Contacts of the helix formed by residues 579 - 600 (chain A) in PDB entry 4ASQ
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 GLY 579 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220A ILE* 4.0 29.3 - - - +
223A ASP* 6.5 1.1 - - - -
224A ILE* 4.1 5.7 - - - +
512A ILE* 4.3 1.3 - - - -
578A SER* 1.3 72.5 + - - +
580A LYS* 1.3 62.9 + - - +
581A ALA 3.4 2.0 - - - -
582A ILE* 3.3 15.7 - - - +
583A ALA* 3.2 24.4 + - - +
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Residues in contact with LYS 580 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
519A LYS* 4.4 11.9 - - - +
578A SER* 3.1 17.6 + - - +
579A GLY* 1.3 77.7 - - - +
581A ALA* 1.3 59.0 + - - +
583A ALA* 3.4 5.9 + - - +
584A GLU* 2.9 46.1 + - - +
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Residues in contact with ALA 581 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
512A ILE 5.4 0.2 - - - +
515A PHE* 3.3 34.8 - - - +
516A GLN* 3.7 16.8 - - + +
519A LYS* 4.1 20.0 - - + +
537A LEU* 4.4 4.2 - - - +
578A SER* 4.4 2.4 + - - +
579A GLY 3.4 0.6 - - - -
580A LYS* 1.3 76.5 - - - +
582A ILE* 1.3 60.4 + - - +
584A GLU* 3.3 8.1 + - - +
585A TYR* 3.0 27.9 + - - +
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Residues in contact with ILE 582 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224A ILE* 3.9 18.2 - - + -
438A LYS 4.6 5.4 - - - +
439A ILE* 3.9 21.1 - - + -
442A LEU* 4.2 16.2 - - + -
511A PHE* 3.7 12.8 - - + +
512A ILE* 4.8 12.5 + - + +
515A PHE* 3.6 46.9 - - + +
578A SER 5.3 0.2 + - - -
579A GLY* 3.3 21.9 - - - +
581A ALA* 1.3 78.8 - - - +
583A ALA* 1.3 64.3 + - - +
585A TYR* 3.4 1.2 + - - +
586A PHE* 3.2 41.8 + - + -
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Residues in contact with ALA 583 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224A ILE* 4.3 15.3 - - + -
227A LEU* 6.0 3.6 - - - -
579A GLY 3.2 18.4 + - - +
580A LYS* 3.7 5.6 - - - +
582A ILE* 1.3 75.4 - - - +
584A GLU* 1.3 59.7 + - - +
586A PHE* 3.4 3.1 + - - -
587A GLU* 2.9 35.2 + - - +
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Residues in contact with GLU 584 (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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519A LYS* 2.8 35.5 + - - +
528A TYR* 2.5 39.6 + - + +
530A PRO* 4.8 4.2 - - - +
537A LEU* 4.7 5.4 - - + +
580A LYS* 2.9 29.2 + - + +
581A ALA 3.3 6.5 + - - +
583A ALA* 1.3 73.7 - - - +
585A TYR* 1.3 66.3 + - - +
586A PHE 3.4 0.2 + - - -
587A GLU* 3.4 16.6 + - - +
588A PRO* 4.0 4.7 - - - +
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Residues in contact with TYR 585 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
403A LEU* 4.4 12.3 + - + +
406A SER* 5.1 2.1 + - - -
407A THR* 5.5 1.2 - - - +
430A GLN* 5.5 2.3 + - - +
431A LEU* 3.5 24.9 - - + +
434A THR* 3.8 23.3 + - + +
515A PHE* 3.6 26.0 - + + -
518A TYR* 3.7 24.8 + + - -
537A LEU* 3.8 30.2 - - + +
538A ASP* 3.8 32.3 + - + +
581A ALA 3.0 12.4 + - - +
582A ILE 3.5 9.2 - - - +
584A GLU* 1.3 79.1 - - - +
586A PHE* 1.3 92.3 + + - +
587A GLU 3.7 0.5 + - - -
588A PRO* 3.7 7.4 - - - +
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Residues in contact with PHE 586 (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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227A LEU* 3.9 18.6 - - + -
431A LEU* 3.6 14.1 - - + -
434A THR* 3.8 16.6 - - + -
435A ALA* 3.5 36.8 - - + -
438A LYS* 3.9 13.2 - - + -
439A ILE* 3.7 25.1 - - + -
515A PHE* 3.8 17.3 - + - -
582A ILE* 3.2 27.6 + - + +
583A ALA 3.7 1.8 - - - +
585A TYR* 1.3 101.3 - + - +
587A GLU* 1.3 60.2 + - - +
588A PRO* 3.3 3.1 - - - -
589A LEU* 2.9 15.7 + - + +
590A ARG* 2.9 27.0 + - - +
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Residues in contact with GLU 587 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
583A ALA* 2.9 19.1 + - - +
584A GLU* 3.6 10.1 - - - +
585A TYR 3.4 0.4 - - - -
586A PHE* 1.3 75.4 - - - +
588A PRO* 1.4 70.3 - - + +
590A ARG* 2.7 51.5 + - - +
591A VAL* 3.1 32.7 + - + +
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Residues in contact with PRO 588 (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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427A ARG* 3.8 32.8 - - - +
428A ILE* 4.1 6.3 - - + +
431A LEU* 3.8 22.0 - - + -
538A ASP* 4.8 0.4 - - - +
584A GLU 4.0 4.3 - - - +
585A TYR 3.7 11.7 - - - +
586A PHE 3.5 1.1 - - - -
587A GLU* 1.4 94.8 - - + +
589A LEU* 1.3 58.8 + - - +
591A VAL* 3.7 6.7 + - + +
592A TRP* 3.3 22.2 + - - +
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Residues in contact with LEU 589 (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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227A LEU* 5.0 4.5 - - + -
