Contacts of the helix formed by residues 497 - 515 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131B LEU* 4.4 20.9 - - + +
132B LYS* 5.2 5.2 - - + +
135B SER* 3.3 19.7 + - - -
409B GLU* 3.4 24.5 - - + +
410B GLY 2.7 36.1 + - - -
411B VAL* 3.1 12.1 + - - -
412B VAL* 3.8 10.2 - - + +
495B ASP 3.2 3.4 + - - -
496B PRO* 1.3 71.3 - - - +
498B LYS* 1.3 56.6 + - - +
500B THR* 3.8 4.7 - - - +
501B ARG* 2.8 35.8 + - + +
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Residues in contact with LYS 498 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84B ALA* 3.5 29.9 + - - -
85B ALA* 4.8 4.0 - - + +
405B ALA* 3.5 30.4 - - + +
408B GLU* 3.1 30.1 + - - +
409B GLU* 3.7 33.1 - - + +
496B PRO 3.0 0.4 - - - -
497B THR* 1.3 80.6 - - - +
499B VAL* 1.3 58.9 + - + +
501B ARG* 3.3 11.2 + - - +
502B SER* 2.8 42.0 + - - +
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Residues in contact with VAL 499 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85B ALA* 3.9 23.6 - - + -
87B ASP* 3.9 28.0 - - + +
88B GLY* 4.5 12.6 - - - +
91B THR* 5.9 1.1 - - - +
402B ALA* 5.1 1.6 - - - -
405B ALA* 4.5 8.1 - - + -
495B ASP* 5.0 4.7 - - + +
496B PRO* 3.1 44.3 + - + +
498B LYS* 1.3 74.7 - - - +
500B THR* 1.3 69.3 + - - +
502B SER* 4.0 2.0 - - - -
503B ALA* 3.0 31.2 + - - +
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Residues in contact with THR 500 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91B THR* 5.8 5.3 - - - +
131B LEU* 4.0 18.3 - - + +
412B VAL* 4.9 4.3 - - + +
418B ALA* 4.7 9.0 - - + +
419B LEU* 3.7 36.4 - - + +
495B ASP* 3.7 28.9 + - - +
496B PRO 3.4 4.1 + - - -
497B THR* 4.0 7.6 - - - -
498B LYS 3.3 0.2 - - - -
499B VAL* 1.3 82.5 - - - +
501B ARG* 1.3 64.3 + - - +
503B ALA* 3.6 4.3 + - - +
504B LEU* 3.4 21.8 + - - +
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Residues in contact with ARG 501 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128B VAL* 3.9 24.3 - - + +
131B LEU* 4.2 16.1 - - + +
132B LYS* 4.4 9.6 - - + +
409B GLU* 2.7 42.7 + - - +
497B THR* 2.8 23.3 + - + +
498B LYS* 3.6 13.8 + - - +
500B THR* 1.3 78.9 - - - +
502B SER* 1.3 74.2 + - - +
504B LEU* 3.5 3.4 + - - +
505B GLN* 3.1 64.7 + - - +
183C LEU* 6.2 1.0 - - - +
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Residues in contact with SER 502 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81B ALA* 5.5 3.1 - - - -
84B ALA* 4.3 14.4 - - - +
85B ALA* 5.3 4.4 + - - -
498B LYS* 2.8 31.0 + - - +
499B VAL* 4.0 5.4 - - - -
501B ARG* 1.3 88.0 + - - +
503B ALA* 1.3 65.6 + - - +
505B GLN* 3.3 6.8 + - - +
506B TYR* 2.9 49.4 + - - -
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Residues in contact with ALA 503 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81B ALA* 5.2 2.7 - - - +
88B GLY 3.9 6.7 - - - +
91B THR* 4.3 7.4 - - + -
92B ALA* 3.5 38.9 - - + +
95B LEU* 3.9 9.2 - - + -
499B VAL 3.0 19.4 + - - +
500B THR* 4.0 6.1 - - - +
501B ARG 3.4 0.2 - - - -
502B SER* 1.3 75.3 - - - +
504B LEU* 1.3 58.4 + - - +
506B TYR* 5.0 0.7 - - - -
507B ALA* 3.0 33.1 + - - +
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Residues in contact with LEU 504 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95B LEU* 3.7 30.6 - - + +
99B ILE* 4.8 11.2 - - + -
124B VAL* 4.5 21.5 - - + +
127B ALA* 4.2 15.3 - - + -
128B VAL* 5.8 3.8 - - + +
131B LEU* 5.5 5.4 - - + -
419B LEU* 4.0 19.1 - - + -
443B ALA* 6.5 0.2 - - + -
447B MET* 4.0 31.9 - - + -
500B THR 3.4 14.6 + - - +
501B ARG* 3.8 4.5 - - - +
502B SER 3.2 0.2 - - - -
503B ALA* 1.3 79.5 - - - +
505B GLN* 1.3 58.0 + - + +
507B ALA* 4.5 0.2 - - - -
508B ALA* 2.9 32.9 + - - +
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Residues in contact with GLN 505 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124B VAL* 4.5 13.2 - - + -
128B VAL* 3.7 28.1 - - + +
501B ARG* 3.1 54.2 + - - +
502B SER* 3.3 6.0 + - - +
504B LEU* 1.3 78.6 - - - +
506B TYR* 1.3 68.8 + - + +
508B ALA* 3.3 3.1 + - - +
509B SER* 2.9 28.8 + - - -
183C LEU* 4.5 25.7 - - + +
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Residues in contact with TYR 506 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77B VAL* 3.3 24.0 - - + +
80B LYS* 3.3 70.0 + - + +
81B ALA* 3.9 4.9 - - - -
84B ALA* 3.7 19.9 - - + +
