Contacts of the helix formed by residues 549 - 569 (chain A) in PDB entry 4IVE
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 PRO 549 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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547A SER 4.7 1.6 - - - +
548A ALA* 1.4 86.1 - - + +
550A PRO* 1.4 76.1 - - + +
551A GLN* 3.3 2.7 - - + +
552A LYS* 2.9 30.2 + - + +
553A GLN* 3.0 10.4 + - - +
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Residues in contact with PRO 550 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
548A ALA 3.7 2.2 - - - +
549A PRO* 1.4 83.6 - - + +
551A GLN* 1.4 60.5 + - - +
553A GLN* 3.2 30.2 + - - +
554A LYS* 3.2 18.0 + - - +
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Residues in contact with GLN 551 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
549A PRO* 3.3 3.4 - - + +
550A PRO* 1.4 75.8 - - - +
552A LYS* 1.4 60.1 + - - +
554A LYS* 3.5 20.1 + - - +
555A GLN* 3.1 43.1 + - - +
544D ARG* 3.9 11.5 - - - +
547D SER 3.2 28.0 + - - +
548D ALA* 4.2 2.0 - - - +
549D PRO* 3.9 21.3 - - + +
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Residues in contact with LYS 552 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
548A ALA* 4.3 6.7 - - + -
549A PRO* 2.9 30.2 + - + +
551A GLN* 1.4 75.5 - - - +
553A GLN* 1.4 58.1 + - - +
555A GLN* 3.2 34.9 + - - +
556A MSE 3.0 71.6 + - + +
559A GLU* 6.3 0.4 - - - +
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Residues in contact with GLN 553 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
545A LEU* 3.0 35.5 + - + +
546A ALA* 4.1 10.0 + - - +
548A ALA 2.7 22.6 + - - +
549A PRO 3.0 9.1 + - - +
550A PRO* 3.2 26.6 + - - +
552A LYS* 1.4 74.8 - - - +
554A LYS* 1.4 55.7 + - + +
556A MSE 3.1 15.1 + - + +
557A LEU* 3.0 34.6 + - - +
585A ASN* 2.7 35.6 + - - +
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Residues in contact with LYS 554 (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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550A PRO 3.2 10.6 + - - +
551A GLN* 3.7 30.1 + - - +
552A LYS 3.4 0.2 - - - -
553A GLN* 1.4 73.7 - - + +
555A GLN* 1.4 55.9 + - - +
557A LEU* 4.6 3.6 - - + +
558A GLY* 2.8 31.4 + - - -
578A GLY 5.6 0.4 + - - -
581A LEU* 3.4 47.5 + - + +
582A GLU* 3.5 33.0 + - - +
585A ASN* 5.6 4.7 - - - +
547D SER* 3.5 19.1 + - - +
548D ALA 6.3 0.2 - - - -
549D PRO* 6.0 4.9 - - - +
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Residues in contact with GLN 555 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
551A GLN* 3.1 34.2 + - - +
552A LYS* 3.2 38.4 + - - +
554A LYS* 1.4 76.2 - - - +
556A MSE 1.4 55.8 + - - +
558A GLY* 3.4 0.5 + - - -
559A GLU* 3.0 38.2 + - + +
543D SER 5.4 0.2 - - - +
544D ARG* 3.3 52.6 + - - +
547D SER* 3.6 14.3 + - - -
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Residues in contact with MSE 556 (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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540A LEU* 4.0 18.3 - - + +
544A ARG* 5.1 7.0 - - - +
545A LEU* 3.7 24.2 - - + -
548A ALA* 3.4 32.3 - - + -
552A LYS* 3.0 45.5 + - + +
553A GLN* 3.1 19.3 + - + +
555A GLN* 1.4 71.0 - - - +
557A LEU* 1.3 65.0 + - - +
559A GLU* 3.5 13.1 + - - +
560A ARG* 3.4 21.0 + - - +
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Residues in contact with LEU 557 (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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540A LEU* 4.2 5.8 - - + -
545A LEU* 3.9 13.0 - - + -
553A GLN 3.0 20.6 + - - +
554A LYS* 4.9 2.7 - - + +
556A MSE 1.3 73.4 - - - +
558A GLY* 1.3 59.6 + - - +
560A ARG* 3.2 6.5 + - - +
561A LEU* 2.9 32.6 + - + +
581A LEU* 3.9 14.6 - - + -
585A ASN* 3.3 36.6 - - + +
588A LEU* 3.7 28.5 - - + -
589A LEU* 3.8 29.4 - - + -
592A LEU* 3.8 16.4 - - + -
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Residues in contact with GLY 558 (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 LYS 2.8 23.5 + - - -
555A GLN 3.7 1.8 - - - -
556A MSE 3.4 0.2 - - - -
557A LEU* 1.3 72.5 - - - +
559A GLU* 1.3 54.9 + - - +
561A LEU* 4.4 1.1 - - - -
562A PHE* 2.9 36.2 + - - +
577A THR* 4.3 6.5 - - - +
581A LEU* 3.6 15.1 - - - +
543D SER* 4.1 6.7 - - - -
547D SER* 3.8 10.1 - - - -
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Residues in contact with GLU 559 (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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552A LYS* 6.3 0.4 - - - +
555A GLN* 3.0 26.4 + - + +
556A MSE 3.7 9.2 - - - +
557A LEU 3.3 0.2 - - - -
558A GLY* 1.3 74.9 - - - +
560A ARG* 1.3 61.5 + - + +
563A PRO* 3.2 22.7 - - - +
541D THR* 4.0 12.2 + - - +
543D SER* 2.6 32.9 + - - -
544D ARG* 4.5 10.3 + - - +
