Contacts of the helix formed by residues 457 - 477 (chain B) in PDB entry 4Z2C
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 LYS 457 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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453B ASP* 3.1 17.5 + - - +
454B ILE 2.9 17.7 + - - +
455B LEU 3.3 1.0 - - - -
456B ALA* 1.3 82.0 - - - +
458B PRO* 1.3 67.6 - - - +
459B GLU* 4.6 4.7 - - + +
460B ARG* 3.3 26.2 + - + +
461B VAL* 3.6 5.0 + - - +
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Residues in contact with PRO 458 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
455B LEU 5.6 0.7 - - - +
456B ALA 3.9 6.1 - - - +
457B LYS* 1.3 84.6 - - + +
459B GLU* 1.3 65.7 + - + +
461B VAL* 3.0 13.4 + - + +
462B SER* 2.9 22.8 + - - -
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Residues in contact with GLU 459 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
457B LYS* 3.3 4.9 - - + -
458B PRO* 1.3 80.1 - - - +
460B ARG* 1.3 58.2 + - + +
462B SER* 3.3 8.8 + - - -
463B GLN* 2.9 29.2 + - - +
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Residues in contact with ARG 460 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
450B ASP* 2.7 39.6 + - - -
453B ASP* 2.7 51.0 + - - +
454B ILE* 3.4 31.1 - - + +
457B LYS* 3.3 19.1 + - + +
458B PRO 3.2 0.6 - - - -
459B GLU* 1.3 75.7 - - + +
461B VAL* 1.3 60.5 + - - +
463B GLN* 3.2 7.9 + - - +
464B ILE* 2.9 37.4 + - + +
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Residues in contact with VAL 461 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356B LYS* 4.4 11.7 - - + +
359B VAL* 3.9 23.6 - - + -
360B VAL* 4.0 29.2 - - + -
454B ILE* 3.8 33.4 - - + +
455B LEU* 5.6 1.3 - - + -
457B LYS 3.6 3.5 + - - +
458B PRO* 3.0 13.3 + - + +
460B ARG* 1.3 75.4 - - - +
462B SER* 1.3 64.0 + - - +
464B ILE* 3.1 11.9 + - - +
465B ILE* 2.9 31.1 + - + +
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Residues in contact with SER 462 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196B MET* 3.2 29.2 + - - +
356B LYS* 5.1 10.4 - - - +
458B PRO 2.9 12.1 + - - -
459B GLU* 3.5 12.6 - - - -
461B VAL* 1.3 77.0 - - - +
463B GLN* 1.3 58.4 + - - +
465B ILE* 3.2 8.3 + - - +
466B LYS* 2.9 35.7 + - - +
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Residues in contact with GLN 463 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
459B GLU 2.9 15.2 + - - +
460B ARG* 3.2 11.2 + - - +
462B SER* 1.3 73.5 - - - +
464B ILE* 1.3 59.8 + - + +
466B LYS* 3.3 31.8 + - - +
467B ASP* 2.9 60.6 + - - +
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Residues in contact with ILE 464 (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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359B VAL* 4.1 11.9 - - + -
362B ARG* 3.6 25.8 - - - +
363B THR* 5.2 1.1 - - - +
454B ILE* 3.7 37.7 - - + -
460B ARG* 2.9 23.7 + - + +
461B VAL* 3.1 15.4 + - - +
463B GLN* 1.3 76.0 - - + +
465B ILE* 1.3 64.4 + - - +
467B ASP* 3.3 8.3 + - - +
468B GLU* 2.9 38.2 + - + +
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Residues in contact with ILE 465 (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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160B ARG* 4.5 8.7 + - - +
196B MET* 3.7 28.0 - - + -
352B ILE* 4.3 2.0 - - + +
355B GLN* 3.6 24.2 - - + +
356B LYS* 3.5 46.9 - - + +
359B VAL* 3.7 19.7 - - + -
461B VAL* 2.9 18.8 + - + +
462B SER* 3.4 7.2 - - - +
464B ILE* 1.3 76.4 - - - +
466B LYS* 1.3 57.5 + - - +
468B GLU* 3.9 1.0 - - - +
469B LEU* 2.9 41.0 + - + +
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Residues in contact with LYS 466 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193B LYS* 4.2 25.4 - - + +
196B MET* 3.8 24.9 - - + -
197B ASP* 3.2 33.8 + - - +
462B SER* 2.9 22.7 + - - +
463B GLN* 3.3 35.2 + - - +
465B ILE* 1.3 75.3 - - - +
467B ASP* 1.3 58.0 + - - +
469B LEU* 3.6 5.6 - - - +
470B ASP* 2.9 38.3 + - - +
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Residues in contact with ASP 467 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
463B GLN* 2.9 48.5 + - - +
464B ILE* 3.7 7.9 - - - +
466B LYS* 1.3 76.5 - - - +
468B GLU* 1.3 59.6 + - + +
470B ASP* 3.1 11.7 + - - +
471B GLU* 2.9 27.0 + - - +
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Residues in contact with GLU 468 (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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160B ARG* 2.8 41.1 + - + +
