Contacts of the strand formed by residues 358 - 362 (chain A) in PDB entry 3M6L
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 358 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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348A LEU* 3.7 21.1 - - + -
351A LEU* 3.7 40.4 - - + +
352A ALA* 3.8 17.7 - - + +
355A LEU* 3.0 33.4 + - + +
356A GLU 3.5 0.2 - - - -
357A GLY* 1.3 73.2 - - - +
359A LEU* 1.3 62.2 + - - +
383A LYS* 2.7 32.2 + - - +
408A LEU* 3.4 26.0 - - + +
410A PHE* 3.6 34.3 - + - -
436A PHE* 4.2 11.2 - + - -
483A TRP* 4.0 15.7 - + - -
487A LEU* 5.1 1.6 - - + -
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Residues in contact with LEU 359 (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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132A LYS* 4.1 28.0 - - + -
357A GLY 3.5 16.4 - - - +
358A PHE* 1.3 75.2 - - - +
360A GLY* 1.3 59.9 + - - +
373A LEU* 4.4 7.4 - - - -
379A PHE* 4.8 3.8 - - + -
383A LYS* 3.5 23.6 - - + +
385A ILE* 4.2 15.5 - - + -
401A PHE* 4.0 31.0 - - + -
407A PHE* 3.9 18.8 - - + -
408A LEU 3.3 5.8 + - - +
409A PRO* 3.2 11.9 - - + +
410A PHE* 3.0 30.8 + - - -
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Residues in contact with GLY 360 (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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359A LEU* 1.3 80.5 - - - +
361A GLY* 1.3 57.9 + - - -
373A LEU* 4.6 0.4 - - - +
383A LYS 3.4 7.2 + - - +
384A ASN* 3.6 4.5 - - - +
385A ILE* 2.9 36.7 + - - +
387A PHE* 4.3 1.6 - - - -
398A ASN* 4.8 2.7 - - - -
409A PRO* 5.1 0.4 - - - -
410A PHE* 3.3 27.5 - - - -
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Residues in contact with GLY 361 (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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360A GLY* 1.3 76.3 - - - -
362A SER* 1.3 61.3 + - - -
371A THR* 4.7 2.7 - - - -
384A ASN* 5.5 0.9 - - - -
385A ILE 3.3 15.0 - - - -
387A PHE* 3.8 9.4 - - - -
394A MSE 3.8 1.2 - - - +
410A PHE* 3.3 23.3 + - - +
411A SER* 3.7 1.2 - - - -
412A ALA* 3.0 24.7 + - - +
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Residues in contact with SER 362 (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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361A GLY* 1.3 74.6 - - - -
363A ALA* 1.3 60.7 + - - +
364A ASP* 3.1 6.3 + - - -
365A LEU* 3.0 16.2 + - - +
366A GLY* 3.5 20.2 - - - -
369A ASN* 2.7 27.0 + - - -
371A THR* 3.6 16.3 + - - -
385A ILE 3.8 2.8 + - - +
386A HIS* 4.4 1.4 - - - -
387A PHE* 3.4 20.6 + - - +
394A MSE 3.9 4.7 - - - -
412A ALA* 3.3 6.7 + - - -
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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