Contacts of the helix formed by residues 238 - 255 (chain A) in PDB entry 4DYL
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 GLN 238 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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90A HIS* 3.6 10.6 + - - -
232A GLU 2.8 28.4 + - - +
233A ILE* 3.3 14.9 + - - +
235A SER* 2.6 34.7 + - - +
236A LEU 3.6 0.4 - - - -
237A VAL* 1.3 80.7 - - - +
239A ASP* 1.3 69.6 + - - +
240A GLU* 4.1 20.7 - - + +
241A VAL* 2.9 24.2 + - + +
242A VAL* 3.0 11.0 + - - -
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Residues in contact with ASP 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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237A VAL 5.5 0.2 - - - +
238A GLN* 1.3 74.1 - - - +
240A GLU* 1.3 58.8 + - + +
242A VAL* 3.3 10.1 + - - +
243A ALA* 2.9 31.6 + - - +
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Residues in contact with GLU 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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86A LEU* 3.4 35.3 - - + +
89A GLN* 5.2 2.7 + - - -
90A HIS* 5.1 0.7 + - - -
238A GLN* 3.3 18.9 - - + +
239A ASP* 1.3 77.6 - - + +
241A VAL* 1.3 60.7 + - - +
243A ALA* 3.7 6.2 + - - +
244A ILE* 3.4 27.2 + - - +
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Residues in contact with VAL 241 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A LEU* 4.1 11.7 - - + -
86A LEU* 3.7 20.0 - - + -
87A LEU* 5.8 0.9 - - + -
90A HIS* 4.4 7.2 - - + -
235A SER 4.0 11.0 - - - +
236A LEU* 2.9 41.1 - - + +
238A GLN* 2.9 13.9 + - + +
240A GLU* 1.3 74.6 - - - +
242A VAL* 1.3 65.6 + - - +
244A ILE* 3.0 6.6 + - - +
245A HIS* 2.8 55.7 + - + +
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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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237A VAL* 3.5 28.5 - - + +
238A GLN 3.0 9.1 + - - +
239A ASP* 3.7 12.1 - - - +
241A VAL* 1.3 75.5 - - - +
243A ALA* 1.3 56.4 + - - +
245A HIS* 3.1 7.9 + - + +
246A ARG* 2.8 68.6 + - + +
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Residues in contact with ALA 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 ASP 2.9 18.0 + - - +
240A GLU* 4.0 7.0 - - - +
241A VAL 3.2 0.2 - - - -
242A VAL* 1.3 76.5 - - - +
244A ILE* 1.3 63.4 + - + +
246A ARG* 3.5 11.8 + - - +
247A GLU* 3.3 28.0 + - - +
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Residues in contact with ILE 244 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A GLN* 3.5 38.3 - - - +
82A GLY* 3.7 31.4 - - - +
83A LEU* 3.7 14.8 - - + +
86A LEU* 3.9 14.6 - - + -
240A GLU 3.4 14.5 + - - +
241A VAL* 3.0 9.2 + - - +
243A ALA* 1.3 78.9 - - + +
245A HIS* 1.3 65.6 + - + +
247A GLU* 3.4 4.7 + - - +
248A MET* 3.1 39.2 + - + +
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Residues in contact with HIS 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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83A LEU* 4.2 25.8 - - + +
241A VAL* 2.8 50.0 + - + +
242A VAL* 3.1 9.4 + - + +
244A ILE* 1.3 80.1 - - + +
246A ARG* 1.3 56.3 + - + +
248A MET* 3.4 23.9 + - + +
249A ALA* 3.0 27.4 + - - +
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Residues in contact with ARG 246 (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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242A VAL* 2.8 50.5 + - + +
243A ALA* 3.9 11.1 - - - +
244A ILE 3.3 0.2 - - - -
245A HIS* 1.3 75.5 - - + +
247A GLU* 1.3 57.4 + - + +
249A ALA* 3.2 7.2 + - - +
250A ALA* 2.8 36.0 + - - +
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Residues in contact with GLU 247 (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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75A GLU* 3.8 14.8 - - - +
