Contacts of the strand formed by residues 245 - 250 (chain B) in PDB entry 3L49
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 245 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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147B ASP* 5.0 7.2 - - + +
219B GLY 3.4 7.6 + - - +
220B ALA* 3.3 4.0 - - - -
221B ILE 2.8 24.8 + - - -
242B THR 3.3 25.4 + - - -
243B ASP* 5.1 4.2 - - - +
244B ILE* 1.3 91.5 + - - +
246B THR* 1.3 62.6 + - - +
247B TYR* 3.4 30.1 - - + +
262B PRO 5.5 3.8 + - - -
264B SER 4.2 3.5 + - - -
265B PRO* 3.2 22.7 - - - +
266B ALA 4.2 3.4 - - - -
267B GLY* 3.7 19.7 - - - +
307B LYS* 4.0 20.2 - - - +
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Residues in contact with THR 246 (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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221B ILE* 3.4 25.1 - - + -
229B MET* 3.9 11.0 - - - -
232B ALA* 3.9 12.8 - - + -
233B THR* 2.9 27.0 + - - +
236B LEU* 3.9 20.6 - - + -
245B ARG* 1.3 75.4 - - - +
247B TYR* 1.3 64.4 + - - +
255B PHE* 3.8 6.6 - - - -
265B PRO 3.0 5.1 + - - +
266B ALA* 3.3 14.0 - - - -
267B GLY* 2.8 25.5 + - - -
268B ALA 3.4 3.8 + - - +
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Residues in contact with TYR 247 (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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140B LEU* 4.2 22.9 - - + -
143B GLN 4.5 1.3 - - - -
144B MET* 3.7 42.7 + - + -
147B ASP* 2.4 44.1 + - - +
148B LEU* 6.0 0.2 - - - +
220B ALA* 4.1 4.9 - - + -
221B ILE 2.8 19.4 + - - +
222B TRP* 3.5 9.4 - - + -
223B ALA 3.0 27.5 + - - +
229B MET* 3.4 7.9 - - - +
245B ARG* 3.4 36.6 - - + +
246B THR* 1.3 77.4 - - - +
248B GLY* 1.3 57.9 + - - +
267B GLY* 4.0 1.3 - - - -
268B ALA* 3.6 33.9 - - + -
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Residues in contact with GLY 248 (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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140B LEU* 3.6 9.4 - - - +
223B ALA 3.6 10.8 - - - -
225B TRP 4.3 5.2 - - - -
226B ASP* 4.3 5.2 - - - -
229B MET* 4.2 10.0 - - - +
247B TYR* 1.3 75.0 - - - +
249B VAL* 1.3 62.9 + - - -
255B PHE* 4.2 3.5 - - - -
268B ALA 3.4 6.5 + - - -
269B VAL* 3.3 11.1 - - - -
270B ALA 3.2 19.2 + - - -
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Residues in contact with VAL 249 (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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136B ILE* 4.0 21.5 - - + -
137B GLY* 6.1 0.2 - - - -
140B LEU* 3.9 16.8 - - + -
169B ARG* 3.6 37.2 - - + +
222B TRP* 6.0 0.2 - - + -
223B ALA 4.4 0.9 - - - +
224B CYS* 3.3 24.0 - - - +
225B TRP* 3.1 3.2 - - - +
226B ASP 2.9 20.3 + - - +
248B GLY* 1.3 78.8 - - - +
250B ASP* 1.3 73.1 + - - +
251B GLY 3.9 0.9 - - - -
269B VAL* 4.1 2.0 - - - -
270B ALA* 3.6 13.9 - - + +
272B GLN* 3.7 14.6 - - + +
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Residues in contact with ASP 250 (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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1B UNL 2.7 39.7 - - - +
43B HIS* 4.8 1.7 + - - -
45B TRP* 3.5 21.1 - - + +
225B TRP* 3.4 12.6 - - - +
226B ASP* 3.6 14.4 - - - +
249B VAL* 1.3 79.4 - - - +
251B GLY* 1.3 62.4 + - - +
252B SER* 4.4 3.6 - - - +
269B VAL* 3.8 0.6 - - - +
270B ALA 2.8 17.6 + - - -
272B GLN* 2.7 58.6 + - - +
274B PRO* 5.0 1.2 - - - +
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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