Contacts of the helix formed by residues 457 - 477 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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453A ASP* 3.0 41.1 + - - +
454A ILE 2.8 19.6 - - - +
455A LEU 3.3 1.3 - - - -
456A ALA* 1.3 85.8 + - + +
458A PRO* 1.3 67.7 - - + +
459A GLU* 4.4 7.6 - - + +
460A ARG* 3.4 25.6 + - + +
461A VAL* 3.7 3.7 + - - +
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Residues in contact with PRO 458 (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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455A LEU 5.7 0.2 - - - +
456A ALA 3.8 7.9 - - - +
457A LYS* 1.3 83.3 - - + +
459A GLU* 1.3 61.4 + - + +
461A VAL* 3.0 13.2 + - + +
462A SER* 2.9 29.1 + - - -
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Residues in contact with GLU 459 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
457A LYS* 5.0 7.4 - - + -
458A PRO* 1.3 81.5 - - + +
460A ARG* 1.3 58.2 + - + +
462A SER* 3.5 7.3 + - - -
463A GLN* 2.9 29.2 + - - +
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Residues in contact with ARG 460 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
450A ASP* 2.8 35.9 + - - -
453A ASP* 2.7 51.4 + - - +
454A ILE* 3.4 30.3 - - + +
457A LYS* 3.4 23.6 + - + +
458A PRO 3.2 0.4 - - - -
459A GLU* 1.3 75.6 - - + +
461A VAL* 1.3 60.6 + - - +
463A GLN* 3.5 7.0 + - - +
464A ILE* 2.9 39.7 + - + +
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Residues in contact with VAL 461 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356A LYS* 4.3 13.2 - - + +
359A VAL* 3.7 26.2 - - + -
360A VAL* 3.9 28.3 - - + -
454A ILE* 3.7 29.4 - - + +
455A LEU* 5.5 1.6 - - + -
457A LYS 3.7 4.9 + - - +
458A PRO* 3.0 12.4 + - + +
460A ARG* 1.3 73.8 - - - +
462A SER* 1.3 66.3 + - - +
464A ILE* 3.2 8.3 + - - +
465A ILE* 2.9 35.4 + - + +
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Residues in contact with SER 462 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196A MET* 3.2 34.3 + - - +
197A ASP* 5.6 0.5 + - - -
356A LYS* 5.2 10.5 - - - +
458A PRO 2.9 12.5 + - - -
459A GLU* 3.6 11.3 + - - -
461A VAL* 1.3 76.1 - - - +
463A GLN* 1.3 58.9 + - - +
465A ILE* 3.2 6.8 + - - +
466A LYS* 2.9 30.7 + - - +
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Residues in contact with GLN 463 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
459A GLU 2.9 19.9 + - - +
460A ARG* 3.7 7.9 - - - +
462A SER* 1.3 77.9 + - - +
464A ILE* 1.3 59.2 + - + +
466A LYS* 3.2 17.4 + - - +
467A ASP* 2.7 69.5 + - - +
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Residues in contact with ILE 464 (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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359A VAL* 4.3 12.8 - - + -
362A ARG* 3.6 14.4 - - - +
363A THR* 5.2 1.3 - - - +
454A ILE* 3.8 40.8 - - + -
460A ARG* 2.9 29.7 + - + +
461A VAL* 3.2 6.3 + - - +
463A GLN* 1.3 75.7 - - + +
465A ILE* 1.3 64.5 + - - +
467A ASP* 3.3 7.7 + - - +
468A GLU* 2.9 49.8 + - + +
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Residues in contact with ILE 465 (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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160A ARG* 5.2 2.2 - - - +
196A MET* 4.1 20.2 - - + -
351A TYR* 6.1 0.2 - - + -
352A ILE* 4.4 2.5 - - + +
355A GLN* 3.7 25.4 - - + -
356A LYS* 3.6 48.5 - - + +
359A VAL* 3.6 19.5 - - + -
461A VAL* 2.9 21.9 + - + +
462A SER* 3.2 10.1 + - - +
464A ILE* 1.3 76.7 - - - +
466A LYS* 1.3 61.9 + - - +
468A GLU* 3.9 3.3 - - - +
469A LEU* 2.9 36.4 + - + +
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Residues in contact with LYS 466 (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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193A LYS* 4.3 23.8 - - + +
196A MET* 3.7 23.3 - - + -
197A ASP* 3.7 28.0 - - - +
462A SER* 2.9 20.5 + - - +
463A GLN* 3.2 20.8 + - - +
465A ILE* 1.3 78.7 - - - +
467A ASP* 1.3 61.2 + - - +
469A LEU* 3.4 6.2 + - - +
470A ASP* 2.9 37.4 + - - +
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Residues in contact with ASP 467 (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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463A GLN* 2.7 51.5 + - - +
464A ILE* 3.8 6.3 - - - +
466A LYS* 1.3 76.1 - - - +
468A GLU* 1.3 60.3 + - + +
