Contacts of the strand formed by residues 414 - 421 (chain A) in PDB entry 4MCS
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 ARG 414 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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364A GLY* 3.5 4.0 - - - -
367A GLU* 3.2 35.5 + - + +
370A ARG* 3.6 28.2 - - + +
372A VAL* 4.5 3.1 - - + -
412A PRO* 3.3 24.8 - - - +
413A ARG* 1.3 82.8 - - + +
415A THR* 1.3 67.3 + - - +
416A ILE* 3.5 1.9 + - - +
447A VAL* 4.1 13.8 - - - +
586A GLU 4.6 0.2 + - - -
587A LEU 2.9 26.0 + - - -
588A ALA* 2.9 24.4 + - - +
590A SER* 2.8 30.5 + - - +
591A ILE 3.1 17.0 + - - -
593A LEU* 3.6 21.3 - - - +
665A ASN* 3.5 10.5 - - - +
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Residues in contact with THR 415 (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 THR* 4.1 10.3 - - + -
362A LEU 3.4 12.6 - - - +
363A ARG* 3.7 3.6 - - - +
364A GLY* 3.0 15.9 + - - +
367A GLU 3.6 2.4 + - - -
368A PRO* 2.7 25.2 + - - +
370A ARG 2.9 16.3 + - - +
371A TYR* 3.5 12.3 - - + -
372A VAL* 2.9 26.9 + - - +
414A ARG* 1.3 72.3 - - - +
416A ILE* 1.3 63.6 + - - +
417A LEU* 3.7 28.7 - - + -
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Residues in contact with ILE 416 (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 3.9 0.3 - - - +
361A THR* 3.6 2.3 - - - -
362A LEU* 2.8 44.2 + - + +
372A VAL* 3.2 11.9 - - + +
374A LEU 5.0 1.1 - - - +
402A PHE* 3.8 37.0 - - + -
412A PRO* 4.0 15.0 - - + -
414A ARG 4.1 3.4 - - - +
415A THR* 1.3 73.2 - - - +
417A LEU* 1.3 69.9 + - - +
418A PHE* 3.4 32.2 - - + -
584A VAL* 3.8 14.8 - - + -
588A ALA* 3.5 33.4 - - + -
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Residues in contact with LEU 417 (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 ILE* 5.3 9.0 - - + -
360A GLY 3.4 3.8 - - - +
361A THR* 3.6 26.0 - - + +
371A TYR* 4.1 35.9 - - + -
372A VAL 2.8 6.9 + - - +
373A ILE* 3.3 20.2 - - + +
374A LEU 2.8 27.0 + - - +
415A THR* 3.7 23.6 - - + -
416A ILE* 1.3 77.1 - - - +
418A PHE* 1.3 63.4 + - - +
434A TRP* 4.1 29.2 - - + -
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Residues in contact with PHE 418 (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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100A TRP* 3.5 22.7 - - + -
105A LEU* 3.7 34.8 - - + -
359A ILE* 3.4 5.5 - - - +
360A GLY 2.7 39.8 + - - +
362A LEU* 4.1 8.1 - - + -
374A LEU* 3.3 34.3 - - + +
395A VAL* 4.8 2.0 - - + -
398A ILE* 4.2 1.8 - - + -
399A VAL* 3.5 24.5 - - + -
402A PHE* 3.7 36.1 - + + -
416A ILE* 3.4 34.1 - - + -
417A LEU* 1.3 74.5 - - - +
419A ALA* 1.3 62.5 + - - +
584A VAL* 5.1 0.2 - - + -
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Residues in contact with ALA 419 (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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100A TRP* 3.8 6.8 - - - -
358A VAL 3.3 3.4 - - - -
359A ILE* 4.0 7.2 - - + -
373A ILE* 5.0 4.0 - - + -
374A LEU 2.9 10.6 + - - +
375A GLY* 3.5 7.1 - - - -
376A GLY 3.1 24.9 + - - +
395A VAL* 4.9 5.4 - - - +
417A LEU* 4.2 0.4 - - + -
418A PHE* 1.3 76.4 - - - +
420A SER* 1.3 58.7 + - - +
421A TRP* 3.4 46.9 - - + -
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Residues in contact with SER 420 (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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96A ILE* 4.5 8.3 - - - +
100A TRP* 3.8 11.8 - - - -
357A ASN* 3.3 2.8 - - - -
358A VAL* 3.0 47.8 + - - -
376A GLY 3.4 5.4 - - - -
377A HIS 5.3 0.2 - - - -
378A ARG* 3.0 43.3 + - - +
392A ALA* 6.1 0.2 - - - +
419A ALA* 1.3 70.8 - - - +
421A TRP* 1.3 59.4 + - - +
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Residues in contact with TRP 421 (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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357A ASN* 3.4 22.4 - - + +
359A ILE* 3.7 20.4 - - + -
373A ILE* 4.8 2.9 - - + -
375A GLY* 3.7 4.9 - - - -
376A GLY 2.9 27.6 + - - -
377A HIS* 3.2 5.7 - - + +
378A ARG* 2.9 29.7 + - - +
419A ALA* 3.4 22.7 - - + -
420A SER* 1.3 72.8 - - - +
422A ASP* 1.3 63.5 + - - +
431A SER* 3.5 24.7 - - - +
434A TRP* 3.4 46.4 - + + -
449A TYR* 2.9 24.9 + + - -
520A ASP* 3.3 37.5 - - + +
524A PHE* 3.6 22.0 - + - -
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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