Contacts of the strand formed by residues 280 - 283 (chain B) in PDB entry 3NUI
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 280 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106B PHE* 3.7 4.5 - - - -
124B MET* 3.0 33.0 - - + -
253B VAL 3.3 2.6 + - - -
254B ILE* 3.5 14.3 - - + -
255B SER 2.8 30.3 + - - -
278B PRO* 3.4 7.2 - - - +
279B ASP* 1.3 82.2 - - - +
281B ILE* 1.3 57.4 + - - +
298B ILE 3.2 11.4 - - - +
299B LEU* 3.9 10.3 - - + -
303B LEU* 4.0 2.2 - - + -
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Residues in contact with ILE 281 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104B SER* 4.5 4.0 - - - -
105B PRO* 3.4 35.9 - - + -
106B PHE* 4.1 12.3 - - + -
124B MET* 4.1 1.1 - - - +
255B SER* 3.3 4.7 - - - +
257B GLU* 3.8 14.4 - - + -
269B TRP* 3.7 39.3 - - + -
271B CYS* 4.4 5.2 - - - -
278B PRO* 4.0 10.1 - - + -
280B ALA* 1.3 78.6 - - - +
282B ILE* 1.3 78.8 + - - +
283B SER* 4.4 0.4 - - - +
296B ALA 3.9 0.3 - - - +
297B VAL* 3.5 4.3 - - - +
298B ILE* 2.8 47.8 + - + +
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Residues in contact with ILE 282 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117B GLY 3.9 1.1 - - - +
120B ALA* 3.6 25.8 - - + +
121B ASN* 3.8 26.2 - - + +
124B MET* 4.1 14.6 - - + -
221B PHE* 3.4 24.5 - - + -
254B ILE* 3.4 28.0 - - + -
255B SER 3.0 7.6 + - - +
256B ASP* 4.3 11.0 - - - +
257B GLU* 2.9 33.3 + - - +
258B VAL* 3.6 19.7 - - + -
281B ILE* 1.3 75.0 - - - +
283B SER* 1.3 63.5 + - - +
296B ALA 3.5 2.9 - - - -
297B VAL* 4.9 1.6 - - + -
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Residues in contact with SER 283 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100B LEU* 5.5 0.4 - - - +
117B GLY* 4.2 4.2 - - - -
120B ALA* 4.3 1.0 - - - +
257B GLU 4.4 5.4 + - - -
258B VAL* 4.1 3.4 - - - -
261B GLY* 5.6 0.5 - - - -
262B PHE* 3.9 23.2 - - - -
269B TRP* 4.4 7.6 - - - -
281B ILE* 4.5 10.5 - - - -
282B ILE* 1.3 76.4 - - - +
284B SER* 1.3 64.0 + - - +
287B LEU* 4.1 10.7 - - - +
295B GLY* 3.2 3.3 - - - -
296B ALA* 2.8 43.4 + - - +
298B ILE* 4.8 7.4 - - - -
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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