Contacts of the helix formed by residues 558 - 582 (chain A) in PDB entry 4PE5
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 PHE 558 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
557A PRO* 1.3 75.1 - - + +
559A GLN* 1.3 70.1 + - - +
561A CYS* 3.2 21.7 + - + +
562A LEU* 3.6 23.6 + - + +
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Residues in contact with GLN 559 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
556A GLN* 3.4 12.3 + - - +
557A PRO* 2.9 10.2 - - - +
558A PHE* 1.3 82.3 - - - +
560A SER* 1.3 62.4 + - - +
561A CYS* 3.4 2.8 + - + +
562A LEU* 4.2 0.5 + - - +
563A TRP* 3.9 13.0 + - - +
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Residues in contact with SER 560 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
559A GLN* 1.3 77.7 - - - +
561A CYS* 1.3 58.6 + - - +
562A LEU 3.6 0.4 - - - -
563A TRP* 3.8 11.9 - - - -
564A LEU* 2.9 32.5 + - - +
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Residues in contact with CYS 561 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
558A PHE* 3.3 12.8 - - + +
559A GLN* 3.2 3.1 - - + +
560A SER* 1.3 78.2 - - - +
562A LEU* 1.3 60.0 - - - +
564A LEU* 3.8 2.1 - - - +
565A LEU* 2.9 30.8 + - - +
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Residues in contact with LEU 562 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
557A PRO 5.2 1.3 - - - +
558A PHE* 3.6 26.4 + - + +
559A GLN 5.0 0.9 - - - +
561A CYS* 1.3 80.3 - - - +
563A TRP* 1.3 58.8 + - - +
565A LEU* 3.7 7.6 - - - +
566A VAL* 2.9 30.5 + - - +
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Residues in contact with TRP 563 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
559A GLN 3.9 7.0 + - - +
560A SER* 3.8 20.1 - - - +
561A CYS 3.2 0.4 - - - -
562A LEU* 1.3 78.9 - - - +
564A LEU* 1.3 58.3 + - - +
566A VAL* 3.4 5.2 + - - +
567A GLY* 2.9 24.8 + - - -
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Residues in contact with LEU 564 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
560A SER* 2.9 21.4 + - - +
561A CYS* 4.1 2.5 - - - +
563A TRP* 1.3 73.9 - - - +
565A LEU* 1.3 61.0 + - - +
567A GLY* 3.7 2.4 - - - +
568A LEU* 2.9 30.7 + - - +
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Residues in contact with LEU 565 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
561A CYS* 2.9 22.2 + - - +
562A LEU* 3.7 9.6 - - - +
563A TRP 3.2 0.2 - - - -
564A LEU* 1.3 77.3 - - - +
566A VAL* 1.3 57.0 + - - +
568A LEU* 3.5 4.8 + - - +
569A SER* 2.9 30.0 + - - -
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Residues in contact with VAL 566 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
562A LEU 2.9 19.0 + - - +
563A TRP* 3.9 4.7 - - - +
565A LEU* 1.3 76.0 - - - +
567A GLY* 1.3 59.0 + - - +
569A SER* 3.7 7.2 - - - -
570A VAL* 2.9 27.7 + - - +
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Residues in contact with GLY 567 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
563A TRP 2.9 16.6 + - - -
564A LEU* 3.8 2.7 - - - -
565A LEU 3.2 0.4 - - - -
566A VAL* 1.3 75.2 - - - +
568A LEU* 1.3 59.1 + - - +
570A VAL* 3.1 8.0 + - - +
571A HIS* 2.9 27.4 + - - +
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Residues in contact with LEU 568 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
564A LEU 2.9 18.8 + - - +
565A LEU* 4.0 4.5 - - - +
567A GLY* 1.3 75.3 - - - +
569A SER* 1.3 56.2 + - - +
571A HIS* 3.4 6.7 + - - +
572A VAL* 2.9 29.5 + - - +
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Residues in contact with SER 569 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
565A LEU 2.9 19.1 + - - -
566A VAL* 3.8 9.2 - - - -
568A LEU* 1.3 76.0 - - - +
570A VAL* 1.3 58.4 + - - +
572A VAL* 3.6 7.2 + - - +
573A VAL* 2.9 27.0 + - - +
822B PHE* 6.3 4.0 - - - -
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Residues in contact with VAL 570 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
566A VAL 2.9 18.2 + - - +
567A GLY* 3.3 9.6 - - - +
569A SER* 1.3 76.7 - - - +
571A HIS* 1.3 58.4 + - - +
573A VAL* 3.2 7.9 + - - +
574A ALA* 2.9 29.1 + - - +
610A SER* 4.7 16.0 - - - -
