Contacts of the helix formed by residues 368 - 384 (chain A) in PDB entry 3K5M
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 GLY 368 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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361A LEU* 3.6 13.4 - - - +
365A ARG* 5.4 2.2 - - - -
366A HIS 3.3 5.3 + - - -
367A GLY* 1.3 72.7 - - - +
369A SER* 1.3 65.4 + - - +
370A VAL 3.3 2.9 - - - -
371A ALA* 3.4 7.7 + - - +
372A ALA* 2.9 24.7 + - - +
800T G 5.8 9.2 - - - -
801T T 6.3 0.9 - - - -
802T C 3.8 15.2 + - - -
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Residues in contact with SER 369 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367A GLY* 3.3 7.2 - - - -
368A GLY* 1.3 75.8 - - - +
370A VAL* 1.3 57.7 + - - +
372A ALA* 3.3 6.4 + - - +
373A PHE* 2.9 30.3 + - - +
498A ALA* 3.5 21.5 - - - +
499A PHE* 5.3 3.2 - - - -
502A VAL* 4.0 6.0 - - - +
802T C 3.3 47.9 + - - -
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Residues in contact with VAL 370 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
369A SER* 1.3 73.6 - - - +
371A ALA* 1.3 68.2 + - - +
373A PHE* 3.3 6.1 + - - +
374A GLY* 3.1 17.7 + - - -
502A VAL* 4.0 18.4 - - + -
505A THR* 5.4 0.7 - - + -
507A ALA* 4.2 21.8 - - + +
508A CYS* 4.4 17.7 - - + -
509A ARG* 5.4 3.1 - - - +
510A PHE* 6.1 0.2 - - - -
801T T 3.9 16.6 - - + -
802T C 3.2 29.1 + - - +
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Residues in contact with ALA 371 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116A MET* 5.8 0.2 - - - +
361A LEU* 4.0 16.8 - - + +
368A GLY* 3.4 11.0 + - - +
369A SER 3.4 0.2 - - - -
370A VAL* 1.3 80.6 - - - +
372A ALA* 1.3 57.6 + - - +
374A GLY* 3.1 3.3 + - - +
375A HIS* 2.9 28.4 + - - +
800T G 5.8 8.7 - - - -
802T C 4.7 0.2 + - - -
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Residues in contact with ALA 372 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
359A ASN* 3.7 36.8 - - + +
361A LEU* 3.8 7.4 - - + +
367A GLY 5.3 0.2 - - - +
368A GLY 2.9 19.3 + - - +
369A SER* 3.5 8.1 - - - +
371A ALA* 1.3 74.2 - - - +
373A PHE* 1.3 66.3 + - - +
375A HIS* 3.2 2.2 + - - +
376A LEU* 3.2 30.0 + - + +
495A ILE* 6.0 2.7 - - + -
499A PHE* 5.0 6.5 - - + -
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Residues in contact with PHE 373 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
369A SER 2.9 17.1 + - - +
370A VAL* 3.5 6.5 - - - +
372A ALA* 1.3 78.2 - - - +
374A GLY* 1.3 56.1 + - - +
376A LEU* 3.8 1.7 - - - +
377A TYR* 2.8 60.7 + + - +
435A PRO* 4.2 7.4 - - + -
466A LEU* 3.9 22.0 - - + -
499A PHE* 3.7 33.8 - + + -
502A VAL* 3.6 23.8 - - + -
503A LEU* 3.9 25.6 - - + -
508A CYS* 4.9 2.2 - - - -
510A PHE* 3.3 41.3 - + + -
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Residues in contact with GLY 374 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116A MET* 4.5 3.4 - - - -
370A VAL 3.1 10.8 + - - -
371A ALA* 3.1 7.8 + - - -
373A PHE* 1.3 82.7 - - - +
375A HIS* 1.3 61.1 + - - +
377A TYR* 4.4 0.9 - - - -
378A PHE* 3.0 49.1 + - - +
509A ARG* 5.8 1.6 - - - -
510A PHE* 4.6 4.3 - - - -
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Residues in contact with HIS 375 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A ARG* 4.7 13.4 + - - -
112A GLU* 4.7 6.9 + - + -
115A LEU* 4.5 5.9 - - - +
116A MET* 3.5 48.8 + - + +
119A PHE 5.8 0.2 - - - -
120A ILE 2.9 31.4 + - - -
121A THR* 4.2 5.8 - - + +
359A ASN 4.3 8.5 - - - +
360A GLY* 3.6 34.2 + - - +
361A LEU* 5.2 2.2 - - + -
371A ALA 2.9 15.6 + - - +
372A ALA* 3.7 4.7 - - - +
374A GLY* 1.3 76.4 - - - +
376A LEU* 1.3 63.2 + - + +
379A PRO* 3.5 17.8 - - - +
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Residues in contact with LEU 376 (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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121A THR* 4.4 18.2 - - + -
358A VAL* 3.6 27.1 - - + +
359A ASN* 4.4 12.3 - - + +
372A ALA* 3.2 15.9 + - + +
373A PHE* 4.0 2.9 - - - +
375A HIS* 1.3 81.7 - - - +
377A TYR* 1.3 63.4 + - - +
379A PRO* 3.9 3.9 - - - +
380A ARG* 2.9 33.5 + - - +
469A ILE* 3.4 21.0 - - + +
473A ILE* 4.0 13.5 - - + -