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Residues in contact with ARG 560 (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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537A GLN* 3.6 42.8 + - - +
538A GLU* 2.9 33.5 + - - +
539A THR* 4.9 1.0 - - - +
540A LEU* 3.5 42.5 - - + +
544A ARG* 4.9 0.6 - - - +
556A MSE 3.4 15.8 + - - +
557A LEU 3.2 4.6 + - - +
559A GLU* 1.3 80.0 - - + +
561A LEU* 1.3 63.3 + - - +
562A PHE 3.6 0.2 - - - -
563A PRO* 3.4 9.8 - - - +
564A LEU* 3.7 18.5 - - - +
592A LEU* 3.6 24.6 - - + +
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Residues in contact with LEU 561 (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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557A LEU* 2.9 24.2 + - + +
558A GLY* 4.0 3.6 - - - +
560A ARG* 1.3 74.4 - - - +
562A PHE* 1.3 65.4 + - - +
564A LEU* 3.2 7.3 + - - +
565A ILE* 2.9 36.6 + - + +
577A THR* 4.5 3.8 - - + -
580A LEU* 5.0 7.4 - - + -
581A LEU* 3.8 22.4 - - + -
588A LEU* 3.8 33.9 - - + +
591A MSE 4.9 2.0 - - + -
592A LEU* 3.7 25.4 - - + +
598A LEU* 3.8 31.2 - - + -
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Residues in contact with PHE 562 (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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558A GLY 2.9 21.7 + - - +
561A LEU* 1.3 72.2 - - - +
563A PRO* 1.4 66.4 - - + +
565A ILE 3.3 0.7 + - - -
566A GLN* 2.9 66.0 + - - +
570A PRO 5.9 0.2 - - - -
573A ALA* 3.6 23.8 - - + -
574A GLY* 3.7 15.5 - - - -
577A THR* 3.5 26.7 - - + +
542D ALA* 3.4 31.0 - - + -
543D SER* 3.7 28.0 - - - -
546D ALA* 4.6 0.2 - - + -
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Residues in contact with PRO 563 (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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559A GLU 3.2 24.0 - - - +
560A ARG* 3.4 11.9 - - - +
562A PHE* 1.4 98.5 - - + +
564A LEU* 1.3 57.9 + - + +
566A GLN* 3.6 11.1 + - + +
567A ALA* 3.1 26.3 + - - +
543D SER* 5.6 0.7 - - - -
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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
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560A ARG 3.7 18.4 - - - +
561A LEU 3.2 7.2 + - - +
563A PRO* 1.3 76.7 - - + +
565A ILE* 1.3 65.4 + - - +
567A ALA* 3.3 16.1 + - + +
568A MSE 3.4 22.0 + - + +
592A LEU* 4.1 26.0 - - + +
598A LEU* 3.8 26.2 - - + -
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Residues in contact with ILE 565 (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 LEU* 2.9 33.8 + - + +
562A PHE 3.9 0.7 - - - +
564A LEU* 1.3 72.7 - - - +
566A GLN* 1.3 60.6 + - - +
568A MSE 3.1 9.3 + - - +
569A HIS 2.8 27.4 + - - +
573A ALA* 3.8 17.0 - - - +
576A ILE* 3.7 31.6 - - + -
577A THR* 3.5 29.6 - - - +
580A LEU* 3.8 26.0 - - + -
598A LEU* 4.3 9.0 - - + -
602A VAL* 3.9 17.0 - - + -
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Residues in contact with GLN 566 (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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562A PHE* 2.9 45.9 + - + +
563A PRO* 3.8 10.1 + - - +
565A ILE* 1.3 76.5 - - - +
567A ALA* 1.3 61.4 + - - +
570A PRO* 3.2 42.0 - - + +
573A ALA* 3.7 18.3 - - + +
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Residues in contact with ALA 567 (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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563A PRO 3.1 14.9 + - - +
564A LEU* 3.4 13.7 - - + +
565A ILE 3.2 0.6 - - - -
566A GLN* 1.3 75.8 - - - +
568A MSE 1.4 61.2 + - + +
570A PRO* 4.6 3.1 - - - +
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Residues in contact with MSE 568 (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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564A LEU* 3.4 15.9 - - + +
565A ILE* 3.1 5.9 + - - +
567A ALA* 1.4 78.4 - - + +
569A HIS* 1.3 72.1 + - + +
570A PRO* 3.8 5.6 - - - +
595A PRO* 4.7 4.3 - - + +
598A LEU* 3.7 35.4 - - + -
599A ARG* 3.5 52.1 + - + +
602A VAL* 3.8 27.6 - - + -
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Residues in contact with HIS 569 (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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565A ILE 2.8 11.1 + - - +
566A GLN 3.7 2.7 - - - -
568A MSE 1.3 83.8 + - + +
570A PRO* 1.3 66.4 - - - +
571A THR 3.3 3.1 + - - -
572A LEU* 4.7 6.7 - - + +
573A ALA* 3.0 22.3 + - - +
576A ILE* 3.7 20.6 - - + -
599A ARG* 3.7 13.6 + - - -
602A VAL* 3.5 26.2 - - + +
603A ASP* 4.2 8.2 + - - -
606A VAL* 3.9 26.3 - - + +
701A CL 3.7 15.7 - - + +
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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
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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