Contacts of the strand formed by residues 180 - 184 (chain G) in PDB entry 1RZR
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 ILE 180 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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169G VAL* 4.0 8.5 - - + -
172G LEU* 4.4 12.8 - - + -
173G ILE* 4.7 2.7 - - + +
177G HIS* 3.5 28.9 - - + -
178G LYS 3.9 12.6 - - - +
179G ASN* 1.3 79.0 - - - +
181G ALA* 1.3 55.7 + - - +
200G TYR* 2.5 41.1 + - + -
204G LEU* 3.1 42.2 - - + -
209G LEU 5.3 0.4 - - - +
212G ARG* 5.8 1.1 - - - +
215G TYR* 3.2 11.5 - - + -
242G ALA* 2.8 26.5 - - + +
244G PHE* 6.3 0.4 - - + -
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Residues in contact with ALA 181 (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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180G ILE* 1.3 76.7 - - - +
182G PHE* 1.3 62.4 + - - +
200G TYR* 3.5 12.4 - - - -
215G TYR* 3.2 25.1 - - + +
233G LEU* 4.1 19.1 - - + -
240G PRO* 3.9 19.7 - - + +
242G ALA 2.8 7.7 + - - -
243G ILE* 3.4 8.1 - - + -
244G PHE* 3.0 21.8 + - - +
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Residues in contact with PHE 182 (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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181G ALA* 1.3 78.3 - - - +
183G VAL* 1.3 66.9 + - - +
184G SER* 3.2 27.8 + - - -
192G ASN* 4.7 0.4 - - - -
196G LYS* 3.7 26.7 - - + -
197G VAL* 3.6 33.2 - - + -
200G TYR* 4.0 24.1 + + + -
215G TYR 3.1 5.9 + - - +
216G ILE* 3.6 24.8 - - + -
217G VAL* 3.2 25.7 + - - +
244G PHE* 2.9 53.6 - + - -
246G GLY* 4.1 9.0 - - - -
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Residues in contact with VAL 183 (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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182G PHE* 1.3 73.1 - - - +
184G SER* 1.3 63.3 + - - +
217G VAL* 3.5 17.0 - - + +
219G GLY* 5.1 2.9 - - - +
225G SER 5.1 1.3 - - - +
226G GLY* 5.2 0.4 - - - -
229G ALA* 3.2 37.0 - - + +
233G LEU* 3.6 13.9 - - + -
243G ILE* 4.0 11.2 - - + +
244G PHE 3.1 9.7 + - - +
245G VAL* 3.7 23.8 - - + -
246G GLY 3.1 21.8 + - - -
250G MSE 4.1 15.5 - - + -
254G VAL* 4.2 11.4 - - + -
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Residues in contact with SER 184 (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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182G PHE* 3.2 38.6 - - - -
183G VAL* 1.3 73.4 - - - +
185G GLY* 1.3 76.9 + - - +
187G LEU* 3.8 15.8 - - - +
192G ASN* 3.6 10.2 + - - -
216G ILE* 4.9 0.3 - - - +
217G VAL 3.3 11.1 + - - -
218G GLU* 3.8 0.5 - - - -
219G GLY 3.0 24.8 + - - +
246G GLY* 4.4 2.0 - - - +
250G MSE 3.4 12.4 - - - +
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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