Contacts of the helix formed by residues 497 - 515 (chain A) in PDB entry 4PKO
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 THR 497 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131A LEU* 3.9 23.3 - - + +
132A LYS* 4.7 4.0 - - + +
135A SER* 3.1 24.9 + - - +
409A GLU* 3.6 18.4 - - + +
410A GLY 2.5 31.3 + - - -
411A VAL* 3.1 12.8 + - - -
412A VAL* 3.5 13.7 - - + +
495A ASP 3.2 3.4 + - - -
496A PRO* 1.3 71.7 - - - +
498A LYS* 1.3 55.7 + - - +
500A THR* 3.4 1.6 + - - -
501A ARG* 2.8 32.1 + - + +
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Residues in contact with LYS 498 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A ALA* 3.8 27.6 + - - +
85A ALA* 5.4 2.5 - - + -
405A ALA* 4.0 23.9 - - + +
408A GLU* 3.0 29.5 + - - +
409A GLU* 3.8 27.5 - - + +
496A PRO 3.1 0.6 - - - -
497A THR* 1.3 80.4 - - - +
499A VAL* 1.3 54.5 + - - +
501A ARG* 3.7 23.7 + - - +
502A SER* 2.6 46.3 + - - +
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Residues in contact with VAL 499 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85A ALA* 3.7 24.7 - - + -
87A ASP* 3.6 31.3 - - + +
88A GLY* 4.7 8.2 - - - -
402A ALA* 5.0 1.8 - - - -
405A ALA* 4.3 8.5 - - + -
495A ASP* 4.9 5.2 - - + +
496A PRO* 3.1 45.3 + - + +
498A LYS* 1.3 72.8 - - - +
500A THR* 1.3 72.2 + - - +
502A SER* 3.9 0.8 - - - -
503A ALA* 2.8 32.7 + - - +
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Residues in contact with THR 500 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91A THR* 6.2 0.3 - - - +
95A LEU* 5.5 0.2 - - - +
131A LEU* 3.6 17.4 - - + +
412A VAL* 4.4 7.5 - - - +
418A ALA* 4.5 5.4 - - + -
419A LEU* 3.4 41.2 - - + +
495A ASP* 3.6 29.8 + - - +
496A PRO 3.4 4.7 + - - -
497A THR 4.0 4.9 - - - -
498A LYS 3.3 0.4 - - - -
499A VAL* 1.3 80.5 - - - +
501A ARG* 1.3 65.7 + - - +
503A ALA* 4.0 4.0 - - - +
504A LEU* 3.2 24.1 + - - +
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Residues in contact with ARG 501 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128A VAL* 4.0 26.6 - - + +
131A LEU* 3.7 18.6 - - + +
132A LYS* 4.2 11.5 - - + +
409A GLU* 2.8 41.5 + - - +
497A THR* 2.8 22.8 + - + +
498A LYS* 3.7 17.1 + - - +
500A THR* 1.3 79.9 - - - +
502A SER* 1.3 73.9 + - - +
504A LEU* 3.8 2.5 - - - +
505A GLN* 3.1 61.4 + - - +
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Residues in contact with SER 502 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A ALA* 5.4 2.7 - - - -
84A ALA* 4.2 15.3 - - - +
85A ALA* 4.8 5.7 - - - +
498A LYS* 2.6 38.7 + - - +
499A VAL* 3.9 5.6 - - - -
501A ARG* 1.3 80.7 + - - +
503A ALA* 1.3 66.4 + - - +
505A GLN* 3.2 9.4 + - - +
506A TYR* 3.1 45.0 + - - -
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Residues in contact with ALA 503 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A ALA* 5.1 5.1 - - + +
88A GLY* 3.8 11.7 - - - +
91A THR* 4.7 5.6 - - + -
92A ALA* 3.3 36.1 - - + +
95A LEU* 3.9 7.2 - - + +
499A VAL 2.8 23.5 + - - +
500A THR* 4.0 5.2 - - - +
502A SER* 1.3 73.6 - - - +
