILE* 4.3 6.7 + - - +
145A LEU* 3.5 41.0 - - - +
146A PHE* 3.5 22.8 - - - -
241A PHE 2.8 17.8 + - - -
242A GLU 2.8 20.4 + - - -
244A LEU* 1.3 71.5 - - - +
246A ARG* 1.3 61.6 + - - +
247A VAL 3.7 0.2 - - - -
107B LYS* 3.6 16.3 + - - +
108B PRO* 3.7 14.5 - - - +
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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