Contacts of the strand formed by residues 253 - 258 (chain F) in PDB entry 3RL7
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 253 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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238F ILE* 3.7 31.6 - - + -
239F ALA 3.4 8.7 - - - +
240F GLY 3.7 5.8 - - - +
241F GLY* 3.5 31.9 - - - +
252F SER* 1.3 72.3 - - - +
254F PHE* 1.3 63.1 + - - +
275F CYS* 3.1 11.4 - - - -
276F ILE* 3.1 42.8 + - + +
284F VAL* 3.5 24.3 + - + +
285F ARG 5.5 0.9 - - - +
287F VAL* 4.8 2.7 - - + +
288F THR 4.8 1.3 - - - +
289F HIS* 4.5 6.1 - - - +
292F ALA* 3.6 27.8 - - + -
296F LEU* 5.5 1.3 - - + -
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Residues in contact with PHE 254 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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245A PRO* 3.8 2.0 - - + -
246A HIS* 3.6 31.6 - - - -
247A ILE* 3.6 30.5 - - + -
238F ILE* 3.1 9.6 - - - -
239F ALA* 2.8 50.0 + - + -
240F GLY* 3.9 9.6 - - - -
252F SER 3.5 13.0 - - - -
253F ILE* 1.3 75.3 - - - +
255F ILE* 1.3 71.4 + - - +
256F THR* 3.9 6.3 - - + -
273F ASN* 4.4 4.3 - - - +
274F ASP 3.2 16.8 - - - +
276F ILE 4.8 0.9 - - - +
2837G SER* 3.3 32.5 - - - -
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Residues in contact with ILE 255 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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245A PRO* 4.1 0.5 - - - +
236F PHE* 3.6 26.9 - - + -
237F SER 3.4 4.9 - - - +
238F ILE* 3.9 1.1 - - + -
254F PHE* 1.3 76.0 - - - +
256F THR* 1.3 58.9 + - - +
257F LYS 3.4 26.7 - - - +
258F ILE* 3.8 19.3 - - + -
270F LEU* 3.7 16.2 - - + -
271F ARG 3.4 22.4 - - - +
272F VAL* 3.4 5.6 - - - +
273F ASN* 2.9 26.5 + - - -
274F ASP* 2.9 20.8 + - + +
276F ILE* 3.7 27.6 - - + -
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Residues in contact with THR 256 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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245A PRO* 3.3 22.2 - - + +
237F SER* 3.0 11.8 + - - -
239F ALA* 3.5 24.7 - - + +
254F PHE* 3.5 6.9 + - + -
255F ILE* 1.3 76.4 - - - +
257F LYS* 1.3 63.5 + - - +
272F VAL* 3.5 12.5 - - - +
2837G SER 3.4 28.7 - - - +
2838G TYR* 3.8 24.4 - - - +
2840L VAL* 3.4 22.0 - - + +
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Residues in contact with LYS 257 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236F PHE* 3.2 9.0 - - - +
237F SER* 2.8 49.8 + - - +
255F ILE* 3.4 3.7 - - - +
256F THR* 1.3 83.9 + - - +
258F ILE* 1.3 67.7 + - - +
259F ILE* 3.5 28.9 - - + +
272F VAL* 4.5 1.1 - - - -
2838G TYR* 3.8 38.6 - - + -
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Residues in contact with ILE 258 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235F GLY 3.7 2.7 - - - -
236F PHE* 4.6 3.6 - - + -
255F ILE* 3.8 11.4 - - + -
257F LYS* 1.3 81.9 - - - +
259F ILE* 1.3 65.2 + - - +
260F THR* 3.3 10.4 + - + +
264F ALA* 4.0 10.1 - - + -
265F ALA* 3.9 35.0 - - + +
270F LEU* 3.2 30.7 - - + +
271F ARG* 3.5 4.3 - - - -
272F VAL* 3.5 33.5 - - + +
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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