Contacts of the strand formed by residues 243 - 248 (chain B) in PDB entry 2XMR
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 VAL 243 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152B LEU* 3.2 10.8 - - + +
154B LEU* 3.9 15.3 - - + -
239B LEU* 3.7 29.4 - - + -
241B CYS* 3.5 20.4 - - - +
242B PRO* 1.3 74.4 - - - +
244B MET* 1.3 62.7 + - - +
245B LEU* 3.8 29.8 - - + -
264B LEU* 4.0 12.3 - - + -
268B GLN 3.0 7.6 + - - +
269B THR* 3.3 13.7 - - + +
270B SER* 2.9 26.7 + - - +
296B PHE* 3.8 3.4 - - - -
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Residues in contact with MET 244 (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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152B LEU 2.8 11.5 + - - +
153B VAL* 3.3 30.0 - - + +
154B LEU 2.8 26.2 + - - -
243B VAL* 1.3 74.0 - - - +
245B LEU* 1.3 65.1 + - - +
246B VAL* 3.9 13.9 - - + -
270B SER* 3.5 16.6 - - - +
272B LEU* 4.6 7.0 - - + -
289B LEU* 4.5 6.1 - - + -
292B ALA* 4.0 29.2 - - + +
293B PHE* 4.0 11.7 - - + +
296B PHE* 3.7 19.7 - - + -
172C LEU* 3.8 29.6 - - - -
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Residues in contact with LEU 245 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154B LEU* 3.5 17.7 - - + -
157B ILE* 3.8 27.4 - - + -
243B VAL* 3.8 17.9 - - + -
244B MET* 1.3 72.4 - - - +
246B VAL* 1.3 62.5 + - - +
257B VAL* 3.7 16.8 - - + +
260B CYS* 4.1 7.2 - - + -
261B ASN* 3.6 48.9 - - + +
264B LEU* 4.1 10.3 - - + -
269B THR* 4.1 2.0 - - + -
270B SER 2.8 12.7 + - - +
271B PHE* 3.5 6.7 - - + -
272B LEU* 2.8 27.7 + - - +
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Residues in contact with VAL 246 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153B VAL* 4.2 7.4 - - + -
154B LEU 3.0 5.5 + - - +
155B ILE* 3.3 27.8 - - + +
156B ASN* 2.9 27.7 + - - +
244B MET* 3.9 23.1 - - + +
245B LEU* 1.3 81.8 - - - +
247B VAL* 1.3 64.9 + - - +
257B VAL* 4.2 3.2 - - - +
271B PHE* 5.2 0.2 - - - -
272B LEU* 3.5 23.1 - - + +
274B MET* 4.1 22.7 - - - -
281B PRO* 4.3 12.1 - - + -
289B LEU* 4.3 9.2 - - + -
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Residues in contact with VAL 247 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156B ASN* 3.6 18.8 - - - +
246B VAL* 1.3 75.7 - - - +
248B GLY* 1.3 72.0 + - - +
251B ALA* 4.6 4.0 - - + -
253B HIS* 3.7 9.4 - - + -
254B GLU* 3.6 37.5 - - + +
257B VAL* 3.7 15.9 - - + +
271B PHE* 4.1 15.9 - - + -
272B LEU 3.3 5.2 + - - +
273B LYS* 3.4 19.2 - - + -
274B MET* 2.9 24.8 + - - +
281B PRO* 4.4 6.3 - - - -
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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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156B ASN* 4.6 1.0 + - - -
247B VAL* 1.3 89.9 - - - +
249B ASP* 1.3 68.2 + - - -
250B GLN 3.4 0.9 + - - -
251B ALA* 3.2 16.4 + - - +
254B GLU* 4.1 2.9 - - - +
274B MET 3.4 0.9 - - - -
277B SER* 3.2 24.5 - - - -
278B GLY 3.5 15.5 + - - -
281B PRO* 4.1 4.0 - - - +
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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