Contacts of the helix formed by residues 229 - 244 (chain A) in PDB entry 5JEI
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 SER 229 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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227A GLY 3.4 4.5 + - - -
228A SER* 1.3 73.7 + - - +
230A LEU* 1.3 62.8 + - - +
231A GLY 3.1 1.3 + - - -
232A ASN* 3.4 17.4 + - - +
233A ALA* 4.3 2.9 + - - +
309A ETE 3.4 20.7 + - - -
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Residues in contact with LEU 230 (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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6A VAL* 4.4 22.9 - - + -
47A CYS* 5.2 1.1 - - + -
49A PHE* 4.2 24.9 - - + -
84A ASP* 4.1 23.3 - - + +
85A ILE* 4.3 14.4 - - + -
224A THR* 4.4 4.0 - - + -
228A SER* 3.1 13.7 + - - +
229A SER* 1.3 80.5 + - - +
231A GLY* 1.3 63.5 + - - +
232A ASN 3.2 0.3 + - - -
233A ALA* 3.4 12.0 + - + +
234A VAL* 3.1 30.5 + - + +
309A ETE 4.2 33.0 - - - +
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Residues in contact with GLY 231 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101A ASP* 5.8 2.9 - - - -
103A SER* 5.7 0.9 - - - -
224A THR* 3.8 25.2 - - - +
228A SER 3.2 9.4 + - - -
229A SER 3.1 2.2 - - - -
230A LEU* 1.3 80.0 - - - +
232A ASN* 1.3 61.4 + - - +
234A VAL* 3.9 2.8 - - - +
235A ASN* 3.0 26.2 + - - +
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Residues in contact with ASN 232 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228A SER 4.7 1.0 + - - -
229A SER 3.4 10.2 + - - +
230A LEU 3.2 1.0 + - - -
231A GLY* 1.3 78.4 - - - +
233A ALA* 1.3 63.5 + - - +
235A ASN* 3.3 6.0 + - - +
236A LEU* 3.0 44.7 + - - +
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Residues in contact with ALA 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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47A CYS* 3.6 22.7 - - + +
229A SER 4.3 2.1 + - - +
230A LEU* 3.4 14.1 + - + +
232A ASN* 1.3 81.6 - - - +
234A VAL* 1.3 59.2 + - - +
236A LEU* 3.3 10.0 + - - +
237A ALA* 2.9 29.3 + - - +
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Residues in contact with VAL 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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43A ILE* 4.0 17.7 - - + -
47A CYS* 4.0 9.2 - - - -
49A PHE* 4.5 1.8 - - + -
85A ILE* 3.6 23.8 - - + -
103A SER* 4.6 3.1 - - - -
222A ILE* 3.4 39.9 - - + +
224A THR* 5.1 2.5 - - + -
230A LEU* 3.1 32.4 + - + +
231A GLY* 3.9 4.9 - - - +
233A ALA* 1.3 75.2 - - - +
235A ASN* 1.3 66.2 + - - +
237A ALA* 3.2 4.2 + - - +
238A VAL* 2.9 23.5 + - + +
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Residues in contact with ASN 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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103A SER* 3.7 16.3 - - - -
104A LYS* 2.9 53.4 + - - +
231A GLY 3.0 18.3 + - - +
232A ASN* 3.6 6.7 + - - +
234A VAL* 1.3 78.4 - - - +
236A LEU* 1.3 69.6 + - - +
238A VAL* 3.2 2.8 + - - +
239A LEU* 3.0 36.5 + - - +
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Residues in contact with LEU 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 ASN* 3.0 44.0 + - - +
233A ALA* 3.8 7.4 - - - +
235A ASN* 1.3 84.0 - - - +
237A ALA* 1.3 56.9 + - - +
239A LEU* 3.3 14.5 + - + +
240A LYS* 2.9 29.6 + - - +
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Residues in contact with ALA 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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43A ILE* 4.6 13.9 - - + -
