Contacts of the strand formed by residues 234 - 244 (chain C) in PDB entry 4AEJ
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 GLU 234 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91C ARG 4.8 1.6 - - - +
92C LYS* 3.6 12.7 + - - +
93C HIS* 3.7 27.7 - - + +
94C TRP 5.3 0.4 - - - +
152C LYS* 3.0 53.6 + - + +
154C SER* 3.8 7.3 - - - -
203C TRP* 3.1 31.9 + - + -
228C ILE* 5.7 0.2 - - - -
231C PRO 5.1 3.7 - - - +
232C ASP 4.1 5.9 - - - +
233C GLN* 1.3 79.7 - - - +
235C PHE* 1.3 68.8 + - - +
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Residues in contact with PHE 235 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89C VAL* 4.6 4.9 - - + -
91C ARG* 4.1 5.4 - - - -
92C LYS 3.0 24.2 + - - -
94C TRP* 3.1 44.4 - + + -
95C TRP 5.3 1.1 - - - -
107C PHE* 4.5 9.6 - + + -
111C MSE 3.8 24.9 - - + -
149C TYR* 3.4 39.9 - + + +
150C HIS 3.0 15.9 - - - +
203C TRP* 3.9 4.5 - - - -
223C ILE* 5.3 1.3 - - + -
225C PRO* 3.9 19.1 - - + -
228C ILE* 4.2 15.7 - - + -
234C GLU* 1.3 81.2 - - - +
236C GLY* 1.3 68.3 + - - +
237C VAL* 4.1 14.4 - - + -
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Residues in contact with GLY 236 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89C VAL* 3.4 13.9 - - - -
90C PRO 3.8 8.1 - - - -
91C ARG* 4.1 4.9 - - - -
149C TYR* 3.7 2.3 - - - -
150C HIS* 2.8 43.0 + - - +
203C TRP* 4.3 0.8 - - - -
235C PHE* 1.3 79.4 - - - +
237C VAL* 1.3 66.3 + - - +
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Residues in contact with VAL 237 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88C ASN* 3.1 9.0 - - - +
89C VAL* 2.8 54.3 + - + +
117C PHE* 4.9 1.6 - - + -
147C ILE* 3.5 33.7 - - + -
148C THR 3.2 12.1 - - - +
149C TYR* 4.6 1.6 - - + -
150C HIS* 4.4 2.2 - - - -
223C ILE* 4.2 23.8 - - + -
235C PHE* 4.1 18.2 - - + -
236C GLY* 1.3 79.6 - - - +
238C ASP* 1.3 69.7 + - - +
239C VAL* 3.9 6.3 - - + -
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Residues in contact with ASP 238 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87C LEU 4.1 4.0 - - - +
88C ASN* 3.5 15.6 + - - +
147C ILE* 3.6 0.7 - - - -
148C THR* 2.8 49.5 + - - +
150C HIS* 2.5 32.8 + - - -
237C VAL* 1.3 78.7 - - - +
239C VAL* 1.3 65.0 + - - +
240C GLY 3.5 2.3 + - - -
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Residues in contact with VAL 239 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84C ALA* 4.1 19.6 + - + +
86C PRO 5.0 1.1 - - - +
87C LEU* 3.1 33.6 + - - +
88C ASN* 5.3 1.8 - - - -
89C VAL* 5.3 0.9 - - + -
117C PHE* 3.9 40.6 - - + -
119C TYR* 3.3 15.0 - - - +
145C GLN* 3.3 24.9 - - - +
146C GLN 4.8 0.2 - - - +
147C ILE* 4.1 19.7 - - + -
220C ILE* 5.5 1.1 - - + -
237C VAL* 4.1 7.2 - - + +
238C ASP* 1.3 72.2 - - - +
240C GLY* 1.3 62.4 + - - +
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Residues in contact with GLY 240 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84C ALA 5.4 0.7 - - - -
119C TYR* 4.6 1.9 - - - -
145C GLN* 2.8 24.6 - - - +
146C GLN* 3.1 24.9 + - - -
238C ASP* 3.5 4.6 + - - -
239C VAL* 1.3 75.8 - - - +
241C PRO* 1.3 74.4 - - - +
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Residues in contact with PRO 241 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72C PHE* 6.0 3.4 - - + -
81C CYS* 3.9 18.8 - - + -
82C ILE 3.2 22.9 - - - +
83C SER* 4.1 13.4 - - - +
84C ALA 4.9 0.7 - - - +
87C LEU* 6.3 2.7 - - + -
144C SER 4.0 1.9 - - - +
145C GLN* 3.4 10.6 - - - +
146C GLN 4.5 1.6 + - - -
239C VAL 4.8 0.7 - - - +
240C GLY* 1.3 87.3 - - - +
242C VAL* 1.3 62.1 + - - +
243C CYS* 3.7 17.8 + - - -
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Residues in contact with VAL 242 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80C THR 3.6 1.4 - - - +
81C CYS* 3.2 1.4 - - - -
82C ILE* 2.8 47.5 + - + +
119C TYR* 4.0 10.7 - - + -
133C LEU* 5.1 1.1 - - + -
143C ALA* 5.1 0.2 - - + -
144C SER 3.7 8.7 - - - +
145C GLN* 4.0 10.0 + - - +
218C LEU* 3.9 16.2 - - + -
219C PRO* 3.6 43.1 - - + -
240C GLY 3.6 1.2 + - - -
241C PRO* 1.3 72.3 - - - +
243C CYS* 1.3 62.5 + - - +
244C PHE* 4.0 28.2 - - + -
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Residues in contact with CYS 243 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79C GLU* 3.7 21.8 - - - +
80C THR 3.2 2.9 - - - -
81C CYS* 2.1 46.9 - - - -
143C ALA* 3.1 5.6 - - - +
144C SER* 2.8 46.5 + - - +
241C PRO* 3.9 16.8 - - - -
242C VAL* 1.3 76.2 - - - +
244C PHE* 1.3 61.1 + - - +
245C LEU 4.4 0.2 + - - -
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Residues in contact with PHE 244 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78C GLY 4.4 0.7 - - - +
79C GLU* 3.3 4.8 - - - -
80C THR* 2.8 47.4 + - - +
82C ILE* 4.0 21.3 - - + -
133C LEU* 4.3 14.4 - - + -
136C LEU* 4.1 30.7 - - + +
137C ARG* 4.0 28.7 - - + -
140C SER* 3.1 22.9 - - - +
142C ARG 3.6 2.9 - - - -
143C ALA* 3.7 22.0 - - + -
215C ALA* 4.0 14.4 - - + -
218C LEU 4.7 4.9 - - - -
219C PRO 5.2 0.2 - - - -
242C VAL* 4.0 27.6 - - + -
243C CYS* 1.3 74.6 - - - +
245C LEU* 1.3 59.2 + - - +
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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