Contacts of the strand formed by residues 243 - 247 (chain B) in PDB entry 4M3P
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 HIS 243 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14B LEU* 4.1 11.9 - - + +
17B LEU* 3.5 61.8 + - + +
18B ASN* 2.8 30.9 + - - -
211B SER* 3.1 20.6 + - - +
212B ILE* 3.3 5.5 - - + -
213B ILE* 2.9 27.9 + - - +
242B ALA* 1.3 76.3 - - - +
244B LEU* 1.3 61.0 + - - +
294B ARG* 5.4 7.6 - - + +
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Residues in contact with LEU 244 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212B ILE* 4.5 1.1 - - - +
213B ILE* 3.3 30.1 - - + +
228B VAL* 4.2 18.4 - - + +
232B LYS* 3.7 46.9 - - + +
235B LEU* 4.7 4.9 - - + -
242B ALA 4.3 8.5 - - - +
243B HIS* 1.3 76.8 - - - +
245B MET* 1.3 62.3 + - - +
291B LEU 4.4 2.2 - - - +
292B GLY* 3.9 28.9 + - - +
293B VAL* 3.2 11.1 - - + +
294B ARG* 3.2 23.9 + - - +
295B TYR* 3.3 6.9 + - - +
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Residues in contact with MET 245 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157B ILE* 4.6 13.2 - - + -
182B ALA* 3.9 22.7 - - - -
183B ALA 5.2 0.4 - - - -
184B THR* 3.4 31.4 - - + +
212B ILE* 3.8 9.0 - - + -
213B ILE 2.8 10.9 + - - +
214B GLY* 3.1 23.6 - - - -
215B VAL 3.3 2.9 + - - -
228B VAL* 4.0 5.6 - - - +
244B LEU* 1.3 76.9 - - - +
246B SER* 1.3 63.1 + - - +
247B GLN* 3.7 25.8 - - + +
293B VAL* 3.8 2.5 - - - -
295B TYR* 3.0 62.4 - - + +
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Residues in contact with SER 246 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215B VAL* 3.7 9.2 - - - -
224B SER* 5.4 1.6 - - - -
225B LEU* 4.1 20.2 - - - +
228B VAL* 4.4 9.4 - - - -
245B MET* 1.3 77.7 - - - +
247B GLN* 1.3 63.0 + - - +
248B PRO* 3.6 3.8 - - - -
284B TYR* 2.8 32.5 + - - -
288B ALA* 4.2 1.2 - - - +
293B VAL* 3.7 14.0 - - - +
295B TYR 3.0 5.9 + - - -
296B ILE* 4.4 0.7 - - - -
297B GLY 2.8 27.9 + - - -
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Residues in contact with GLN 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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25B GLY* 4.0 7.6 - - - -
26B ASP 3.4 4.5 - - - +
72B GLN* 2.9 26.1 + - - +
157B ILE* 5.3 0.2 - - - +
159B GLU* 4.0 10.7 + - - -
184B THR* 5.6 0.6 + - - -
215B VAL* 2.9 10.1 + - - +
216B ASN* 3.1 16.0 - - + +
217B CYS 2.9 22.9 + - - -
245B MET* 3.7 29.7 - - + +
246B SER* 1.3 80.3 - - - +
248B PRO* 1.3 66.7 - - - +
295B TYR* 4.4 3.1 - - + -
297B GLY* 3.5 8.3 - - - +
298B GLY 3.3 24.9 + - - +
299B CYS* 3.2 6.5 - - + +
503B K 3.1 19.0 - - - -
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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