362B ARG* 3.1 32.2 + - - -
464B ILE* 2.9 26.8 + - + +
465B ILE 4.1 2.0 - - - +
467B ASP* 1.3 74.6 - - + +
469B LEU* 1.3 60.2 + - - +
471B GLU* 3.1 10.0 + - - +
472B VAL* 2.9 31.5 + - + +
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Residues in contact with LEU 469 (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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160B ARG* 3.3 28.0 - - - +
161B PHE* 4.6 0.2 - - - -
162B PRO* 4.5 4.3 - - + -
189B ILE* 3.2 42.5 - - + +
192B VAL* 4.1 26.9 - - + -
193B LYS* 4.7 8.5 - - + -
196B MET* 5.0 3.4 - - - -
351B TYR* 3.8 18.8 - - + +
355B GLN* 5.6 2.2 - - + +
465B ILE* 2.9 36.8 + - + +
466B LYS* 3.6 4.5 - - - +
468B GLU* 1.3 77.4 - - - +
470B ASP* 1.3 57.5 + - - +
472B VAL* 3.1 4.3 + - + +
473B LYS 2.9 24.1 + - - -
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Residues in contact with ASP 470 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193B LYS* 2.6 39.7 + - - +
466B LYS* 2.9 20.0 + - - +
467B ASP* 3.1 13.6 + - - +
469B LEU* 1.3 75.4 - - - +
471B GLU* 1.3 58.1 + - - +
473B LYS* 3.3 15.7 + - - +
474B ARG* 2.9 28.5 + - - +
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Residues in contact with GLU 471 (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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467B ASP 2.9 11.5 + - - +
468B GLU* 3.1 12.7 + - - +
470B ASP* 1.3 76.2 - - - +
472B VAL* 1.3 59.4 + - - +
474B ARG* 2.5 42.6 + - - +
475B LYS* 2.9 47.0 + - + +
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Residues in contact with VAL 472 (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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128B ILE* 5.5 0.2 - - + -
131B GLU* 3.6 35.4 - - + +
160B ARG* 4.2 15.0 - - + +
161B PHE* 4.1 16.4 - - + -
185B LEU* 4.0 15.9 - - + -
189B ILE* 3.9 14.6 - - + -
468B GLU* 2.9 16.4 + - + +
469B LEU* 3.1 9.2 + - - +
471B GLU* 1.3 77.2 - - - +
473B LYS* 1.3 62.8 + - - +
475B LYS* 3.1 3.3 + - + -
476B PHE* 2.9 38.1 + - + +
477B SER 4.1 0.3 + - - -
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Residues in contact with LYS 473 (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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185B LEU* 5.0 0.9 - - - -
186B GLY* 3.8 27.4 - - - +
189B ILE* 3.6 21.3 - - + -
190B ASP* 2.9 32.7 + - - +
193B LYS* 4.6 6.1 - - - +
469B LEU 2.9 8.2 + - - +
470B ASP* 3.4 21.3 + - - +
472B VAL* 1.3 76.4 - - - +
474B ARG* 1.3 63.7 + - - +
477B SER* 3.2 31.4 + - - +
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Residues in contact with ARG 474 (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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470B ASP 2.9 16.1 + - - +
471B GLU* 2.5 42.5 + - - +
472B VAL 3.2 0.2 - - - -
473B LYS* 1.3 78.5 - - - +
475B LYS* 1.3 82.4 + - - +
476B PHE 3.6 0.2 + - - -
477B SER 4.9 1.0 + - - +
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Residues in contact with LYS 475 (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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131B GLU* 5.4 4.5 - - - +
471B GLU* 2.9 34.7 + - + +
472B VAL* 3.1 3.6 + - + +
474B ARG* 1.3 105.5 - - - +
476B PHE* 1.3 91.4 + - + +
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Residues in contact with PHE 476 (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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98B TYR* 4.0 10.2 - - + -
127B LYS* 3.9 34.5 - - + -
128B ILE* 3.9 26.5 - - + -
131B GLU* 3.7 32.5 - - + -
185B LEU* 3.7 13.5 - - + -
472B VAL* 2.9 25.5 + - + +
474B ARG 3.5 0.2 - - - -
475B LYS* 1.3 105.6 - - + +
477B SER* 1.3 70.2 + - - +
478B ASP* 3.5 7.4 + - - +
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Residues in contact with SER 477 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98B TYR* 4.1 0.4 - - - -
184B ASN* 3.5 4.2 + - - -
185B LEU* 3.8 13.9 - - - +
186B GLY* 3.1 33.8 + - - -
473B LYS* 3.2 24.2 + - - +
474B ARG 4.9 1.1 + - - +
476B PHE* 1.3 81.4 - - - +
478B ASP* 1.3 72.2 + - - +
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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
------------------------------------------------------------
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