Contacts of the helix formed by residues 285 - 297 (chain A) in PDB entry 3T5D
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 285 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281A VAL* 2.9 31.7 + - + +
284A ASN* 1.3 86.8 - - + +
286A HIS* 1.3 69.6 + - + +
287A TYR 3.4 1.3 - - - -
288A GLU* 3.5 0.9 + - - +
289A ASN* 2.9 51.4 + - - +
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Residues in contact with HIS 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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119A PHE* 4.0 11.8 - - + -
165A HIS 3.4 24.2 - - - -
166A GLU* 3.4 26.6 + - - +
167A LYS 4.0 16.8 - - - +
168A VAL* 3.5 14.5 + - - -
169A ASN* 2.8 37.1 + - - -
281A VAL* 3.4 12.0 + - + +
282A THR* 3.5 25.4 - - + +
285A VAL* 1.3 82.6 - - + +
287A TYR* 1.3 61.6 + - - +
289A ASN* 3.7 3.7 + - - +
290A TYR* 3.3 20.4 + - - +
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Residues in contact with TYR 287 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119A PHE* 3.6 51.3 - + + -
122A TYR* 3.3 24.9 - + + -
123A LEU* 3.3 25.5 - - + +
126A GLU* 2.9 34.0 + - - -
138A ARG* 3.3 24.9 - - - +
282A THR 2.9 20.4 + - - +
283A ASN* 3.6 9.2 - - - +
286A HIS* 1.3 72.4 - - - +
288A GLU* 1.3 82.2 + - - +
290A TYR* 3.3 7.2 + + - +
291A ARG* 2.9 30.2 + - + +
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Residues in contact with GLU 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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126A GLU* 5.4 0.7 - - - +
283A ASN* 3.5 11.7 - - - +
284A ASN* 3.3 28.3 - - - +
285A VAL 3.5 2.1 + - - +
286A HIS 3.4 0.2 - - - -
287A TYR* 1.3 94.9 - - - +
289A ASN* 1.3 62.1 + - - +
291A ARG* 3.6 24.8 + - - +
292A SER* 3.0 35.1 + - - +
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Residues in contact with ASN 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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166A GLU* 5.1 13.2 + - + +
285A VAL* 2.9 42.5 + - - +
286A HIS* 4.0 5.5 + - - +
288A GLU* 1.3 75.0 - - - +
290A TYR* 1.3 64.0 + - - +
292A SER* 3.7 6.9 + - - +
293A ARG* 3.2 23.9 + - - +
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Residues in contact with TYR 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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116A ASP* 3.4 39.2 + - + +
119A PHE* 3.5 41.3 - + + -
120A GLU* 3.3 28.5 - - - +
123A LEU* 4.1 14.7 - - + +
167A LYS* 5.0 5.2 - - - +
286A HIS 3.3 12.4 + - - +
287A TYR* 3.3 13.8 + + - +
289A ASN* 1.3 78.8 - - - +
291A ARG* 1.3 67.6 + - - +
293A ARG* 3.3 8.5 + - - +
294A LYS* 3.1 63.4 + - + +
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Residues in contact with ARG 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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123A LEU* 3.7 24.8 - - + +
126A GLU* 3.9 22.5 + - - -
287A TYR* 2.9 23.3 + - + +
288A GLU* 3.6 28.7 + - - +
289A ASN 3.3 0.2 - - - -
290A TYR* 1.3 83.0 - - + +
292A SER* 1.3 66.8 + - - +
294A LYS* 3.6 0.9 + - - +
295A LEU* 3.4 47.1 + - + +
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Residues in contact with SER 292 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288A GLU* 3.0 21.2 + - - +
289A ASN* 4.1 6.5 + - - -
291A ARG* 1.3 82.6 + - - +
293A ARG* 1.3 61.0 + - - +
295A LEU* 5.2 1.6 - - - -
296A ALA* 3.4 27.0 + - - +
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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
----------------------------------------------------------
116A ASP* 4.9 1.0 + - - -
167A LYS* 3.4 28.9 - - - +
289A ASN 3.2 18.8 + - - +
290A TYR* 3.6 9.1 - - - +
291A ARG 3.2 0.2 - - - -
292A SER* 1.3 79.1 - - - +
294A LYS* 1.3 85.9 + - + +
295A LEU 3.4 1.0 + - - -
296A ALA* 4.5 1.5 - - - +
297A ALA* 3.8 20.8 + - - +
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Residues in contact with LYS 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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116A ASP* 5.4 5.3 + - - +
123A LEU* 4.9 10.1 - - + -
290A TYR* 3.1 60.6 + - + +
291A ARG 4.4 2.0 - - - +
292A SER 3.5 0.2 - - - -
293A ARG* 1.3 100.6 - - + +
295A LEU* 1.3 61.9 + - - +
297A ALA* 4.8 7.4 + - - +
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Residues in contact with LEU 295 (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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123A LEU* 4.6 17.7 - - + -
291A ARG* 3.4 56.2 + - + +
292A SER* 4.8 2.0 - - - +
293A ARG 3.3 0.4 - - - -
294A LYS* 1.3 82.8 - - - +
296A ALA* 1.3 64.2 + - - +
297A ALA 3.4 5.1 - - - -
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Residues in contact with ALA 296 (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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292A SER 3.4 19.8 + - - +
293A ARG* 3.9 2.2 + - - +
295A LEU* 1.3 80.8 - - - +
297A ALA* 1.3 63.4 + - - +
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Residues in contact with ALA 297 (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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293A ARG 3.8 14.0 + - - +
294A LYS* 5.3 6.3 - - - +
295A LEU 3.4 6.0 - - - +
296A ALA* 1.3 83.9 - - - +
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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