Contacts of the strand formed by residues 274 - 277 (chain F) in PDB entry 4LQL
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 ALA 274 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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176F ILE* 5.5 1.1 - - + -
177F LYS 3.6 3.4 + - - +
178F ILE* 3.3 15.7 - - + -
179F ALA 3.1 23.2 + - - -
267F LEU* 4.1 6.9 - - - +
272F TYR* 3.1 5.7 - - - +
273F ASP* 1.3 79.6 - - - +
275F PHE* 1.3 61.1 + - - +
302F GLY* 3.0 31.6 - - - +
312F ALA 4.6 7.6 - - - +
313F GLY* 5.0 2.0 - - - -
316F ARG* 4.3 12.1 - - + -
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Residues in contact with PHE 275 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178F ILE* 4.1 2.6 - - - +
179F ALA* 3.3 13.7 - - + +
181F PHE* 5.1 8.3 - - + +
263F ILE* 4.8 14.1 - - + -
267F LEU* 3.7 30.5 - - + -
274F ALA* 1.3 75.0 - - - +
276F THR* 1.3 70.8 + - - +
277F ASP* 4.2 11.0 - - + -
289F PRO* 5.2 2.2 - - + -
293F VAL* 3.4 32.5 - - + -
296F LEU* 3.5 28.7 - - + -
301F TYR 5.9 0.2 - - - -
302F GLY 2.8 25.0 + - - +
303F PHE* 3.5 30.7 - + + -
304F GLY 3.1 23.6 + - - -
312F ALA* 4.3 1.8 - - - +
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Residues in contact with THR 276 (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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178F ILE* 5.4 1.3 - - + -
179F ALA 3.2 7.7 + - - +
180F ARG* 3.0 28.1 - - + +
181F PHE* 3.0 30.0 + - - +
182F GLY 4.0 4.8 + - - +
275F PHE* 1.3 78.6 - - - +
277F ASP* 1.3 59.5 + - - +
278F ASN* 4.2 0.6 - - - -
304F GLY 3.2 16.4 - - - +
307F GLY* 3.2 33.6 + - - +
309F PHE* 3.9 8.5 - - + +
312F ALA* 3.9 19.7 - - + -
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Residues in contact with ASP 277 (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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181F PHE* 4.2 9.6 - - + -
275F PHE* 4.2 12.3 - - + -
276F THR* 1.3 71.9 - - - +
278F ASN* 1.3 62.6 + - - +
282F LEU* 4.9 3.6 - - - -
285F LEU* 6.3 0.2 - - - -
288F LEU* 4.3 12.9 - - - +
289F PRO* 3.5 37.2 - - + -
303F PHE* 3.9 24.0 - - + -
304F GLY 3.6 5.3 + - - -
305F PRO 2.5 25.3 + - - +
306F GLU* 4.3 0.2 - - - -
349F MET* 5.4 2.4 - - - +
351F GLU* 4.9 3.7 - - - +
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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