Contacts of the helix formed by residues 438 - 458 (chain B) in PDB entry 1P1K
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 ASP 438 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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323B SER* 5.3 2.8 - - - -
324B GLY 5.4 3.1 + - - -
352B LEU* 4.1 9.9 - - - +
354B ASN* 4.4 2.2 - - - +
356B ASP* 4.4 1.4 - - - +
410B ASP* 3.0 20.0 + - - +
412B LYS* 3.7 41.8 + - + +
436B CYS* 3.1 11.9 + - - -
437B GLU* 1.3 70.6 - - - +
439B SER* 1.3 57.6 + - - +
441B LEU* 3.1 11.8 + - - +
442B ALA* 3.0 23.0 + - - +
660B NAI 3.1 40.9 + - - +
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Residues in contact with SER 439 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76B ASN* 3.0 21.4 - - - +
77B ASN* 3.4 10.1 + - - -
80B THR* 4.0 18.6 - - - -
163B VAL* 4.1 7.2 - - - -
410B ASP* 2.9 24.3 + - - -
437B GLU 3.2 1.0 - - - -
438B ASP* 1.3 71.8 - - - +
440B LEU* 1.3 57.0 + - - +
441B LEU 3.0 5.8 - - - -
442B ALA 4.2 0.2 - - - +
443B THR* 2.8 37.3 + - - -
660B NAI 3.0 13.9 + - - -
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Residues in contact with LEU 440 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
422A LEU* 3.9 20.6 - - + +
423A MET* 3.8 34.6 - - + +
424A LEU 5.3 1.3 - - - +
426A GLY* 3.4 34.1 - - - +
80B THR* 4.2 7.4 - - + -
106B PHE 4.7 1.2 - - - +
107B GLY* 5.3 0.3 - - - -
163B VAL* 4.1 11.9 - - + +
164B LEU* 4.0 24.9 - - + -
437B GLU* 2.9 38.7 + - + +
439B SER* 1.3 76.6 - - - +
441B LEU* 1.3 62.0 + - - +
443B THR* 4.9 0.2 - - - -
444B PRO* 3.2 18.9 - - - +
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Residues in contact with LEU 441 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341A ILE* 4.0 18.8 - - + -
422A LEU* 3.8 28.3 - - + -
428A ASN* 5.5 4.9 - - - +
107B GLY* 5.2 4.1 - - - +
324B GLY* 4.0 30.5 - - - +
434B ASN* 5.9 3.6 - - - +
436B CYS* 3.7 29.6 - - - -
437B GLU 3.7 0.4 + - - -
438B ASP* 3.1 12.9 + - - +
439B SER 3.0 0.2 - - - -
440B LEU* 1.3 82.2 - - - +
442B ALA* 1.3 60.6 + - - +
443B THR 3.4 0.2 - - - -
444B PRO* 3.1 19.4 - - + +
445B LEU* 3.5 12.2 + - - +
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Residues in contact with ALA 442 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77B ASN* 3.3 29.8 - - - +
321B LEU* 4.5 5.1 - - + +
438B ASP 3.0 9.0 + - - +
439B SER 4.0 0.4 - - - +
441B LEU* 1.3 76.7 - - - +
443B THR* 1.3 65.8 + - - +
445B LEU* 3.1 12.3 + - - +
446B ILE* 2.8 25.8 + - - +
660B NAI 3.6 30.3 - - + -
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Residues in contact with THR 443 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423A MET* 3.9 13.2 - - + -
77B ASN* 3.9 10.0 + - - -
80B THR* 3.1 28.6 - - - +
81B LEU* 3.7 30.3 - - + +
84B SER* 3.9 12.8 - - - +
439B SER 2.8 24.8 + - - -
442B ALA* 1.3 71.1 - - - +
444B PRO* 1.3 63.2 - - + +
446B ILE* 2.7 34.0 + - - +
447B ILE* 2.9 11.3 + - + +
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Residues in contact with PRO 444 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423A MET* 3.5 22.9 - - + -
106B PHE 4.2 0.2 - - - +
107B GLY* 3.4 35.4 - - - +
108B SER* 3.6 6.2 + - - +
440B LEU 3.2 24.9 - - - +
441B LEU* 3.1 19.1 - - - +
443B THR* 1.3 95.5 - - - +
445B LEU* 1.3 59.4 + - - -
447B ILE* 3.3 11.7 + - + +
448B ASP* 3.0 29.9 + - - +
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Residues in contact with LEU 445 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107B GLY 4.8 1.3 + - - -