46A HIS* 4.1 20.6 - - + -
47A CYS* 3.9 17.7 - - - -
233A ALA 2.9 17.8 + - - +
234A VAL* 3.5 5.6 - - - +
236A LEU* 1.3 73.8 - - - +
238A VAL* 1.3 59.9 + - - +
240A LYS* 3.2 6.5 + - - +
241A LEU* 2.9 38.4 + - + +
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Residues in contact with VAL 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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39A LEU* 5.6 2.2 - - + -
43A ILE* 4.4 11.0 - - + -
103A SER* 3.9 10.1 - - - +
104A LYS* 3.7 23.6 - - + +
105A PRO 4.0 7.0 - - - +
106A PHE* 4.0 21.8 - - + -
222A ILE* 3.8 28.9 - - + -
234A VAL 2.9 18.0 + - - +
235A ASN* 3.6 7.9 - - - +
237A ALA* 1.3 75.3 - - - +
239A LEU* 1.3 60.7 + - + +
241A LEU* 3.8 7.4 - - - +
242A ASN* 2.9 28.8 + - + +
247A LEU* 4.1 5.7 - - + +
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Residues in contact with LEU 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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104A LYS* 4.1 24.9 - - + -
105A PRO 6.0 1.1 - - - +
235A ASN* 3.0 36.7 + - - +
236A LEU* 3.7 18.4 - - + +
237A ALA 3.2 0.2 - - - -
238A VAL* 1.3 77.9 - - + +
240A LYS* 1.3 57.9 + - - +
242A ASN* 3.4 10.7 + - + +
243A GLU* 2.9 47.3 + - - +
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Residues in contact with LYS 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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46A HIS* 3.7 31.1 - - + +
236A LEU 2.9 17.6 + - - +
237A ALA* 3.2 6.7 + - - +
239A LEU* 1.3 76.8 - - - +
241A LEU* 1.3 58.7 + - + +
243A GLU* 3.2 7.3 + - - +
244A GLN* 2.9 59.5 + - + +
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Residues in contact with LEU 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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39A LEU* 3.9 21.1 - - + -
42A GLU* 3.9 29.8 - - + +
43A ILE* 4.2 15.3 - - + +
46A HIS* 3.7 30.7 - - + +
237A ALA* 2.9 26.0 + - + +
238A VAL* 3.9 4.3 - - - +
240A LYS* 1.3 73.1 - - + +
242A ASN* 1.3 62.7 + - - +
244A GLN* 3.6 11.8 + - - +
245A GLY 3.4 2.3 + - - -
246A LEU* 3.0 42.7 + - + +
247A LEU* 3.5 16.1 + - + -
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Residues in contact with ASN 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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105A PRO 5.2 1.6 + - - +
238A VAL* 2.9 20.0 + - + +
239A LEU* 3.6 11.9 - - + +
241A LEU* 1.3 76.5 - - - +
243A GLU* 1.3 60.9 - - + +
245A GLY* 3.0 20.8 + - - -
247A LEU* 3.6 15.0 + - + +
248A ASP* 4.6 6.2 - - - +
306A TOE 3.2 53.4 - - - +
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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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239A LEU* 2.9 34.1 + - - +
240A LYS* 3.8 6.3 - - - +
242A ASN* 1.3 78.2 - - + +
244A GLN* 1.3 60.4 + - + +
245A GLY 3.7 0.3 + - - -
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Residues in contact with GLN 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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46A HIS* 4.5 8.4 + - - -
240A LYS* 2.9 45.1 + - + +
241A LEU* 4.0 20.0 - - - +
242A ASN 3.2 0.4 - - - -
243A GLU* 1.3 76.0 - - + +
245A GLY* 1.3 59.7 + - - +
246A LEU* 3.7 6.2 + - + +
249A LYS* 5.7 1.2 - - - +
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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