Contacts of the strand formed by residues 284 - 294 (chain E) in PDB entry 4A63
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 VAL 284 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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121E TYR* 4.1 23.1 + - + -
276E THR* 5.0 1.8 - - - -
277E LEU 3.9 3.8 - - - +
278E GLU* 4.6 9.6 - - + +
282E GLY 4.1 9.4 - - - +
283E GLN* 1.3 74.1 - - - +
285E LEU* 1.4 63.5 + - - +
286E GLY 3.6 22.0 - - - +
287E ARG* 3.6 35.2 - - + +
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Residues in contact with LEU 285 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121E TYR* 3.7 7.6 - - - -
122E PRO 4.0 2.3 - - - +
123E GLY* 3.4 22.5 - - - -
124E PRO* 3.5 29.6 - - + +
125E HIS* 4.0 12.3 + - + +
169E PRO* 4.5 4.5 - - + -
170E PRO* 3.9 17.0 - - + -
173E THR* 4.0 20.0 - - + +
277E LEU* 2.8 25.4 + - + +
278E GLU 4.2 0.2 - - - -
279E MET* 3.5 45.3 - - + +
283E GLN 3.7 0.2 + - - -
284E VAL* 1.4 74.3 - - - +
286E GLY* 1.3 56.1 + - - +
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Residues in contact with GLY 286 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121E TYR* 3.2 16.5 - - - -
122E PRO 4.3 0.2 - - - -
127E PHE* 3.8 17.0 - - - -
276E THR* 3.4 4.7 - - - -
277E LEU* 2.9 32.0 + - - +
284E VAL* 3.6 6.6 - - - +
285E LEU* 1.3 78.4 - - - +
287E ARG* 1.3 62.7 + - - +
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Residues in contact with ARG 287 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117E SER* 3.4 46.6 + - - +
118E ASN 4.0 4.7 - - - -
119E THR 3.6 20.7 + - - +
120E ASP* 4.2 1.1 - - - -
121E TYR* 2.6 41.0 + - + +
127E PHE* 3.7 3.5 - - - -
274E ILE* 3.5 12.5 - - + +
275E ILE 3.3 6.3 - - - +
276E THR* 2.6 48.8 + - + +
278E GLU* 5.5 1.0 + - - -
284E VAL* 3.6 30.6 - - + +
286E GLY* 1.3 72.9 - - - +
288E ARG* 1.3 74.9 + - - +
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Residues in contact with ARG 288 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120E ASP* 3.4 30.1 + - - +
122E PRO* 3.5 34.8 - - - +
126E HIS 5.2 0.2 - - - -
127E PHE* 2.7 33.3 + - + +
128E GLU* 4.0 18.2 - - - +
129E VAL* 3.7 39.7 - - + +
274E ILE* 3.9 0.2 - - - -
275E ILE* 2.8 34.9 + - - +
287E ARG* 1.3 84.3 + - - +
289E SER* 1.3 61.3 + - - +
290E PHE* 5.0 2.2 - - + -
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Residues in contact with SER 289 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118E ASN* 2.8 42.7 + - - +
120E ASP* 3.2 17.0 + - - +
149E LYS* 5.3 3.5 - - - +
272E LEU* 4.7 8.0 - - - +
273E ILE 3.2 13.5 - - - -
274E ILE* 4.1 9.6 - - - -
288E ARG* 1.3 74.6 - - - +
290E PHE* 1.3 67.8 + - - +
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Residues in contact with PHE 290 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129E VAL* 3.9 18.4 - - + -
131E PHE* 3.7 28.0 - + - -
144E TYR* 4.4 8.7 - + + +
149E LYS* 3.5 21.3 - - + +
151E LEU* 4.0 17.5 - - + -
161E ILE* 3.8 17.3 - - + -
272E LEU* 3.3 10.6 - - - +
273E ILE* 2.8 62.9 + - + +
275E ILE* 3.9 21.8 - - + -
288E ARG* 4.9 1.6 - - + -
289E SER* 1.3 81.8 - - - +
291E GLU* 1.3 73.3 + - - +
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Residues in contact with GLU 291 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148E LEU 5.2 3.0 - - - +
149E LYS 3.0 16.0 + - - +
150E LYS* 3.4 39.5 + - + +
151E LEU 2.8 25.4 + - - -
182E LYS* 3.2 36.3 + - + +
270E PRO* 3.7 17.5 - - - +
271E ILE 3.2 19.3 - - - +
272E LEU* 4.0 8.6 - - + +
290E PHE* 1.3 81.0 - - - +
292E GLY* 1.3 64.2 + - - +
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Residues in contact with GLY 292 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150E LYS* 5.1 0.2 - - - -
151E LEU* 3.4 6.1 - - - -
260E SER* 4.4 2.6 + - - -
270E PRO* 5.1 2.1 - - - +
271E ILE* 2.9 36.6 + - - +
273E ILE* 3.7 25.2 - - - +
290E PHE 3.8 1.4 + - - -
291E GLU* 1.3 81.2 - - - +
293E ARG* 1.3 61.3 + - - +
294E ILE* 4.7 3.1 - - - -
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Residues in contact with ARG 293 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150E LYS* 3.9 21.8 - - - +
151E LEU 2.7 13.3 + - - +
152E TYR* 3.2 24.2 - - + -
153E CYS 2.8 31.5 + - - +
260E SER* 3.7 21.4 - - - +
261E SER* 5.8 0.8 - - - +
268E ARG 5.8 1.6 + - - -
292E GLY* 1.3 74.8 - - - +
294E ILE* 1.3 60.1 + - - +
295E CYS* 3.6 20.7 + - + +
301E ASP* 2.7 32.2 + - - -
305E ASP* 4.9 1.8 - - - -
1094F GLU* 4.1 25.7 + - - +
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Residues in contact with ILE 294 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151E LEU* 5.6 1.3 - - + +
153E CYS* 3.2 17.3 - - + +
154E GLN 4.0 1.8 - - - -
155E ILE* 3.7 24.9 - - - +
214E LEU* 5.1 0.4 - - + -
256E PHE* 3.5 43.7 - - + +
258E CYS 3.3 27.8 - - - +
259E ASN* 3.5 7.5 - - - +
260E SER* 2.8 41.3 + - - +
261E SER* 4.6 0.5 + - - -
266E MET* 4.5 12.3 - - + -
271E ILE* 5.2 4.9 - - + -
273E ILE* 5.2 1.3 - - + -
292E GLY* 4.7 5.6 - - - -
293E ARG* 1.3 83.3 - - - +
295E CYS* 1.3 61.4 + - - +
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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