92B ALA* 5.4 0.4 - - + -
502B SER* 2.9 31.8 + - - +
503B ALA* 4.3 2.0 - - - +
505B GLN* 1.3 83.5 - - + +
507B ALA* 1.3 66.0 + - - +
509B SER* 3.3 17.1 + - - -
510B VAL* 3.4 14.4 + - - +
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Residues in contact with ALA 507 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77B VAL* 3.1 14.0 - - + +
92B ALA 3.3 23.6 - - - +
95B LEU* 3.7 10.3 - - + -
96B ALA* 3.5 16.1 - - - +
99B ILE* 4.4 2.9 - - + -
503B ALA 3.0 20.1 + - - +
504B LEU 3.8 2.5 - - - +
506B TYR* 1.3 76.2 - - - +
508B ALA* 1.3 57.8 + - - +
510B VAL* 3.7 1.9 - - - +
511B ALA* 2.9 33.5 + - - +
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Residues in contact with ALA 508 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99B ILE* 4.0 15.0 - - + +
117B LYS* 4.7 0.3 + - - -
120B ILE* 4.5 4.1 - - + +
121B ASP* 4.4 13.3 - - - +
124B VAL* 3.4 33.7 - - + -
504B LEU 2.9 19.1 + - - +
505B GLN 3.6 4.5 - - - +
507B ALA* 1.3 75.3 - - - +
509B SER* 1.3 59.3 + - - +
511B ALA* 4.5 0.7 - - - -
512B GLY* 2.7 31.0 + - - -
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Residues in contact with SER 509 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117B LYS* 4.3 8.6 + - - +
121B ASP* 5.3 1.8 - - - -
505B GLN 2.9 16.6 + - - -
506B TYR* 3.3 14.5 + - - -
508B ALA* 1.3 79.6 - - - +
510B VAL* 1.3 65.2 + - - +
512B GLY* 4.2 0.2 - - - -
513B LEU* 3.4 27.3 + - - +
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Residues in contact with VAL 510 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73B MET 4.0 14.4 - - - +
74B VAL* 4.9 1.3 - - + -
76B GLU* 4.4 23.3 - - + +
77B VAL* 3.5 27.6 - - + +
96B ALA* 4.8 2.9 - - + -
506B TYR 3.4 16.4 - - - +
507B ALA 3.7 4.3 - - - +
509B SER* 1.3 81.2 - - - +
511B ALA* 1.3 64.8 + - + +
513B LEU* 3.5 6.0 + - - +
514B MET* 2.9 52.1 + - + +
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Residues in contact with ALA 511 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96B ALA* 3.8 9.0 - - + +
99B ILE* 3.7 23.3 - - + -
100B ILE* 3.6 29.6 - - + -
507B ALA 2.9 23.0 + - - +
508B ALA 4.3 0.4 - - - +
510B VAL* 1.3 75.4 - - - +
512B GLY* 1.3 65.9 + - - +
514B MET* 3.2 8.8 + - - +
515B ILE* 3.3 23.0 + - - +
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Residues in contact with GLY 512 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99B ILE* 4.8 0.8 - - - +
117B LYS* 3.5 24.6 - - - +
120B ILE* 4.8 11.2 - - - -
121B ASP* 5.6 0.9 - - - -
508B ALA 2.7 23.0 + - - -
509B SER 4.2 0.2 - - - -
511B ALA* 1.3 73.5 - - - +
513B LEU* 1.3 60.2 + - - +
515B ILE* 3.2 25.2 - - - +
516B THR* 3.5 9.5 - - - +
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Residues in contact with LEU 513 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114B MET* 6.3 1.3 - - + -
117B LYS* 3.9 23.0 - - + +
509B SER* 3.4 21.0 + - - +
510B VAL* 3.9 6.1 - - - +
511B ALA 3.3 0.4 - - - -
512B GLY* 1.3 75.5 - - - +
514B MET* 1.3 60.5 + - - +
516B THR* 2.4 27.0 + - + +
517B THR* 4.3 2.8 + - - -
37C ASN* 4.2 19.7 - - - +
49C ILE* 4.3 34.7 - - + +
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Residues in contact with MET 514 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16B MET* 3.3 33.9 - - + +
20B VAL* 4.4 4.9 - - - -
70B GLY 4.2 4.3 - - - +
73B MET* 3.7 41.5 - - + +
74B VAL* 3.4 32.5 - - + -
100B ILE* 3.6 13.5 - - + -
104B LEU* 4.9 0.2 - - - +
510B VAL* 2.9 55.8 + - + +
511B ALA* 3.7 7.2 - - - +
512B GLY 3.2 0.4 - - - -
513B LEU* 1.3 79.1 - - - +
515B ILE* 1.3 57.8 + - - +
516B THR 3.1 0.9 - - - -
517B THR* 2.8 22.1 + - - +
49C ILE* 5.7 2.9 - - + -
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Residues in contact with ILE 515 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13B ARG* 5.2 0.9 + - - -
99B ILE 4.5 1.3 - - - +
100B ILE* 3.8 38.1 - - + +
103B GLY* 4.3 20.2 - - - -
104B LEU* 4.2 17.6 - - + +
107B VAL* 3.8 12.6 - - + +
113B PRO* 3.7 15.0 - - + +
116B LEU* 4.2 21.8 - - + -
117B LYS 4.8 2.7 - - - +
120B ILE* 4.0 28.0 - - + -
511B ALA 3.4 12.3 - - - +
512B GLY 3.2 18.2 - - - +
514B MET* 1.3 76.4 - - - +
516B THR* 1.3 59.7 + - + +
517B THR 3.3 6.5 + - - +
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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