Contacts of the strand formed by residues 244 - 248 (chain B) in PDB entry 1M7X
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 SER 244 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242B PRO 4.0 0.8 - - - -
243B ILE* 1.3 72.1 - - - +
245B ILE* 1.3 60.8 + - - +
280B GLY 4.7 1.8 - - - -
281B PHE* 3.5 19.0 - - - +
282B THR* 3.0 34.8 + - - -
283B HIS 3.2 6.1 + - - -
558B TRP* 3.8 11.3 + - - -
564B LYS* 3.5 6.4 - - - +
607B ASN* 2.5 30.4 + - - -
610B TYR* 4.4 14.6 - - - -
611B ARG* 5.6 0.7 - - - -
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Residues in contact with ILE 245 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243B ILE* 3.9 17.3 - - + -
244B SER* 1.3 74.9 + - - +
246B TYR* 1.3 62.1 + - - +
281B PHE* 3.8 5.9 - - - -
283B HIS* 3.6 12.3 - - + +
285B GLU* 3.4 35.7 - - + +
333B ILE* 3.5 28.0 - - + -
456B MET* 4.4 13.7 - - + -
481B TRP* 6.1 0.2 - - - +
520B VAL* 4.6 8.3 - - + -
564B LYS 2.7 20.2 + - - +
565B LEU* 3.3 26.6 - - + -
566B LEU* 2.7 32.7 + - - +
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Residues in contact with TYR 246 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245B ILE* 1.3 72.0 - - - +
247B GLU* 1.3 61.6 + - - +
248B VAL* 3.6 25.2 + - + -
253B TRP* 3.2 20.2 + - - -
272B LEU* 4.1 4.7 - - + -
275B TYR* 3.7 12.0 - + - -
276B ALA* 4.1 10.8 - - + -
281B PHE* 3.6 39.9 - + + -
283B HIS 3.1 12.0 + - - +
284B LEU* 3.7 18.5 - - + +
285B GLU 3.0 19.1 + - - +
566B LEU* 3.4 10.8 - - + -
567B PHE 4.3 0.9 - - - -
568B MET* 3.2 29.1 - - + +
569B GLY 4.0 0.5 + - - -
571B GLU* 2.5 46.0 + - + -
584B LEU* 4.1 1.2 - - - +
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Residues in contact with GLU 247 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245B ILE 3.7 1.4 + - - -
246B TYR* 1.3 71.9 - - - +
248B VAL* 1.3 65.4 + - - +
285B GLU* 3.4 31.6 - - + +
287B LEU* 3.5 12.5 - - + +
335B ASP* 4.5 2.8 - - - +
481B TRP* 4.1 4.7 - - - -
524B SER* 3.2 14.4 - - - -
525B HIS* 2.6 53.5 + - - -
565B LEU* 3.9 14.0 - - + +
566B LEU 2.8 14.7 + - - +
567B PHE* 3.1 15.9 - - + -
568B MET* 2.9 29.3 + - - +
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Residues in contact with VAL 248 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246B TYR* 3.6 37.5 - - + +
247B GLU* 1.3 83.3 - - - +
249B HIS* 1.3 75.0 + - - +
250B LEU* 3.7 21.0 + - + -
253B TRP* 4.0 10.1 - - + -
272B LEU* 4.0 12.3 - - + -
284B LEU* 4.1 8.7 - - + -
285B GLU 2.7 12.9 + - - +
286B LEU* 3.4 11.2 - - + +
287B LEU* 2.9 33.0 + - - +
567B PHE* 4.3 0.9 - - - -
568B MET* 3.9 9.9 - - + -
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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