Contacts of the helix formed by residues 567 - 587 (chain A) in PDB entry 4DAY
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 567 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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563A GLN 3.7 4.0 + - - +
564A SER 2.8 28.1 - - - +
565A LYS 3.3 3.4 - - - -
566A LYS* 1.3 78.6 - - + +
568A PRO* 1.3 64.9 - - - +
569A LEU* 3.1 31.8 + - - +
570A GLN* 3.3 33.1 + - + -
571A TYR 3.3 4.0 + - - -
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Residues in contact with PRO 568 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
565A LYS 3.8 3.8 - - - +
566A LYS 3.9 6.7 - - - +
567A ASP* 1.3 85.6 - - - +
569A LEU* 1.3 64.2 + - + +
570A GLN 3.1 1.8 - - - -
571A TYR* 2.9 24.6 + - + +
572A GLN* 2.9 14.2 + - - +
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Residues in contact with LEU 569 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
567A ASP* 3.1 9.7 + - - +
568A PRO* 1.3 82.3 - - + +
570A GLN* 1.3 78.5 + - - +
572A GLN* 3.4 12.7 - - + +
573A LYS* 3.3 29.1 + - + +
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Residues in contact with GLN 570 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
556A PHE* 3.9 6.9 - - + -
563A GLN 5.2 0.9 - - - +
564A SER* 3.4 26.9 - - - -
567A ASP* 3.3 38.4 + - + +
568A PRO 3.1 0.6 - - - -
569A LEU* 1.3 95.4 - - - +
571A TYR* 1.3 64.1 + - - +
573A LYS* 3.4 11.9 + - - +
574A PHE* 3.2 15.6 + - - +
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Residues in contact with TYR 571 (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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561A MET* 5.1 5.6 - - - -
564A SER* 2.9 35.8 + - - +
565A LYS* 3.9 28.1 - - + +
567A ASP 4.0 0.7 - - - +
568A PRO* 2.9 15.7 + - + +
570A GLN* 1.3 75.7 - - - +
572A GLN* 1.3 54.8 + - - +
574A PHE* 2.8 22.2 + + - +
575A LEU* 2.7 72.6 + - + +
1226C ASP 6.0 0.2 + - - -
1228C PHE* 5.3 7.3 - + - -
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Residues in contact with GLN 572 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
568A PRO 2.9 11.2 + - - +
569A LEU* 3.4 20.0 - - + +
571A TYR* 1.3 75.7 - - - +
573A LYS* 1.3 63.7 + - + +
575A LEU* 3.1 27.2 + - - +
576A GLU* 3.0 52.8 + - - +
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Residues in contact with LYS 573 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
556A PHE* 3.7 18.3 - - + -
569A LEU* 3.3 20.5 + - + +
570A GLN* 3.6 17.7 - - - +
571A TYR 3.1 0.6 - - - -
572A GLN* 1.3 78.5 - - + +
574A PHE* 1.3 59.8 + - - +
576A GLU* 3.6 19.4 - - - +
577A GLY* 3.3 15.1 + - - -
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Residues in contact with PHE 574 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
528A TRP* 3.7 24.7 - + - -
554A ILE* 4.1 9.2 - - + -
556A PHE* 3.6 35.6 - + + -
561A MET* 3.3 32.3 - - + -
564A SER* 3.8 11.4 - - - +
570A GLN 3.2 12.5 + - - +
571A TYR* 2.8 26.6 + + - +
573A LYS* 1.3 74.5 - - - +
575A LEU* 1.3 75.6 + - + +
576A GLU 3.0 1.1 - - - -
577A GLY* 2.8 14.9 + - - -
578A LEU* 2.9 42.5 + - + +
1228C PHE* 4.1 13.7 - + - -
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Residues in contact with LEU 575 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
571A TYR* 2.7 56.7 + - + +
572A GLN* 3.4 30.3 - - - +
574A PHE* 1.3 83.4 - - + +
576A GLU* 1.3 62.4 + - - +
578A LEU* 3.4 11.8 + - + +
579A GLN* 3.3 22.2 + - - +
1228C PHE* 6.4 0.9 - - + -
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Residues in contact with GLU 576 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
572A GLN* 3.0 48.6 + - - +
573A LYS* 3.6 21.5 + - - +
574A PHE 2.9 1.0 + - - -
575A LEU* 1.3 71.6 - - - +
577A GLY* 1.3 55.3 + - - +
578A LEU 2.7 15.1 + - - -
579A GLN* 2.9 21.3 + - - +
580A LYS* 2.7 24.5 + - + +
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Residues in contact with GLY 577 (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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554A ILE* 3.5 33.9 - - - -
556A PHE* 5.2 0.4 - - - -
573A LYS 3.3 8.1 + - - -
574A PHE 2.8 10.7 + - - -
576A GLU* 1.3 74.6 - - - +
578A LEU* 1.3 54.7 + - - +
580A LYS* 3.5 12.6 - - - +
581A CYS* 2.9 26.0 + - - +
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Residues in contact with LEU 578 (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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521A LEU* 4.1 18.2 - - + -
528A TRP* 5.3 0.7 - - + -
554A ILE* 3.9 27.1 - - + +