504A LEU* 1.3 61.9 + - - +
506A TYR* 4.4 0.4 - - - -
507A ALA* 3.3 26.0 + - - +
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Residues in contact with LEU 504 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95A LEU* 3.6 26.2 - - + +
99A ILE* 5.4 7.9 - - + -
124A VAL* 3.4 45.5 - - + +
127A ALA* 5.2 2.7 - - + -
128A VAL* 5.1 3.6 - - + -
131A LEU* 5.4 3.8 - - + -
419A LEU* 4.4 9.0 - - + -
447A MET* 4.2 37.9 - - + -
500A THR 3.2 16.5 + - - +
501A ARG* 3.8 4.9 - - - +
503A ALA* 1.3 80.9 - - - +
505A GLN* 1.3 64.8 + - + +
507A ALA* 4.0 1.0 - - - +
508A ALA* 3.2 19.8 + - + +
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Residues in contact with GLN 505 (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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124A VAL* 4.6 9.2 - - + -
128A VAL* 3.6 30.5 - - + +
501A ARG* 3.1 53.8 + - - +
502A SER* 3.2 7.0 + - - +
504A LEU* 1.3 79.9 - - - +
506A TYR* 1.3 67.2 + - + +
508A ALA* 3.3 4.2 + - - +
509A SER* 3.0 28.9 + - - -
183B LEU* 4.7 19.6 - - + +
384B ALA* 5.6 4.9 - - + +
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Residues in contact with TYR 506 (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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77A VAL* 3.4 18.9 - - + +
80A LYS* 3.3 46.2 + - + +
81A ALA* 3.5 21.3 - - + -
84A ALA* 3.8 23.1 - - + +
502A SER* 3.1 29.0 + - - +
503A ALA 4.4 1.8 - - - +
505A GLN* 1.3 83.9 - - + +
507A ALA* 1.3 66.8 + - - +
509A SER* 3.2 12.7 + - - -
510A VAL* 3.3 18.4 + - - +
384B ALA* 3.7 27.3 + - + -
385B THR* 3.7 17.2 - - + +
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Residues in contact with ALA 507 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A VAL* 3.2 12.9 - - + +
92A ALA 3.2 27.1 - - - +
95A LEU* 3.9 8.7 - - + -
96A ALA* 3.6 18.6 - - + +
99A ILE* 4.1 3.1 - - + -
503A ALA 3.3 14.7 + - - +
504A LEU 4.0 2.0 - - - +
506A TYR* 1.3 78.4 - - - +
508A ALA* 1.3 60.4 + - - +
510A VAL* 3.7 1.4 - - - +
511A ALA* 3.0 31.9 + - - +
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Residues in contact with ALA 508 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99A ILE* 3.7 18.6 - - + +
117A LYS* 4.8 0.2 + - - -
120A ILE* 4.4 9.4 - - + +
121A ASP* 4.6 10.6 - - - +
124A VAL* 3.7 28.7 - - + -
504A LEU* 3.2 17.6 + - + +
505A GLN* 3.6 4.7 - - - +
507A ALA* 1.3 76.7 - - - +
509A SER* 1.3 60.2 + - - +
511A ALA* 4.7 0.2 - - - -
512A GLY* 2.8 28.4 + - - -
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Residues in contact with SER 509 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A LYS* 4.0 10.8 + - - +
121A ASP* 5.2 2.9 - - - -
505A GLN 3.0 16.6 + - - -
506A TYR* 3.2 6.7 + - - -
508A ALA* 1.3 79.6 - - - +
510A VAL* 1.3 61.7 + - - +
513A LEU* 3.3 23.3 + - - +
384B ALA* 3.8 11.5 - - - +
385B THR* 3.4 22.8 + - - -
388B GLU* 3.2 26.0 + - - +
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Residues in contact with VAL 510 (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 MET 4.8 7.6 - - - +