231A ILE* 4.7 8.7 - - + -
428A ILE* 4.3 12.6 - - + +
431A LEU* 3.9 24.8 - - + +
432A PHE* 3.9 38.6 - - + +
435A ALA* 3.6 31.6 - - + -
586A PHE* 2.9 20.5 + - + +
588A PRO* 1.3 77.7 - - - +
590A ARG* 1.3 57.0 + - - +
592A TRP* 3.3 16.8 + - + -
593A LEU* 2.8 43.9 + - + +
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Residues in contact with ARG 590 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227A LEU* 4.1 34.2 - - + +
230A GLN* 6.3 0.4 - - + -
586A PHE 2.9 12.2 + - - +
587A GLU* 2.7 48.8 + - - +
589A LEU* 1.3 75.9 - - - +
591A VAL* 1.3 75.5 + - - +
593A LEU* 4.1 1.3 - - - +
594A GLU* 2.8 79.5 + - + +
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Residues in contact with VAL 591 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
587A GLU* 3.1 33.9 + - + +
588A PRO* 4.0 7.0 - - + +
590A ARG* 1.3 88.8 - - - +
592A TRP* 1.3 63.6 + - - +
594A GLU* 4.1 3.7 - - - +
595A ALA* 3.4 21.1 + - + +
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Residues in contact with TRP 592 (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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234A TYR* 4.3 7.4 - + - -
276A PRO* 3.3 38.6 - - + -
277A PHE* 3.5 34.7 - + - -
428A ILE* 3.7 32.1 - - + -
432A PHE* 5.2 0.4 - + - -
588A PRO 3.3 14.1 + - - +
589A LEU* 3.3 9.5 + - + +
591A VAL* 1.3 79.0 - - - +
593A LEU* 1.3 93.7 + - + +
595A ALA* 3.3 8.8 + - + +
596A GLU* 2.9 65.5 + - + +
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Residues in contact with LEU 593 (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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227A LEU* 4.4 8.1 - - + -
230A GLN* 3.8 9.0 - - + -
231A ILE* 3.6 43.7 - - + +
234A TYR* 3.8 35.0 - - + -
432A PHE* 4.3 11.2 - - + -
589A LEU* 2.8 27.1 + - + +
590A ARG* 4.1 2.9 - - - +
592A TRP* 1.3 92.3 - - + +
594A GLU* 1.3 60.4 + - - +
596A GLU* 3.7 0.6 - - + -
597A ASN* 2.9 40.0 + - - +
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Residues in contact with GLU 594 (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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226A PRO* 6.2 0.2 - - - +
227A LEU* 6.5 0.2 - - + -
230A GLN* 3.8 31.4 - - + +
590A ARG* 2.8 61.5 + - + +
591A VAL* 4.1 4.4 - - - +
593A LEU* 1.3 75.6 - - - +
595A ALA* 1.3 62.6 + - - +
597A ASN* 3.6 2.1 + - - +
598A ILE* 3.2 34.9 + - + +
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Residues in contact with ALA 595 (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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591A VAL* 3.4 12.1 + - + +
592A TRP* 3.3 10.7 + - + +
593A LEU 3.2 0.2 - - - -
594A GLU* 1.3 79.1 - - - +
596A GLU* 1.3 57.1 + - - +
598A ILE* 3.4 9.0 + - - +
599A LYS* 2.9 37.4 + - - +
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Residues in contact with GLU 596 (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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234A TYR* 3.9 18.3 + - + -
276A PRO 5.7 0.7 - - - +
277A PHE* 5.6 2.2 - - - -
592A TRP* 2.9 63.0 + - + +
593A LEU* 3.2 5.1 + - + +
595A ALA* 1.3 73.4 - - - +
597A ASN* 1.3 61.1 + - - +
599A LYS* 3.4 23.9 + - - +
600A ASN* 3.0 57.3 + - - +
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Residues in contact with ASN 597 (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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230A GLN* 2.9 56.2 + - - +
234A TYR* 3.4 24.0 - - - +
593A LEU* 2.9 21.7 + - - +
594A GLU 3.9 1.6 - - - +
596A GLU* 1.3 74.8 - - - +
598A ILE* 1.3 60.5 + - + +
600A ASN 3.5 0.2 + - - -
601A ASN 3.0 6.8 + - - -
602A VAL* 2.8 58.6 + - + +
604A ILE* 3.9 7.7 - - + +
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Residues in contact with ILE 598 (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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594A GLU* 3.2 25.4 + - + +
595A ALA* 3.7 7.6 - - - +
597A ASN* 1.3 76.8 - - + +
599A LYS* 1.3 67.4 + - - +
601A ASN* 3.1 14.7 + - - +
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Residues in contact with LYS 599 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
595A ALA* 2.9 23.0 + - - +
596A GLU* 3.5 29.9 + - - +
598A ILE* 1.3 79.6 - - - +
600A ASN* 1.3 61.9 - - - +
601A ASN* 3.7 1.2 + - - +
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Residues in contact with ASN 600 (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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234A TYR* 5.1 1.6 - - + -
237A PHE* 3.8 33.2 - - + -
596A GLU* 3.0 52.3 + - - +
599A LYS* 1.3 81.5 - - - +
601A ASN* 1.3 70.6 + - - +
602A VAL* 3.2 19.0 + - + +
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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