Contacts of the strand formed by residues 283 - 290 (chain G) in PDB entry 1R8Y
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 TYR 283 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137G GLY* 4.5 3.0 - - - -
138G ASN* 4.1 22.1 - - + +
173G ASP* 3.6 18.6 - - - +
174G HIS 3.8 2.7 - - - -
175G ARG* 4.2 33.7 + - - -
190G LYS* 4.2 5.6 - - + -
191G ASN* 3.8 35.6 + - - +
192G ILE* 3.1 41.1 - - + -
193G TYR* 3.8 18.4 - + - +
268G GLY 2.6 27.2 - - - +
269G ASP* 3.0 5.9 + - - +
281G PRO* 3.4 9.2 - - - +
282G CYS* 1.3 85.8 - - + +
284G PHE* 1.3 61.8 + - - +
285G ILE* 4.1 2.7 - - + -
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Residues in contact with PHE 284 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173G ASP* 3.2 2.8 - - - +
174G HIS* 2.8 65.5 + + + +
176G ASN* 3.5 44.4 - - + -
178G ASP* 4.2 3.8 - - + -
247G LEU* 3.8 35.9 - - + -
266G VAL* 5.3 2.9 - - + -
267G LEU 3.6 13.7 - - - -
273G TYR* 3.7 47.8 - + + -
281G PRO* 3.8 9.9 - - + -
283G TYR* 1.3 75.4 - - - +
285G ILE* 1.3 63.6 + - - +
286G HIS* 3.9 3.0 + - + +
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Residues in contact with ILE 285 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47G TRP* 3.7 29.4 - - + -
136G LEU* 4.3 8.1 - - + -
171G VAL* 3.8 16.4 - - + -
172G ILE 4.6 0.4 - - - +
173G ASP* 3.9 4.5 - - + -
192G ILE* 4.5 2.0 - - + -
193G TYR* 3.7 20.0 - - - +
265G SER 3.8 0.5 - - - +
266G VAL* 3.5 2.0 - - - -
267G LEU* 2.6 50.2 + - + +
268G GLY 4.9 1.1 - - - +
269G ASP 3.7 13.9 - - - +
270G PHE* 3.6 40.8 - - + -
283G TYR* 4.8 3.6 - - + -
284G PHE* 1.3 79.5 - - - +
286G HIS* 1.3 64.2 + - - +
287G VAL* 5.3 0.4 - - + -
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Residues in contact with HIS 286 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170G LEU 3.4 2.0 - - - +
171G VAL* 3.3 3.3 - - - +
172G ILE* 2.8 50.2 + - + +
174G HIS* 3.0 30.0 + + - -
247G LEU* 3.6 15.0 - - + +
250G PHE* 3.2 31.9 - + + -
251G THR* 3.7 11.7 - - - -
254G VAL* 4.8 0.4 - - + -
264G HIS* 3.3 22.1 - + + -
265G SER 3.6 3.1 - - - -
266G VAL* 3.5 24.5 - - + +
284G PHE* 4.1 4.1 - - + +
285G ILE* 1.3 76.1 - - - +
287G VAL* 1.3 60.9 + - - +
288G LEU* 4.1 16.2 - - + -
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Residues in contact with VAL 287 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47G TRP* 5.3 0.2 - - + -
51G LEU* 4.2 30.5 - - + -
55G HIS* 5.1 3.6 - - + -
169G LEU* 4.2 19.7 - - + -
170G LEU 3.3 4.9 - - - +
171G VAL* 4.5 5.8 - - + -
263G GLN 3.8 1.7 - - - +
264G HIS* 3.8 0.5 - - - -
265G SER* 3.1 45.5 + - - +
267G LEU* 4.3 26.9 - - + -
285G ILE* 4.8 1.8 - - + +
286G HIS* 1.3 75.0 - - - +
288G LEU* 1.3 70.0 + - - +
289G LYS* 6.1 0.2 - - + -
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Residues in contact with LEU 288 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169G LEU* 3.1 22.6 - - - +
170G LEU* 2.8 31.6 + - + +
172G ILE* 4.7 1.3 - - + -
254G VAL* 3.8 33.9 - - + +
255G ARG* 4.8 0.9 - - - -
258G PHE* 3.7 39.9 - - + -
262G CYS* 4.0 19.1 - - - -
263G GLN 3.3 4.3 - - - +
264G HIS* 3.6 22.2 - - + +
286G HIS* 4.1 18.4 - - + +
287G VAL* 1.3 79.8 - - - +
289G LYS* 1.3 59.9 + - - +
290G LYS 4.2 0.7 - - - -
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Residues in contact with LYS 289 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55G HIS* 3.4 32.3 + - + +
167G GLY* 4.2 20.7 + - - +
168G GLY 3.4 8.3 - - - +
169G LEU* 3.7 16.4 - - + +
258G PHE* 5.3 0.4 - - - -
262G CYS* 3.1 3.3 - - - -
263G GLN* 2.7 64.8 + - + +
287G VAL* 6.1 0.2 - - + -
288G LEU* 1.3 75.1 - - - +
290G LYS* 1.3 63.1 + - - +
291G THR* 2.7 18.1 + - + +
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Residues in contact with LYS 290 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161G ALA* 3.4 21.8 + - - +
162G SER* 5.1 3.6 - - - +
164G VAL* 3.3 30.0 + - + +
165G ARG 3.5 23.1 - - - +
166G PRO* 3.9 9.4 - - + -
167G GLY* 2.7 31.8 + - - +
168G GLY 3.1 12.4 + - - +
258G PHE* 3.8 35.6 + - + +
261G ARG* 4.6 16.0 - - - +
288G LEU 4.2 0.4 - - - -
289G LYS* 1.3 68.6 - - - +
291G THR* 1.3 66.7 + - - +
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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