Contacts of the strand formed by residues 234 - 244 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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91A ARG 4.6 1.4 - - - +
92A LYS* 3.4 27.0 - - - +
93A HIS* 3.5 19.3 + - + +
151A CYS* 3.8 1.0 - - - -
152A LYS* 3.0 59.9 + - + +
154A SER* 4.2 4.6 - - - -
203A TRP* 3.6 25.0 + - + -
228A ILE* 5.5 0.2 - - - -
231A PRO 5.3 1.6 - - - +
232A ASP 3.5 8.2 + - - +
233A GLN* 1.3 76.8 - - - +
235A PHE* 1.3 65.0 + - - +
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Residues in contact with PHE 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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89A VAL* 4.6 1.3 - - + -
91A ARG* 4.0 4.7 - - - -
92A LYS 3.1 26.4 + - - -
94A TRP* 3.1 42.7 + + + -
95A TRP 5.3 0.7 - - - -
107A PHE* 4.1 12.1 - + - -
111A MSE 3.6 29.4 - - + -
149A TYR* 3.4 31.6 - + + +
150A HIS 3.2 12.8 - - - +
203A TRP* 4.1 2.7 - - - -
223A ILE* 5.2 1.6 - - + -
225A PRO* 3.9 24.2 - - + -
228A ILE* 3.7 26.2 - - + -
233A GLN 5.7 0.4 - - - -
234A GLU* 1.3 75.9 - - - +
236A GLY* 1.3 60.8 + - - +
237A VAL* 4.0 22.0 - - + -
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Residues in contact with GLY 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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89A VAL* 3.3 13.0 - - - -
90A PRO 4.1 0.7 - - - -
91A ARG* 4.0 11.4 - - - -
149A TYR* 3.6 2.8 - - - -
150A HIS* 2.8 45.5 + - - +
203A TRP* 4.2 1.2 - - - -
235A PHE* 1.3 77.3 - - - +
237A VAL* 1.3 67.8 + - - +
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Residues in contact with VAL 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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88A ASN* 2.9 9.3 - - - +
89A VAL* 2.7 55.3 + - + +
117A PHE* 4.5 7.4 - - + -
147A ILE* 3.6 29.2 - - + -
148A THR 3.3 5.4 - - - +
149A TYR* 4.6 2.0 - - + -
150A HIS* 4.4 2.8 - - - -
223A ILE* 4.3 22.4 - - + -
235A PHE* 4.0 20.2 - - + -
236A GLY* 1.3 79.1 - - - +
238A ASP* 1.3 61.5 - - - +
239A VAL* 3.9 16.8 - - + -
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Residues in contact with ASP 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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87A LEU* 4.0 2.9 - - - +
88A ASN* 3.3 25.1 + - - +
147A ILE* 3.6 2.3 - - - +
148A THR* 2.9 47.1 + - - +
150A HIS* 2.6 30.9 + - - -
237A VAL* 1.3 71.9 - - - +
239A VAL* 1.3 63.9 + - - +
240A GLY 3.5 2.1 + - - -
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Residues in contact with VAL 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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84A ALA* 3.5 22.9 + - + +
86A PRO 4.9 1.3 - - - +
87A LEU* 3.0 30.4 + - - +
88A ASN* 4.9 3.1 - - - -
89A VAL* 5.3 0.2 - - + -
117A PHE* 3.8 41.3 - - + -
119A TYR* 3.4 25.1 - - - +
145A GLN* 3.5 5.2 - - - +
147A ILE* 3.8 11.2 - - + -
237A VAL* 4.0 9.9 - - + -
238A ASP* 1.3 72.3 - - - +
240A GLY* 1.3 71.5 + - - +
241A PRO* 3.9 1.4 - - - +
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Residues in contact with GLY 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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84A ALA* 4.6 1.0 - - - +
119A TYR* 4.3 1.7 - - - -
145A GLN* 2.8 27.1 + - - -
146A GLN* 2.8 30.5 + - - -
238A ASP 3.5 3.4 + - - -
239A VAL* 1.3 79.0 - - - +
241A PRO* 1.3 70.4 - - - +
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Residues in contact with PRO 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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72A PHE* 6.5 0.2 - - + -
81A CYS* 4.0 16.8 - - + +
82A ILE 3.1 31.0 - - - +
83A SER* 4.0 13.7 - - - +
84A ALA 4.8 0.2 - - - +
87A LEU* 6.5 0.9 - - + -
144A SER 3.9 2.4 - - - +
145A GLN* 3.4 11.1 - - - +
146A GLN 4.5 0.9 + - - -
239A VAL 4.4 1.1 - - - +
240A GLY* 1.3 87.2 - - - +
242A VAL* 1.3 63.3 + - - +
243A CYS* 3.5 11.0 + - - -
1246A GOL 5.7 4.0 - - - +
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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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80A THR 3.4 2.8 - - - +
81A CYS* 3.3 1.0 - - - -
82A ILE* 2.8 41.4 + - + +
119A TYR* 3.8 17.9 - - + -
133A LEU* 4.6 3.1 - - + -
144A SER 3.7 7.6 - - - +
145A GLN* 3.8 15.8 - - - +
218A LEU* 4.0 25.4 - - + -
219A PRO* 3.9 12.1 - - + -
240A GLY 3.8 1.8 + - - -
241A PRO* 1.3 71.7 - - - +
243A CYS* 1.3 62.7 + - - +
244A PHE* 3.5 38.2 + - + -
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Residues in contact with CYS 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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79A GLU* 3.8 19.2 - - + +
80A THR 3.3 3.1 - - - -
81A CYS* 2.1 48.0 - - - -
143A ALA* 3.1 6.3 - - - +
144A SER* 2.8 44.0 + - - +
241A PRO* 3.9 13.9 - - - -
242A VAL* 1.3 75.1 - - - +
244A PHE* 1.3 62.1 + - - +
1246A GOL 3.8 20.4 - - - -
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Residues in contact with PHE 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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78A GLY 4.2 0.2 - - - +
79A GLU* 3.2 5.6 - - - -
80A THR* 2.7 49.0 + - - +
82A ILE* 3.9 13.5 - - + -
133A LEU* 3.9 11.9 - - + -
136A LEU* 3.7 40.4 - - + -
137A ARG* 3.8 37.7 - - + -
140A SER* 3.4 15.5 - - - +
142A ARG 3.6 1.8 - - - -
143A ALA* 3.8 21.3 - - + -
215A ALA* 4.3 4.5 - - + -
218A LEU 4.9 2.0 - - - -
219A PRO* 4.9 0.2 - - + -
242A VAL* 3.5 35.4 - - + -
243A CYS* 1.3 73.8 - - - +
245A LEU* 1.3 61.8 + - - +
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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