321B LEU* 4.0 22.7 - - + +
322B LYS* 3.8 21.5 - - + +
327B LYS* 6.2 1.6 - - + +
441B LEU 3.5 11.2 + - - +
442B ALA* 3.1 12.4 + - - +
444B PRO* 1.3 77.9 - - - +
446B ILE* 1.3 67.7 + - - +
448B ASP* 3.2 9.7 + - - +
449B LEU* 3.0 34.9 + - + +
487B TRP* 3.0 54.7 - - + +
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Residues in contact with ILE 446 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70B LEU* 4.7 4.9 - - + -
77B ASN* 3.8 31.6 - - + +
81B LEU* 3.8 23.1 - - + -
242B LEU* 3.9 28.0 - - + -
244B THR* 3.9 13.9 - - + +
321B LEU* 4.0 24.9 - - + -
442B ALA 2.8 15.5 + - - +
443B THR* 2.7 12.4 + - - +
445B LEU* 1.3 79.3 - - - +
447B ILE* 1.3 61.1 + - - +
449B LEU* 3.2 7.1 + - - +
450B LEU* 3.1 31.5 + - + +
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Residues in contact with ILE 447 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423A MET* 4.6 1.1 - - + -
81B LEU* 3.5 21.3 - - + -
84B SER* 4.0 13.2 - - - +
85B VAL* 5.4 0.7 - - + -
105B TYR* 3.5 37.5 - - + -
108B SER* 4.2 12.6 - - - +
111B GLN* 4.4 2.7 - - + -
139B PRO* 3.8 30.3 - - + -
142B PHE* 4.4 9.0 - - + -
443B THR* 2.9 12.3 + - + +
444B PRO* 3.4 17.7 - - + +
445B LEU 3.2 0.2 - - - -
446B ILE* 1.3 77.6 - - - +
448B ASP* 1.3 62.7 + - - +
450B LEU* 3.4 2.5 + - - +
451B VAL* 3.0 30.6 + - + +
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Residues in contact with ASP 448 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107B GLY 4.2 2.8 - - - +
108B SER* 2.4 26.3 + - - -
109B MET* 2.7 30.5 + - - +
110B THR* 2.7 28.0 + - + -
444B PRO 3.0 17.8 + - - +
445B LEU* 3.2 5.7 + - - +
447B ILE* 1.3 75.3 - - - +
449B LEU* 1.3 58.1 + - - +
451B VAL* 3.4 0.7 + - - +
452B MET* 3.0 35.3 + - - +
487B TRP* 3.5 32.9 + - + +
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Residues in contact with LEU 449 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242B LEU* 4.6 3.8 - - + -
293B ILE* 4.2 26.5 - - + -
321B LEU* 3.9 18.4 - - + -
445B LEU* 3.0 36.1 + - + +
446B ILE* 3.2 10.7 + - - +
448B ASP* 1.3 78.0 - - - +
450B LEU* 1.3 57.6 + - - +
452B MET* 3.5 3.3 + - - +
453B THR* 2.8 35.5 + - - -
484B LEU* 3.9 26.3 - - + +
487B TRP* 3.6 35.7 - - + +
488B LEU* 4.5 7.9 - - + -
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Residues in contact with LEU 450 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66B LEU* 4.3 0.6 - - - +
68B ILE* 3.6 41.7 - - + -
70B LEU* 4.9 0.9 - - + -
81B LEU* 5.2 4.0 - - + -
142B PHE* 4.0 23.8 - - + -
240B ILE* 3.5 34.3 - - + +
242B LEU* 3.7 28.3 - - + -
293B ILE* 4.1 2.0 - - + -
446B ILE* 3.1 33.4 + - + +
447B ILE* 3.9 4.3 - - - +
449B LEU* 1.3 76.7 - - - +
451B VAL* 1.3 63.3 + - - +
453B THR* 4.5 1.1 - - - -
454B GLU* 3.1 26.0 + - - +
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Residues in contact with VAL 451 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66B LEU* 5.7 0.2 - - - -
110B THR* 3.9 24.5 - - + +
111B GLN* 4.1 14.4 - - - +
136B MET* 4.1 23.4 - - + +
137B VAL* 3.3 30.2 + - - +
139B PRO* 4.5 1.6 - - + -
142B PHE* 3.9 17.0 - - + -
447B ILE* 3.0 25.3 + - + +
448B ASP 3.8 3.6 - - - +
450B LEU* 1.3 77.8 - - - +
452B MET* 1.3 59.3 + - - +
454B GLU* 3.6 6.4 + - - +
455B PHE* 3.0 24.1 + - - +
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Residues in contact with MET 452 (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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110B THR* 4.0 8.7 - - + -
