Contacts of the strand formed by residues 268 - 271 (chain B) in PDB entry 3DLX
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 ARG 268 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41B LYS* 3.3 4.5 - - + -
43B TYR* 3.6 36.0 + - + -
48B GLU 4.9 1.6 + - - -
49B ALA 3.0 23.9 + - - -
52B ASP* 2.8 42.8 + - - -
207B PHE* 4.1 10.1 - - - -
240B THR* 3.6 24.1 + - + +
241B THR 2.9 12.3 + - - +
242B VAL* 3.4 20.3 - - + -
243B VAL* 2.8 33.6 + - - +
266B VAL* 4.0 3.4 - - - +
267B HIS* 1.3 83.8 - - + +
269B LEU* 1.3 58.2 + - - +
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Residues in contact with LEU 269 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40B THR* 3.9 23.6 - - + -
41B LYS 2.9 6.3 + - - +
42B PHE* 3.3 31.9 - - + +
43B TYR* 3.0 26.3 + - - +
215B ALA* 3.3 26.2 - - + -
219B GLY* 4.0 9.4 - - - +
221B VAL* 4.5 1.1 - - + -
242B VAL* 5.8 0.4 - - - -
243B VAL* 3.3 32.3 - - + +
245B VAL* 3.8 26.5 - - + -
248B ILE* 5.2 0.7 - - + -
266B VAL* 4.1 7.6 - - + -
268B ARG* 1.3 75.9 - - - +
270B ILE* 1.3 65.3 + - - +
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Residues in contact with ILE 270 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43B TYR* 2.8 46.2 - - + +
44B THR* 4.7 1.8 - - - -
45B ASP 4.4 9.2 - - - +
46B PRO* 4.3 19.5 - - + -
49B ALA* 4.4 10.5 - - + -
72B ASN* 4.5 4.5 - - + -
73B LEU* 4.3 20.6 - - + -
242B VAL* 5.2 0.7 - - + -
243B VAL 3.0 5.0 + - - +
244B GLU* 3.2 32.8 - - + -
245B VAL* 2.9 29.8 + - - +
248B ILE* 5.4 2.2 - - - -
269B LEU* 1.3 73.1 - - - +
271B LYS* 1.3 61.4 + - - +
272B GLY* 4.0 16.4 - - - -
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Residues in contact with LYS 271 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43B TYR 4.8 1.0 + - - -
46B PRO* 6.1 0.3 - - - +
245B VAL* 3.3 16.5 - - + +
246B GLU 3.7 28.0 - - - +
247B GLU* 4.1 9.9 - - + +
248B ILE* 4.3 21.0 - - + +
270B ILE* 1.3 76.3 - - - +
272B GLY* 1.3 72.2 + - - +
273B GLU* 3.6 1.7 + - - +
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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
------------------------------------------------------------
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