Contacts of the strand formed by residues 322 - 325 (chain F) in PDB entry 1R4N
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 LEU 322 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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496E PHE* 5.8 3.1 - - + -
522E TYR* 5.8 1.6 - - + -
527E GLN* 4.0 36.8 - - - +
188F ASN* 3.0 8.3 - - - +
189F ALA* 2.9 40.4 + - + +
299F ILE* 5.5 2.7 - - + -
302F VAL* 4.2 19.3 - - + -
318F LEU* 4.0 7.9 - - + -
321F TYR* 1.3 84.3 - - - +
323F VAL* 1.3 101.4 + - - +
324F PHE* 4.2 3.4 - - + +
332F THR* 3.6 24.0 - - + -
333F TYR 3.4 11.4 - - - +
334F THR* 4.5 2.7 - - + +
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Residues in contact with VAL 323 (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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186F LYS* 6.0 1.3 - - + -
187F GLY 3.5 9.9 - - - +
188F ASN* 4.3 0.2 - - - +
321F TYR* 3.6 18.8 - - + -
322F LEU* 1.3 93.5 - - - +
324F PHE* 1.3 66.4 + - - +
331F TYR* 4.5 1.9 - - + -
332F THR* 3.0 17.5 - - - -
333F TYR* 3.0 14.1 + - + +
335F PHE* 4.8 0.2 - - + -
108K LEU* 3.8 30.5 - - + -
170K VAL* 3.2 32.5 - - + -
171K LEU* 3.8 18.4 - - + +
173K LEU* 5.4 2.0 - - + -
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Residues in contact with PHE 324 (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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496E PHE* 4.5 9.9 - + - -
500E ALA* 4.6 4.9 - - + -
520E TYR* 4.8 3.6 - - - -
185F PHE 3.7 13.5 - - - -
186F LYS* 3.2 6.2 - - - +
187F GLY 2.7 40.8 + - - +
295F THR* 4.9 9.4 - - + -
298F VAL* 3.6 42.0 - - + -
299F ILE* 4.3 10.3 - - + -
322F LEU* 4.7 2.5 - - + -
323F VAL* 1.3 79.8 - - - +
325F ASN* 1.3 68.9 + - - +
326F ASP* 3.1 39.0 - - - -
330F LEU* 4.5 13.7 - - + -
331F TYR* 3.4 3.8 - - - -
332F THR* 3.3 27.4 - - + -
108K LEU* 5.8 0.2 - - - +
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Residues in contact with ASN 325 (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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177E ASP* 3.4 15.4 - - - +
185F PHE* 3.7 7.4 + - - +
186F LYS* 3.5 26.9 - - - +
324F PHE* 1.3 80.4 - - - +
326F ASP* 1.3 70.2 + - - +
327F VAL* 2.9 25.7 - - - +
328F ASP 4.7 1.9 - - - +
329F GLY 3.3 12.6 - - - +
330F LEU* 3.8 0.9 - - - -
331F TYR* 3.0 32.4 + - + +
108K LEU* 3.1 34.5 - - + +
109K THR* 3.7 5.7 - - + +
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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