Contacts of the strand formed by residues 284 - 294 (chain A) in PDB entry 4G83
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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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121A TYR* 4.0 28.4 + - + -
276A THR* 4.5 19.5 - - + -
277A LEU 3.9 4.3 - - - +
278A GLU* 4.5 7.0 - - + +
282A GLY 4.1 8.3 - - - +
283A GLN* 1.3 76.4 + - - +
285A LEU* 1.3 58.9 + - - +
286A GLY 3.4 29.8 - - - +
287A ARG* 4.2 11.9 - - + +
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Residues in contact with LEU 285 (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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121A TYR* 5.0 3.1 - - - -
123A GLY* 2.8 24.7 - - - -
124A PRO* 3.1 16.3 - - + +
125A HIS* 4.5 12.4 + - + +
127A PHE* 4.9 0.2 - - - +
169A PRO 4.0 20.2 - - - +
170A PRO* 4.1 10.8 - - + -
173A THR* 4.4 5.2 - - + -
277A LEU* 2.9 28.5 + - + +
278A GLU 4.2 0.7 - - - -
279A MET* 3.2 43.5 - - + +
283A GLN* 3.2 17.7 - - + +
284A VAL* 1.3 74.3 - - - +
286A GLY* 1.3 58.0 + - - +
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Residues in contact with GLY 286 (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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121A TYR* 3.4 9.0 - - - -
123A GLY* 3.9 0.9 - - - -
127A PHE* 3.6 25.6 - - - -
276A THR* 3.6 1.0 - - - -
277A LEU* 3.0 28.4 + - - +
284A VAL* 3.4 10.1 - - - +
285A LEU* 1.3 81.0 - - - +
287A ARG* 1.3 65.3 + - - +
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Residues in contact with ARG 287 (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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117A SER* 2.0 62.1 + - - +
118A ASN* 3.1 4.2 - - - +
119A THR* 2.9 34.9 + - - +
121A TYR* 2.5 53.1 + - + +
127A PHE* 3.3 8.8 - - - -
274A ILE* 5.0 14.8 - - + +
275A ILE 3.7 3.8 - - - +
276A THR* 3.9 23.3 - - + +
284A VAL* 4.2 9.6 - - + +
286A GLY* 1.3 78.5 - - - +
288A ARG* 1.3 80.3 + - - +
289A SER* 5.7 1.8 - - - -
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Residues in contact with ARG 288 (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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120A ASP* 3.0 34.7 + - - +
122A PRO* 3.1 39.7 - - - +
126A HIS* 5.9 1.6 - - - -
127A PHE* 2.5 30.9 + - + -
128A GLU* 4.3 16.5 - - - +
129A VAL* 3.3 47.1 - - + +
149A LYS* 3.9 11.4 - - - +
274A ILE* 4.1 0.5 - - - -
275A ILE* 3.2 30.5 + - - +
287A ARG* 1.3 95.5 + - - +
289A SER* 1.3 69.9 + - - +
290A PHE* 5.7 0.2 - - - -
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Residues in contact with SER 289 (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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118A ASN 4.7 11.0 - - - -
119A THR 5.2 1.1 - - - -
120A ASP* 3.2 20.2 + - - +
149A LYS* 2.8 32.6 + - - -
272A LEU* 3.9 21.0 - - - +
273A ILE 3.8 11.2 + - - -
274A ILE* 4.6 8.1 - - - +
287A ARG* 5.7 2.5 - - - -
288A ARG* 1.3 82.6 - - - +
290A PHE* 1.3 77.4 + - - +
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Residues in contact with PHE 290 (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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129A VAL* 4.4 15.9 - - + -
131A PHE* 3.6 33.7 - + - -
144A TYR* 4.5 5.6 - + + -
149A LYS* 3.4 27.8 - - + +
151A LEU* 4.5 21.8 - - + -
161A ILE* 5.2 9.6 - - + -
256A PHE* 5.6 2.7 - + - -
272A LEU* 3.2 5.5 - - - +
273A ILE* 2.8 67.0 + - + -
275A ILE* 4.4 17.3 - - + -
288A ARG 6.1 0.2 - - - -
289A SER* 1.3 84.1 + - - +
291A GLU* 1.3 67.6 + - - +
292A GLY 5.2 0.2 - - - -
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Residues in contact with GLU 291 (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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148A LEU* 2.8 33.3 - - - +
149A LYS 3.4 11.9 - - - +
150A LYS* 3.0 40.8 + - + +
151A LEU 3.0 23.2 + - - -
182A LYS* 5.8 7.3 - - + +
270A PRO* 5.0 11.3 - - + +
271A ILE 3.2 12.1 - - - +
272A LEU* 3.8 14.3 - - + +
290A PHE* 1.3 73.7 - - - +
292A GLY* 1.3 59.8 + - - +
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Residues in contact with GLY 292 (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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150A LYS* 4.8 1.7 - - - +
151A LEU* 3.8 9.2 - - - -
260A SER* 3.7 2.6 + - - -
270A PRO* 4.8 3.1 - - - +
271A ILE* 2.2 63.5 + - - +
272A LEU* 4.2 0.4 - - - +
273A ILE* 4.5 8.6 - - - +
290A PHE* 3.8 2.8 + - - -
291A GLU* 1.3 69.7 - - - +
293A ARG* 1.3 61.0 + - - +
294A ILE* 4.4 2.0 - - - -
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Residues in contact with ARG 293 (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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150A LYS* 4.3 11.2 - - + +
151A LEU 2.9 21.1 + - - +
152A TYR* 3.2 33.5 - - + +
153A CYS 3.1 14.7 + - - -
260A SER* 3.4 17.4 - - - +
291A GLU 4.3 0.4 + - - -
292A GLY* 1.3 73.7 - - - +
294A ILE* 1.3 65.9 + - - +
295A CYS* 3.8 16.5 + - - +
301A ASP* 2.5 37.7 + - - +
305A ASP* 4.4 9.4 + - - -
415F G 3.1 50.6 + - - -
416F G 4.7 0.6 + - - -
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Residues in contact with ILE 294 (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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153A CYS* 3.4 18.8 - - + +
154A GLN 4.0 3.8 - - - +
155A ILE* 4.0 17.7 - - + +
214A LEU* 5.3 1.1 - - + -
256A PHE* 3.9 37.0 - - + -
258A CYS 3.7 21.8 - - - +
259A ASN* 3.0 37.2 - - - +
260A SER* 3.0 22.1 + - - +
266A MET* 4.7 4.5 - - + -
271A ILE* 3.9 27.8 - - + -
292A GLY* 4.4 0.4 - - - -
293A ARG* 1.3 79.6 - - - +
295A CYS* 1.3 57.5 + - - +
416F G 4.3 0.5 + - - -
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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