79A GLN* 3.7 29.4 - - + +
243A ALA* 3.3 13.9 + - + +
244A ILE 3.4 8.3 + - - +
246A ARG* 1.3 74.4 - - + +
248A MET* 1.3 67.1 + - - +
250A ALA* 3.5 7.0 + - - +
251A ALA* 2.9 24.4 + - - +
254A ARG* 4.7 8.5 + - - -
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Residues in contact with MET 248 (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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76A ILE* 3.8 30.6 - - + +
79A GLN* 3.5 20.9 - - + -
80A THR* 3.6 24.9 - - - +
83A LEU* 5.1 7.2 - - + -
244A ILE* 3.1 30.7 + - + +
245A HIS* 3.6 35.0 - - + +
247A GLU* 1.3 77.0 - - - +
249A ALA* 1.3 57.5 + - - +
251A ALA* 3.3 3.5 + - - +
252A ALA* 3.0 29.5 + - - +
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Residues in contact with ALA 249 (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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245A HIS 3.0 17.0 + - - +
246A ARG* 3.2 8.3 + - - +
248A MET* 1.3 76.6 - - - +
250A ALA* 1.3 57.2 + - - +
252A ALA* 3.6 6.4 + - - +
253A ALA* 3.1 30.4 + - - +
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Residues in contact with ALA 250 (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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246A ARG 2.8 17.0 + - - +
247A GLU* 3.9 10.8 - - - +
249A ALA* 1.3 75.2 - - - +
251A ALA* 1.3 64.8 + - - +
253A ALA* 3.3 6.2 + - - +
254A ARG* 3.1 44.8 + - - +
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Residues in contact with ALA 251 (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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72A SER* 2.8 37.7 + - - +
75A GLU* 3.7 30.5 - - + -
76A ILE* 4.0 4.9 - - + -
247A GLU 2.9 18.7 + - - +
248A MET 3.5 4.9 - - - +
250A ALA* 1.3 79.7 - - - +
252A ALA* 1.3 61.4 + - - +
254A ARG* 3.4 21.0 + - - +
255A ILE 3.9 0.2 + - - -
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Residues in contact with ALA 252 (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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76A ILE* 3.9 12.9 - - + +
248A MET 3.0 16.2 + - - +
249A ALA* 3.9 6.5 - - - +
251A ALA* 1.3 76.9 - - - +
253A ALA* 1.3 61.9 + - - +
255A ILE* 3.2 34.6 + - + +
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Residues in contact with ALA 253 (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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249A ALA 3.1 18.7 + - - +
250A ALA* 3.3 6.5 + - - +
251A ALA 3.3 0.2 - - - -
252A ALA* 1.3 75.5 - - - +
254A ARG* 1.3 64.6 + - - +
255A ILE 3.2 7.4 + - - +
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Residues in contact with ARG 254 (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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68A PRO* 5.2 3.7 - - - +
72A SER* 4.4 6.0 + - - +
75A GLU* 4.5 10.3 - - - +
247A GLU* 4.7 7.7 + - - -
250A ALA* 3.1 31.9 + - - +
251A ALA* 3.4 34.1 + - - +
252A ALA 3.2 0.4 - - - -
253A ALA* 1.3 75.8 - - - +
255A ILE* 1.3 66.0 + - - +
256A GLN* 3.0 9.2 + - - +
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Residues in contact with ILE 255 (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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68A PRO* 4.4 6.3 - - + +
69A ILE* 3.6 41.3 - - + +
72A SER* 3.6 30.7 - - - +
76A ILE* 5.8 1.8 - - + -
252A ALA* 3.3 24.2 - - + +
253A ALA 3.2 7.6 - - - +
254A ARG* 1.3 76.4 - - - +
256A GLN* 1.3 59.2 + - - +
257A PRO* 3.5 22.7 - - + +
260A GLU* 5.4 0.9 - - - +
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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