130B PHE* 3.9 17.7 - - + -
136B MET* 3.8 30.7 - - + +
448B ASP 3.0 20.5 + - - +
449B LEU 4.2 1.3 - - - +
451B VAL* 1.3 74.2 - - - +
453B THR* 1.3 61.7 + - - +
455B PHE* 3.5 16.4 - - + +
456B CYS* 3.0 42.1 + - - -
484B LEU* 4.1 18.4 - - + -
487B TRP* 3.7 19.7 - - + -
510B LEU* 3.8 25.6 - - + -
513B PHE* 5.6 4.5 - - + -
514B LEU* 4.7 7.9 - - + -
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Residues in contact with THR 453 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240B ILE* 4.0 8.1 - - + -
291B PRO* 3.6 33.0 - - + -
293B ILE* 3.2 24.1 - - + +
315B PHE* 5.0 0.4 - - + -
449B LEU 2.8 24.3 + - - -
450B LEU 3.9 2.9 - - - -
452B MET* 1.3 73.9 - - - +
454B GLU* 1.3 66.3 + - - +
456B CYS* 3.2 3.1 + - - +
457B THR* 3.1 27.9 + - + +
481B LEU* 4.1 20.1 - - + +
484B LEU* 3.4 15.1 - - - +
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Residues in contact with GLU 454 (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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63B PRO* 3.4 2.6 - - + +
66B LEU* 3.7 28.5 - - + -
137B VAL* 3.1 25.5 + - + +
238B LYS* 2.9 31.2 + - - +
240B ILE* 3.8 6.5 - - + +
450B LEU 3.1 16.3 + - - +
451B VAL* 3.7 5.6 - - - +
453B THR* 1.3 80.5 - - - +
455B PHE* 1.3 61.4 + - - +
457B THR* 2.5 25.0 + - - -
458B ARG* 3.0 40.9 + - - -
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Residues in contact with PHE 455 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58B LEU* 4.2 12.1 - - + +
134B LEU* 3.7 30.5 - - + -
135B PRO 3.6 20.2 - - - -
136B MET* 3.6 22.7 - - + -
451B VAL 3.0 19.2 + - - +
452B MET* 3.5 18.4 - - + +
454B GLU* 1.3 82.7 + - - +
456B CYS* 1.3 73.9 + - - +
458B ARG* 3.1 24.4 + - - +
459B VAL* 3.7 15.0 - - + +
513B PHE* 4.1 7.0 - + - -
514B LEU* 3.8 15.0 - - + -
517B LEU* 3.5 32.3 - - + -
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Residues in contact with CYS 456 (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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315B PHE* 3.2 19.9 - - + -
452B MET* 3.0 31.8 + - - +
453B THR 3.2 4.2 + - - +
455B PHE* 1.3 82.4 - - - +
457B THR* 1.3 60.9 + - - +
458B ARG 3.0 6.1 - - - -
459B VAL* 3.1 23.9 + - - +
477B PHE* 3.9 30.9 - - + +
481B LEU* 4.1 13.7 - - + -
483B PHE* 4.9 6.7 - - - -
484B LEU* 4.9 11.0 - - - -
513B PHE* 4.9 3.1 - - - -
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Residues in contact with THR 457 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238B LYS* 2.9 26.3 + - - +
291B PRO* 3.8 26.0 - - + -
315B PHE* 3.5 24.9 - - + -
453B THR* 3.1 15.2 + - + +
454B GLU* 2.5 23.2 + - - -
456B CYS* 1.3 77.5 - - - +
458B ARG* 1.3 58.1 + - - +
459B VAL 3.3 3.3 + - - +
476B ASN* 4.5 9.7 - - - +
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Residues in contact with ARG 458 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57B LYS 3.5 1.2 - - - +
58B LEU* 3.2 13.5 - - + +
59B ASP* 2.8 72.7 + - + +
60B LEU 4.0 1.4 + - - -
61B LYS 3.4 19.1 - - - -
62B LYS* 3.5 21.7 - - - +
63B PRO* 4.6 1.8 - - - -
135B PRO* 3.0 43.0 + - - +
136B MET* 4.1 4.8 - - - +
238B LYS* 4.8 5.8 - - + +
454B GLU* 3.0 41.5 + - - +
455B PHE* 3.1 19.0 + - - +
456B CYS 3.0 1.2 - - - -
457B THR* 1.3 81.9 + - - +
459B VAL* 1.3 59.5 + - - +
460B SER* 5.1 1.1 + - - -
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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