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Residues in contact with HIS 571 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
567A GLY 2.9 14.9 + - - +
568A LEU* 3.8 8.7 - - - +
569A SER 3.4 0.2 - - - -
570A VAL* 1.3 76.5 - - - +
572A VAL* 1.3 56.4 + - - +
574A ALA* 3.4 6.5 + - - +
575A VAL* 2.9 29.0 + - - +
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Residues in contact with VAL 572 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
568A LEU 2.9 18.6 + - - +
569A SER* 3.8 8.7 - - - +
571A HIS* 1.3 76.5 - - - +
573A VAL* 1.3 58.6 + - - +
575A VAL* 3.8 6.8 - - - +
576A MET* 2.9 29.5 + - - +
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Residues in contact with VAL 573 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
569A SER 2.9 19.7 + - - +
570A VAL* 3.2 9.8 + - - +
572A VAL* 1.3 75.2 - - - +
574A ALA* 1.3 59.8 + - - +
576A MET* 3.8 5.0 - - - +
577A LEU* 2.9 30.4 + - - +
610A SER* 5.8 3.8 - - - -
636A TRP* 5.4 13.2 - - + -
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Residues in contact with ALA 574 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
570A VAL 2.9 16.1 + - - +
571A HIS* 3.8 7.6 - - - +
573A VAL* 1.3 76.1 - - - +
575A VAL* 1.3 59.1 + - - +
577A LEU* 3.8 5.9 - - - +
578A TYR* 2.9 30.1 + - - +
606A ALA* 4.0 29.6 - - + +
607A MET* 4.9 4.0 - - + +
610A SER* 4.9 7.1 - - - -
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Residues in contact with VAL 575 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
571A HIS 2.9 18.1 + - - +
572A VAL* 3.8 8.7 - - - +
574A ALA* 1.3 76.2 - - - +
576A MET* 1.3 59.5 + - - +
578A TYR* 3.4 6.1 + - - +
579A LEU* 2.9 29.5 + - - +
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Residues in contact with MET 576 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
572A VAL 2.9 19.0 + - - +
573A VAL* 3.9 5.8 - - - +
575A VAL* 1.3 73.2 - - - +
577A LEU* 1.3 61.3 + - - +
579A LEU* 3.3 7.6 + - - +
580A LEU* 2.9 29.8 + - - +
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Residues in contact with LEU 577 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
573A VAL 2.9 18.6 + - - +
574A ALA* 3.8 7.4 - - - +
576A MET* 1.3 77.4 - - - +
578A TYR* 1.3 58.0 + - - +
580A LEU* 3.3 6.3 + - - +
581A ASP* 2.9 30.1 + - - +
606A ALA* 4.6 10.5 - - + -
629A ALA* 4.4 17.0 - - + +
632A LEU* 6.2 2.7 - - + -
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Residues in contact with TYR 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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574A ALA 2.9 18.2 + - - +
575A VAL* 3.7 7.2 - - - +
576A MET 3.3 0.2 - - - -
577A LEU* 1.3 77.4 - - - +
579A LEU* 1.3 58.0 + - - +
581A ASP* 4.0 4.7 - - - +
582A ARG* 3.1 30.0 + - - +
606A ALA* 5.0 7.8 - - + +
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Residues in contact with LEU 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 VAL 2.9 17.9 + - - +
576A MET* 3.7 8.1 - - - +
577A LEU 3.2 0.2 - - - -
578A TYR* 1.3 77.4 - - - +
580A LEU* 1.3 59.9 + - - +
582A ARG 4.2 12.1 - - - -
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Residues in contact with LEU 580 (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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576A MET 2.9 16.8 + - - +
577A LEU 3.3 0.6 + - - +
579A LEU* 1.3 76.9 - - - +
581A ASP* 1.3 62.9 + - - +
582A ARG 5.1 0.2 - - - -
627A PHE 3.2 11.7 - - - +
628A SER* 4.2 15.1 - - - +
629A ALA* 3.8 24.7 - - + -
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Residues in contact with ASP 581 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
577A LEU 2.9 17.7 + - - +
578A TYR* 4.0 5.8 - - - +
579A LEU 3.4 0.2 - - - -
580A LEU* 1.3 81.4 - - - +
582A ARG* 1.3 61.8 + - + +
627A PHE* 3.9 27.4 - - + +
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Residues in contact with ARG 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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578A TYR 3.1 15.5 + - - +
579A LEU* 4.2 12.3 - - - -
581A ASP* 1.3 81.4 - - + +
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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