Contacts of the strand formed by residues 355 - 361 (chain A) in PDB entry 5MCO
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 GLN 355 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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250A TRP* 3.7 26.2 - - - -
251A TYR 5.6 0.4 + - - -
349A MET* 4.4 2.8 - - - +
350A GLY* 2.8 32.9 + - - -
351A GLU* 3.2 25.1 + - - +
352A VAL* 3.2 34.3 + - + +
353A THR 3.0 1.8 + - - +
354A ASN* 1.3 79.6 + - - +
356A SER* 1.3 80.8 + - - +
357A PHE* 4.2 1.2 - - - +
434A PRO* 3.9 21.7 - - + +
435A PHE 3.3 5.8 - - - +
436A VAL* 4.7 2.7 - - + +
437A THR* 4.2 2.6 - - - +
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Residues in contact with SER 356 (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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265A VAL* 3.8 15.7 - - - +
347A TYR* 4.0 9.8 - - - -
348A LEU 3.2 18.6 - - - -
349A MET* 4.6 0.2 - - - -
350A GLY 3.7 1.3 - - - +
355A GLN* 1.3 89.0 + - - +
357A PHE* 1.3 64.0 + - - +
434A PRO* 3.5 1.0 - - - +
435A PHE* 2.8 40.0 + - - +
437A THR* 3.0 24.0 - - - +
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Residues in contact with PHE 357 (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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250A TRP* 3.4 57.4 - + + -
251A TYR 3.3 32.3 - - - -
252A THR* 3.8 10.5 - - - -
347A TYR* 3.1 3.9 - - - -
348A LEU* 2.8 62.1 + - + +
349A MET 3.9 4.5 - - - -
350A GLY* 4.5 0.2 - - - -
355A GLN* 4.4 3.4 - - - -
356A SER* 1.3 76.9 - - - +
358A ARG* 1.3 72.1 + - - +
359A ILE* 4.0 12.8 - - + -
415A PHE* 4.1 5.6 - + - -
431A VAL* 4.0 4.7 - - + -
432A GLU 3.2 14.8 - - - +
433A GLY* 4.1 0.7 - - - -
435A PHE* 3.7 7.4 - - - -
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Residues in contact with ARG 358 (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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268A GLU* 4.2 3.8 + - - -
345A SER* 3.7 18.1 + - - -
346A LEU 3.0 12.8 - - - +
347A TYR* 2.9 48.8 + - + -
357A PHE* 1.3 77.0 - - - +
359A ILE* 1.3 64.9 + - - +
360A THR* 4.1 5.2 + - - +
430A ALA 4.0 0.5 - - - +
431A VAL* 3.2 7.8 - - - +
432A GLU* 2.8 74.0 + - + +
435A PHE* 3.6 31.8 - - + -
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Residues in contact with ILE 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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344A ILE 3.7 0.5 - - - +
345A SER* 3.2 4.3 - - - -
346A LEU* 2.8 52.0 + - + +
348A LEU* 4.3 6.7 - - + +
357A PHE* 4.0 11.2 - - + -
358A ARG* 1.3 76.2 - - - +
360A THR* 1.3 64.0 + - - +
361A ILE* 4.3 0.9 - - + -
394A MET* 3.7 30.1 - - + -
398A ILE* 3.8 19.3 - - + -
402A PHE* 3.7 17.0 - - + -
415A PHE* 3.8 37.7 - - + -
430A ALA 3.4 4.5 - - - -
431A VAL* 4.2 7.4 - - + -
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Residues in contact with THR 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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343A VAL* 3.6 34.1 - - + -
344A ILE 3.3 5.2 - - - +
345A SER* 2.7 26.4 + - - +
358A ARG* 4.1 12.1 + - - +
359A ILE* 1.3 74.3 - - - +
361A ILE* 1.3 63.2 + - - +
362A LEU* 5.3 2.7 - - + -
402A PHE* 3.4 5.9 - - - -
428A THR 5.4 2.0 - - - +
429A ALA* 3.2 8.7 - - - -
430A ALA* 2.8 41.9 + - + -
432A GLU* 4.5 3.8 + - - -
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Residues in contact with ILE 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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295A LEU* 4.8 4.5 - - + -
342A PRO 4.7 0.2 - - - +
343A VAL* 3.3 7.8 - - - +
344A ILE* 3.0 49.2 + - + +
346A LEU* 6.5 0.4 - - + -
359A ILE* 5.5 1.1 - - + -
360A THR* 1.3 73.4 - - - +
362A LEU* 1.3 65.0 + - - +
365A GLN* 3.6 15.9 - - + +
366A TYR* 4.1 19.5 - - + -
397A VAL* 3.9 28.7 - - + +
398A ILE* 3.7 29.4 - - + -
401A GLY* 5.2 0.2 - - - -
402A PHE* 3.5 30.3 - - + -
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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