Contacts of the strand formed by residues 388 - 392 (chain A) in PDB entry 3CMM
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 PHE 388 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162A ASN* 5.1 8.1 - - + -
163A THR 3.9 10.1 - - - -
164A PHE* 3.5 35.4 - + + -
269A LEU* 3.8 16.4 - - + -
272A GLN* 3.7 32.3 - - + -
273A LEU* 4.1 6.5 - - + -
276A PRO* 3.9 10.3 - - + -
277A GLU 2.8 17.9 + - - +
278A PHE* 3.3 17.5 - - + -
279A VAL* 2.8 28.9 + - - -
293A HIS* 3.6 20.6 - + - -
385A LEU* 3.8 3.5 - - - +
387A GLN* 1.3 73.6 - - - +
389A MET* 1.3 59.2 + - - +
390A TYR* 3.2 32.1 - + + -
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Residues in contact with MET 389 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162A ASN* 3.1 7.6 - - - +
163A THR* 3.0 36.8 + - + -
278A PHE* 5.5 0.2 - - - -
279A VAL* 3.2 22.2 - - - +
280A PHE 4.7 0.4 - - - -
281A SER* 3.8 17.5 - - - -
365A PHE* 3.8 21.1 - - + -
366A PHE* 3.7 35.4 - - + -
369A LEU* 4.1 12.8 - - + -
385A LEU* 4.0 19.5 - - + +
388A PHE* 1.3 74.3 - - - +
390A TYR* 1.3 74.1 + - - +
391A PHE* 4.6 1.1 - - + -
906A PHE* 3.6 28.0 - - + -
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Residues in contact with TYR 390 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161A GLY 3.5 2.0 - - - -
162A ASN* 3.3 32.5 + - + -
273A LEU* 5.7 0.3 - - - +
278A PHE* 3.7 21.7 - + - -
279A VAL 4.5 1.4 + - - -
280A PHE* 5.4 0.2 - - - -
281A SER* 2.6 31.7 + - - -
289A ALA* 3.9 21.3 - - + +
292A LEU* 3.8 36.8 - - + -
293A HIS* 2.7 53.0 + - + -
296A PHE* 3.8 10.8 - + - +
297A GLN* 6.0 0.2 - - - +
388A PHE* 3.2 30.2 - + - -
389A MET* 1.3 78.3 - - - +
391A PHE* 1.3 53.0 + - - +
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Residues in contact with PHE 391 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159A LEU 4.5 4.7 - - - -
160A PHE* 3.4 5.0 - - - +
161A GLY 2.8 26.4 + - - +
281A SER* 3.6 22.9 - - - +
282A ASP* 5.9 2.7 - - + -
292A LEU* 4.1 8.0 - - - +
296A PHE* 5.5 0.2 - - - -
362A VAL* 4.7 9.6 - - + -
365A PHE* 4.0 20.2 - + + -
366A PHE* 3.6 33.2 - + + -
389A MET* 4.6 0.2 - - + -
390A TYR* 1.3 75.1 - - - +
392A ASP* 1.3 91.9 + - - +
393A SER* 4.0 6.7 - - - -
876A LEU* 4.1 20.2 - - + -
879A LEU* 3.7 31.4 - - + -
908A PHE* 4.4 15.9 - + - -
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Residues in contact with ASP 392 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159A LEU 3.1 9.0 - - - +
160A PHE* 3.6 24.9 - - + -
281A SER* 4.9 0.4 + - - -
285A LYS* 2.7 35.6 + - - +
288A ARG* 2.6 40.6 + - - +
292A LEU* 4.6 5.3 - - + +
347A LEU* 4.4 1.9 - - - +
391A PHE* 1.3 91.9 - - - +
393A SER* 1.3 61.4 + - - +
394A LEU* 2.9 19.2 + - + +
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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