Contacts of the helix formed by residues 236 - 245 (chain A) in PDB entry 6V99
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 ASP 236 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223A ASP* 3.6 7.2 - - - +
228A THR 4.7 1.0 - - - +
229A SER* 3.3 29.0 - - - +
230A SER* 3.0 30.7 + - - -
231A ARG 3.3 0.7 + - - -
232A ASP* 3.0 34.3 + - - +
234A GLY 3.6 0.6 - - - -
235A LYS* 1.3 88.5 + - - +
237A ILE* 1.3 68.1 + - - +
238A ILE 3.4 0.7 - - - -
239A PRO* 3.6 1.1 - - - +
240A TYR* 3.2 23.0 + - - +
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Residues in contact with ILE 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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111A ALA* 3.8 20.0 - - + -
211A PHE* 4.5 8.1 - - + -
216A LEU* 5.2 0.9 - - + -
219A ALA* 3.9 22.7 - - + +
220A LEU* 4.2 11.9 - - + -
223A ASP* 3.7 30.5 - - + -
232A ASP 3.0 15.3 + - - +
233A PHE* 3.8 28.3 - - + +
236A ASP* 1.3 75.2 - - - +
238A ILE* 1.3 64.5 + - - +
240A TYR* 3.2 9.3 - - - +
241A ILE* 3.1 37.3 - - + +
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Residues in contact with ILE 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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156A VAL* 3.6 38.1 - - + +
158A ILE* 3.6 25.6 - - + -
174A MET* 4.7 10.5 - - + -
185A PHE* 5.0 4.5 - - + -
209A TYR* 3.9 25.4 - - + -
211A PHE* 4.3 11.2 - - + -
233A PHE* 2.8 28.9 + - + +
234A GLY* 4.4 4.5 - - - +
237A ILE* 1.3 74.9 - - + +
239A PRO* 1.3 68.9 - - + +
241A ILE* 2.9 15.6 + - + +
242A VAL* 3.0 26.8 + - + +
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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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185A PHE* 3.6 22.2 - - + +
234A GLY 3.1 24.2 - - - +
235A LYS 3.2 26.0 - - - +
236A ASP 3.6 5.2 - - - +
238A ILE* 1.3 89.1 - - + +
240A TYR* 1.3 62.9 + - - +
242A VAL* 3.3 12.2 + - + +
243A GLU* 3.3 22.9 + - - +
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Residues in contact with TYR 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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222A ARG* 3.3 46.0 + - + -
236A ASP 3.2 12.8 + - - +
237A ILE* 3.2 12.8 - - - +
239A PRO* 1.3 80.5 - - - +
241A ILE* 1.3 64.3 + - + +
243A GLU* 3.3 4.0 + - - +
244A HIS* 3.0 57.0 + + + +
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Residues in contact with ILE 241 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155A ASP* 3.6 28.0 - - + +
156A VAL* 3.9 25.4 - - + -
211A PHE* 4.1 6.3 - - + -
215A PHE* 3.8 26.2 - - + -
219A ALA* 5.3 3.6 - - + -
222A ARG* 5.6 2.9 - - - +
237A ILE* 3.1 35.7 - - + +
238A ILE* 2.9 5.0 + - - +
240A TYR* 1.3 81.4 - - + +
242A VAL* 1.3 65.6 + - - +
245A GLY* 2.7 46.9 + - - +
246A LYS 4.1 2.9 - - - +
247A ALA* 4.9 1.3 - - - -
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Residues in contact with VAL 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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182A ILE* 3.3 41.7 - - + +
183A ILE* 3.5 8.0 - - - +
184A ASP* 3.5 26.5 - - - +
185A PHE* 4.5 8.3 - - + +
238A ILE* 3.0 33.9 + - + +
239A PRO* 3.6 10.3 - - + +
241A ILE* 1.3 75.8 - - - +
243A GLU* 1.3 64.0 + - - +
245A GLY 3.6 7.2 - - - +
247A ALA* 4.2 15.0 - - + +
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Residues in contact with GLU 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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183A ILE 6.0 0.7 - - - -
239A PRO 3.3 9.7 + - - +
240A TYR* 3.7 6.1 - - - +
241A ILE 3.1 0.4 - - - -
242A VAL* 1.3 83.0 - - - +
244A HIS* 1.3 86.6 + - + +
245A GLY 4.2 1.6 - - - +
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Residues in contact with HIS 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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240A TYR* 3.0 52.3 + + + +
243A GLU* 1.3 106.7 - - + +
245A GLY* 1.3 58.9 + - - +
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Residues in contact with GLY 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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155A ASP* 3.4 14.8 - - - -
241A ILE* 2.7 31.4 + - - +
242A VAL 3.6 9.7 - - - +
243A GLU 4.2 1.4 - - - +
244A HIS* 1.3 76.9 - - - +
246A LYS* 1.3 58.3 + - - -
247A ALA 4.1 0.2 + - - -
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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