574A PHE* 2.9 37.0 + - + +
575A LEU* 3.4 18.2 - - + +
576A GLU 2.7 5.7 + - - -
577A GLY* 1.3 71.3 - - - +
579A GLN* 1.3 57.9 + - - +
580A LYS 3.1 1.1 - - - -
581A CYS* 3.2 6.5 + - - +
582A GLN 3.1 20.1 + - - -
1228C PHE* 3.8 26.0 - - + -
1230C VAL* 3.2 33.2 - - + +
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Residues in contact with GLN 579 (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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575A LEU 3.4 15.5 - - - +
576A GLU* 2.9 20.9 + - - +
578A LEU* 1.3 71.6 - - - +
580A LYS* 1.3 62.1 + - - +
581A CYS 3.2 0.2 - - - -
582A GLN* 3.6 16.6 - - + +
583A ARG* 3.0 27.0 + - - +
1230C VAL* 5.0 1.1 - - - -
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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
----------------------------------------------------------
552A SER 4.2 6.1 + - - -
553A LEU* 3.2 32.4 + - - +
554A ILE 5.7 0.7 - - - -
576A GLU* 2.7 17.6 + - + +
577A GLY* 3.5 12.3 - - - +
579A GLN* 1.3 79.5 + - - +
581A CYS* 1.3 58.3 + - - +
583A ARG* 3.1 36.5 + - - +
584A ASP* 2.9 54.8 + - - +
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Residues in contact with CYS 581 (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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521A LEU* 5.7 1.1 - - - -
550A LEU* 4.9 6.1 - - - -
553A LEU* 3.8 24.2 - - - +
554A ILE* 3.6 30.7 - - + -
577A GLY 2.9 15.4 + - - +
578A LEU* 3.2 11.9 + - + +
580A LYS* 1.3 77.2 - - - +
582A GLN* 1.3 62.6 + - - +
584A ASP* 3.0 8.0 + - - +
585A LEU* 3.0 43.5 + - - +
1230C VAL* 4.4 10.3 - - - -
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Residues in contact with GLN 582 (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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517A LEU* 5.9 0.2 - - + -
578A LEU 3.1 11.3 + - - +
579A GLN* 3.6 17.6 - - - +
580A LYS 3.3 0.2 - - - -
581A CYS* 1.3 77.6 - - - +
583A ARG* 1.3 59.9 + - - +
585A LEU* 3.6 7.9 + - + +
586A ILE* 2.9 37.7 + - - +
91B ARG 5.5 2.3 - - - +
1230C VAL* 3.9 27.6 - - + +
1231C THR 4.0 23.0 + - - +
1232C PHE* 4.5 14.5 - - + +
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Residues in contact with ARG 583 (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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579A GLN 3.0 18.7 + - - +
580A LYS* 3.1 49.9 + - - +
582A GLN* 1.3 76.9 + - - +
584A ASP* 1.3 93.1 + - - +
586A ILE* 3.3 9.3 + - - +
587A ASP* 3.2 28.9 + - - +
92B GLY* 3.9 26.7 - - - +
93B ARG* 3.1 47.7 - - - +
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Residues in contact with ASP 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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553A LEU* 3.1 31.4 - - + +
580A LYS* 2.9 42.2 + - - +
581A CYS 3.0 9.4 + - - +
583A ARG* 1.3 108.9 + - - +
585A LEU* 1.3 56.9 + - - +
587A ASP* 3.2 6.2 + - - +
588A LEU* 3.0 32.1 + - + +
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Residues in contact with LEU 585 (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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514A ILE* 3.8 27.5 - - + +
517A LEU* 4.4 20.0 - - + -
530A ILE* 5.2 5.8 - - + -
545A PHE* 4.8 14.1 - - + -
550A LEU* 5.3 6.5 - - + -
553A LEU* 4.0 22.4 - - + -
581A CYS* 3.0 35.5 + - - +
582A GLN* 3.9 5.4 - - - +
584A ASP* 1.3 73.0 - - - +
586A ILE* 1.3 66.9 + - - +
588A LEU* 3.5 21.4 + - + +
1230C VAL* 4.4 13.5 - - + -
1232C PHE* 3.5 24.3 - - + -
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Residues in contact with ILE 586 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
582A GLN* 2.9 36.9 + - - +
583A ARG* 3.4 11.7 - - - +
584A ASP 3.3 0.2 - - - -
585A LEU* 1.3 76.6 - - - +
587A ASP* 1.3 66.8 + - - +
588A LEU 3.3 0.7 + - - +
90B PRO* 3.3 35.7 - - + +
91B ARG* 4.1 13.7 - - - +
92B GLY* 3.5 23.3 - - - +
121B LYS* 2.8 31.3 + - - +
122B MET* 4.6 7.9 - - + +
123B THR* 3.5 4.9 - - - +
1232C PHE* 3.4 28.5 - - + -
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Residues in contact with ASP 587 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
583A ARG* 3.2 25.5 + - - +
584A ASP* 3.2 5.6 + - - +
586A ILE* 1.3 87.9 - - - +
588A LEU* 1.3 60.1 + - - +
589A CYS* 3.6 2.9 + - - +
92B GLY* 3.9 16.9 + - - -
93B ARG* 4.7 8.1 + - - +
122B MET* 5.1 2.4 - - - +
123B THR* 3.6 11.1 - - - +
124B ASP* 3.3 47.1 + - - +
125B LEU* 5.2 1.2 - - - +
127B ASP* 4.7 8.3 - - - +
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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