74A VAL* 5.3 1.3 - - + -
76A GLU* 4.7 9.2 - - + -
77A VAL* 3.6 28.3 - - + +
96A ALA* 5.3 2.2 - - + -
506A TYR 3.5 15.9 - - - +
507A ALA* 3.7 4.7 - - - +
509A SER* 1.3 74.0 - - - +
511A ALA* 1.3 65.9 + - + +
513A LEU* 3.3 8.3 + - - +
514A MET* 2.9 45.9 + - + +
49B ILE* 5.2 0.7 - - - +
385B THR* 3.9 26.0 - - + +
387B VAL* 3.9 17.5 - - + -
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Residues in contact with ALA 511 (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 ALA* 4.1 3.8 - - - +
99A ILE* 3.7 24.7 - - + -
100A ILE* 3.2 35.6 - - + +
507A ALA 3.0 18.5 + - - +
508A ALA 4.3 0.2 - - - +
510A VAL* 1.3 78.6 - - + +
512A GLY* 1.3 66.9 + - - +
514A MET* 3.1 10.2 + - - +
515A ILE* 3.3 21.3 + - - +
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Residues in contact with GLY 512 (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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99A ILE* 4.9 0.8 - - - +
117A LYS* 3.5 25.9 - - - +
120A ILE* 4.7 11.0 - - - -
121A ASP* 5.8 0.4 - - - -
508A ALA 2.8 20.4 + - - -
509A SER 4.1 0.7 - - - -
511A ALA* 1.3 77.2 - - - +
513A LEU* 1.3 59.4 + - - +
515A ILE* 3.3 23.8 - - - +
516A THR* 3.5 10.2 - - - +
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Residues in contact with LEU 513 (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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117A LYS* 4.1 17.0 - - + +
509A SER 3.3 14.7 + - - +
510A VAL* 3.3 9.8 + - - +
512A GLY* 1.3 76.1 - - - +
514A MET* 1.3 60.4 + - - +
516A THR* 2.3 31.6 + - + +
517A THR* 4.3 1.2 + - - -
37B ASN* 4.3 17.7 - - - +
49B ILE* 4.1 28.4 - - + +
387B VAL* 4.2 14.8 - - + +
388B GLU* 3.5 44.6 - - + +
391B GLU* 4.6 17.0 - - + +
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Residues in contact with MET 514 (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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16A MET* 3.5 33.8 - - + +
20A VAL* 4.4 9.4 - - - -
70A GLY 4.4 1.1 - - - +
73A MET* 3.8 42.2 - - + -
74A VAL* 3.9 21.5 - - + -
100A ILE* 3.6 24.0 - - + -
104A LEU* 4.3 0.2 - - - +
510A VAL* 2.9 37.8 + - + +
511A ALA* 3.1 9.3 + - - +
513A LEU* 1.3 73.2 - - - +
515A ILE* 1.3 59.8 + - + +
516A THR 3.1 4.9 - - - -
517A THR* 2.6 24.9 + - - +
49B ILE* 4.5 5.8 - - + -
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Residues in contact with ILE 515 (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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13A ARG* 5.2 1.4 + - - -
99A ILE* 5.0 1.6 - - + +
100A ILE* 4.1 12.6 - - + +
103A GLY* 3.9 22.0 - - - +
104A LEU* 3.6 40.7 - - + +
107A VAL* 4.0 11.0 - - + +
113A PRO* 3.3 19.1 - - - +
116A LEU* 4.0 30.3 - - + -
117A LYS 4.7 1.8 - - - +
120A ILE* 4.3 18.4 - - + -
511A ALA 3.5 11.7 - - - +
512A GLY* 3.3 18.4 - - - +
514A MET* 1.3 75.3 - - - +
516A THR* 1.3 60.7 + - + +
517A THR 3.2 7.9 + - - +
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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