470A ASP* 3.1 15.5 + - - +
471A GLU* 2.9 26.6 + - - +
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Residues in contact with GLU 468 (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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134A ARG* 5.9 2.6 - - - -
160A ARG* 2.6 37.6 + - + +
362A ARG* 2.9 35.0 + - - -
464A ILE* 2.9 28.1 + - + +
465A ILE 4.1 2.0 - - - +
467A ASP* 1.3 73.9 - - + +
469A LEU* 1.3 60.7 + - - +
471A GLU* 3.2 9.0 + - - +
472A VAL* 2.9 33.8 + - + +
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Residues in contact with LEU 469 (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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160A ARG 3.7 21.8 - - - +
162A PRO* 4.4 4.5 - - + -
189A ILE* 3.5 43.4 - - + +
192A VAL* 4.3 24.2 - - + -
193A LYS* 4.4 11.0 - - + -
196A MET* 5.0 4.3 - - - -
351A TYR* 3.9 18.6 - - + +
355A GLN* 5.4 2.0 - - - +
465A ILE* 2.9 37.1 + - + +
466A LYS* 3.4 5.4 - - - +
468A GLU* 1.3 76.3 - - - +
470A ASP* 1.3 57.2 + - - +
472A VAL* 3.1 6.7 + - - +
473A LYS* 2.9 25.8 + - - +
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Residues in contact with ASP 470 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189A ILE* 4.7 1.9 - - - +
193A LYS* 2.6 42.8 + - - +
466A LYS* 2.9 22.3 + - - +
467A ASP* 3.1 17.0 + - - +
469A LEU* 1.3 76.0 - - - +
471A GLU* 1.3 57.7 + - - +
473A LYS* 3.6 13.8 + - - +
474A ARG* 2.9 29.2 + - - +
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Residues in contact with GLU 471 (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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467A ASP 2.9 12.7 + - - +
468A GLU* 3.5 11.0 - - - +
469A LEU 3.2 0.4 - - - -
470A ASP* 1.3 74.8 - - - +
472A VAL* 1.3 59.3 + - + +
474A ARG* 2.3 46.0 + - - +
475A LYS* 2.9 32.7 + - + +
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Residues in contact with VAL 472 (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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128A ILE* 5.6 0.2 - - + -
131A GLU* 3.5 34.1 - - + +
160A ARG* 3.9 17.5 - - + +
161A PHE* 4.0 25.4 - - + -
185A LEU* 4.5 7.4 - - + -
189A ILE* 4.2 8.5 - - + -
468A GLU* 2.9 17.1 + - + +
469A LEU* 3.1 8.7 + - - +
471A GLU* 1.3 76.3 - - + +
473A LYS* 1.3 58.1 + - - +
475A LYS* 3.1 1.4 + - - -
476A PHE* 2.9 47.1 + - + +
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Residues in contact with LYS 473 (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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185A LEU* 4.8 2.7 - - - -
186A GLY* 3.8 28.0 - - - +
189A ILE* 3.6 23.6 - - + -
190A ASP* 2.8 31.2 + - - +
193A LYS* 5.2 3.0 - - - +
469A LEU 2.9 15.9 + - - +
470A ASP* 3.8 14.5 + - - +
472A VAL* 1.3 77.0 - - - +
474A ARG* 1.3 65.5 + - - +
477A SER* 3.0 37.0 + - - +
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Residues in contact with ARG 474 (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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470A ASP 2.9 20.5 + - - +
471A GLU* 2.3 40.8 + - - +
473A LYS* 1.3 78.9 - - - +
475A LYS* 1.3 68.9 + - - +
477A SER 5.0 0.3 + - - -
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Residues in contact with LYS 475 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
471A GLU* 2.9 18.6 + - + +
472A VAL 3.1 3.5 + - - +
474A ARG* 1.3 90.9 - - - +
476A PHE* 1.3 85.6 + - + +
477A SER 4.0 0.2 - - - -
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Residues in contact with PHE 476 (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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98A TYR* 3.7 15.1 - - + -
127A LYS* 3.4 44.2 - - + -
128A ILE* 4.2 22.0 - - + -
131A GLU* 3.8 29.4 - - + -
185A LEU* 3.7 14.8 - - + -
472A VAL* 2.9 33.9 + - + +
475A LYS* 1.3 99.2 - - + +
477A SER* 1.3 68.2 + - - +
478A ASP* 4.6 2.3 - - - +
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Residues in contact with SER 477 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184A ASN* 3.9 1.4 + - - -
185A LEU* 3.9 10.2 - - - +
186A GLY* 3.1 30.7 + - - -
473A LYS* 3.0 31.0 + - - -
474A ARG 4.9 0.4 + - - -
476A PHE* 1.3 82.1 - - - +
478A ASP* 1.3 75.0 + - - +
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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