495A ILE* 5.8 0.4 - - + -
499A PHE* 3.9 25.4 - - + -
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Residues in contact with TYR 377 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A PHE* 4.9 0.2 - + - -
373A PHE* 2.8 45.9 + + + +
374A GLY* 4.1 2.7 - - - +
376A LEU* 1.3 74.5 - - - +
378A PHE* 1.3 58.6 + - - +
380A ARG* 3.3 5.4 + - - +
381A MET* 2.9 52.3 + - + +
434A ASP* 2.7 31.0 + - - -
435A PRO* 3.1 15.5 - - + +
436A VAL* 2.9 29.8 + - + +
465A CYS* 3.6 15.0 - - + +
466A LEU* 3.8 7.6 - - + -
469A ILE* 3.9 17.4 - - + +
510A PHE* 3.8 28.0 - + + -
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Residues in contact with PHE 378 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105A GLU* 3.0 35.2 - - + -
108A VAL* 3.9 14.6 - - + -
113A ARG* 4.5 1.3 - - - -
116A MET* 3.5 25.1 - - + -
117A GLU* 4.1 1.6 - - - +
374A GLY* 3.0 37.2 + - - +
377A TYR* 1.3 75.3 - - - +
379A PRO* 1.3 65.9 - - + +
381A MET* 3.2 8.1 + - + +
382A HIS* 2.8 47.0 + + - -
388A ALA* 3.5 27.4 - - + -
509A ARG* 3.7 24.2 - - - -
510A PHE* 4.1 16.2 - + - -
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Residues in contact with PRO 379 (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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116A MET* 3.3 26.9 - - + +
117A GLU* 3.7 11.2 - - - +
119A PHE* 3.9 26.2 - - + -
375A HIS 3.5 15.9 - - - +
376A LEU* 3.9 8.1 - - - +
377A TYR 3.7 1.1 - - - -
378A PHE* 1.3 95.1 - - + +
380A ARG* 1.3 62.8 + - - +
382A HIS* 3.5 0.3 + - - +
383A ARG* 2.8 53.3 + - - +
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Residues in contact with ARG 380 (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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119A PHE* 4.0 34.5 - - + -
376A LEU* 2.9 32.8 + - - +
377A TYR 3.3 4.9 + - - +
378A PHE 3.2 0.4 - - - -
379A PRO* 1.3 77.4 - - - +
381A MET* 1.3 65.6 + - - +
383A ARG* 3.1 10.2 + - - +
384A ALA* 3.0 22.5 + - - +
465A CYS* 3.7 22.4 + - + -
468A GLU* 5.1 6.0 + - + +
469A ILE* 3.3 41.6 - - - +
472A ASN* 3.7 22.6 + - - +
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Residues in contact with MET 381 (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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73A PHE* 4.1 5.2 - - - -
105A GLU* 3.4 2.0 - - - +
377A TYR* 2.9 30.6 + - + +
378A PHE* 3.5 9.4 - - + +
380A ARG* 1.3 74.5 - - - +
382A HIS* 1.3 94.5 + - + +
384A ALA* 3.0 15.5 + - - +
386A TYR* 3.1 34.7 + - + +
387A VAL 3.8 1.8 - - - -
388A ALA* 3.0 48.7 - - + +
436A VAL* 4.0 9.2 - - + -
465A CYS* 3.8 10.5 - - - -
510A PHE* 3.9 18.8 - - - -
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Residues in contact with HIS 382 (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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44A PHE* 4.5 5.2 - + - -
70A LEU* 3.5 22.8 - - + +
105A GLU* 2.7 40.0 + - - -
113A ARG* 4.3 4.3 - - - -
117A GLU* 2.8 41.1 + - - +
378A PHE* 2.8 28.4 + + - +
379A PRO 3.7 4.7 - - - +
381A MET* 1.3 82.9 - - + +
383A ARG* 1.3 59.6 + - - +
385A GLY* 3.0 15.2 + - - -
386A TYR 2.9 28.7 - - - -
387A VAL* 4.2 7.9 - - + +
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Residues in contact with ARG 383 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A GLU* 3.1 35.2 + - - +
118A ARG* 5.0 0.8 - - - +
119A PHE* 3.1 37.9 - - - -
379A PRO* 2.8 39.8 + - - +
380A ARG* 3.1 8.9 + - - +
382A HIS* 1.3 76.9 - - - +
384A ALA* 1.3 60.0 + - - +
385A GLY* 3.1 1.9 + - - -
463A LYS* 4.9 2.1 + - - -
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Residues in contact with ALA 384 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
380A ARG 3.0 11.1 + - - +
381A MET* 3.0 13.7 + - - +
383A ARG* 1.3 77.5 - - - +
385A GLY* 1.3 60.2 + - - +
386A TYR* 3.5 8.3 - - + -
436A VAL* 4.3 8.5 - - + -
463A LYS* 3.1 49.3 + - + +
464A HIS 5.9 0.2 - - - +
465A CYS* 4.1 15.0 - - - -
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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
------------------------------------------------------------
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