Contacts of the strand formed by residues 322 - 325 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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496C PHE* 5.8 3.4 - - + -
522C TYR* 5.8 1.3 - - + -
527C GLN* 4.0 36.8 - - - +
188D ASN* 3.0 9.0 - - - +
189D ALA* 2.9 40.2 + - + +
299D ILE* 5.5 2.9 - - + -
302D VAL* 4.2 19.7 - - + -
318D LEU* 4.0 8.3 - - + -
321D TYR* 1.3 84.3 - - - +
323D VAL* 1.3 99.2 + - - +
324D PHE* 4.2 4.0 - - + +
332D THR* 3.6 24.0 - - + -
333D TYR 3.4 11.2 - - - +
334D THR* 4.5 3.6 - - + +
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Residues in contact with VAL 323 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186D LYS* 6.0 1.1 - - + -
187D GLY 3.5 9.0 - - - +
188D ASN* 4.3 0.2 - - - +
321D TYR* 3.6 18.4 - - + -
322D LEU* 1.3 93.8 - - - +
324D PHE* 1.3 66.8 + - - +
331D TYR* 3.7 1.7 - - + +
332D THR* 3.0 17.8 - - - -
333D TYR* 2.9 14.8 + - + +
335D PHE* 4.8 0.2 - - + -
108J LEU* 3.8 29.6 - - + -
170J VAL* 3.4 31.9 - - + -
171J LEU* 3.8 17.9 - - + +
173J LEU* 5.3 3.4 - - + -
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Residues in contact with PHE 324 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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496C PHE* 4.4 9.2 - + - -
500C ALA* 4.6 6.5 - - + -
520C TYR* 4.8 4.9 - - - -
185D PHE 3.7 12.6 - - - -
186D LYS* 3.2 6.2 - - - +
187D GLY* 2.7 42.3 + - - +
295D THR* 4.9 10.3 - - + -
298D VAL* 3.5 43.7 - - + -
299D ILE* 4.3 9.9 - - + -
322D LEU* 4.7 2.2 - - + -
323D VAL* 1.3 79.4 - - - +
325D ASN* 1.3 68.2 + - - +
326D ASP* 3.1 38.8 - - - -
330D LEU* 4.5 10.5 - - + -
331D TYR* 3.4 3.8 - - - -
332D THR* 3.3 26.2 - - + -
108J LEU* 6.1 0.2 - - - +
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Residues in contact with ASN 325 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177C ASP* 3.4 15.6 - - - +
185D PHE* 3.7 6.4 + - - +
186D LYS* 3.6 26.3 - - + +
324D PHE* 1.3 80.8 - - - +
326D ASP* 1.3 65.2 + - - +
327D VAL* 2.8 31.8 - - - +
328D ASP 4.6 2.3 + - - +
329D GLY 3.3 6.6 - - - +
330D LEU* 3.8 1.2 - - - -
331D TYR* 3.0 38.9 + - + +
108J LEU* 3.3 33.2 - - + +
109J THR* 3.8 5.2 - - + +
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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