Contacts of the helix formed by residues 548 - 564 (chain A) in PDB entry 6R4E
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 HIS 548 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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545A ARG 3.1 17.2 + - - +
546A GLY 2.9 1.6 + - - -
547A TYR* 1.3 83.3 - - + +
549A TYR* 1.3 65.2 + - - +
550A ALA 3.3 1.1 - - - -
551A THR* 3.3 11.2 + - - +
552A CYS* 3.2 25.1 + - - -
592A ILE* 3.7 22.0 - - + +
594A MET* 3.2 34.3 - - + +
596A ASP* 4.0 18.2 + - - -
598A THR* 5.9 0.9 - - - -
642A ASP 5.0 0.2 + - - -
645A GLN* 3.5 34.5 - - + +
646A GLY* 3.8 3.9 - - - -
649A SER* 3.1 28.4 + - - -
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Residues in contact with TYR 549 (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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382A VAL* 4.2 17.3 - - + -
544A GLY 4.5 7.4 - - - -
545A ARG 3.7 3.0 + - - -
546A GLY 3.1 15.8 + - - +
548A HIS* 1.3 76.7 - - - +
550A ALA* 1.3 62.4 + - - +
552A CYS* 3.1 15.2 + - + +
553A LEU* 3.1 45.6 + - + +
569A GLY 5.4 1.1 - - - -
570A ILE 5.0 1.1 - - - -
571A LEU* 3.7 57.3 - - + +
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Residues in contact with ALA 550 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
379A HIS* 3.6 11.8 - - - +
382A VAL* 3.8 13.8 - - + +
383A ALA* 3.5 46.2 - - + +
478A TYR* 3.9 4.7 - - - +
546A GLY 4.7 0.6 + - - -
547A TYR 4.5 3.9 + - - +
548A HIS* 3.3 0.8 - - - +
549A TYR* 1.3 78.2 - - - +
551A THR* 1.3 58.5 + - - +
553A LEU* 3.8 6.8 - - - +
554A GLU* 2.8 33.8 + - - +
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Residues in contact with THR 551 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
478A TYR* 4.5 4.9 + - - -
542A ILE* 5.0 1.6 - - + +
547A TYR 4.3 0.9 + - - -
548A HIS* 3.3 21.5 + - - +
549A TYR 3.2 0.4 - - - -
550A ALA* 1.3 79.3 - - - +
552A CYS* 1.3 57.4 + - - +
554A GLU* 4.1 3.8 - - - +
555A GLY* 2.9 27.0 + - - -
592A ILE* 3.3 25.4 - - + -
619A ILE* 6.1 0.2 - - + -
646A GLY* 3.8 13.3 + - - -
649A SER* 3.1 41.2 + - - +
650A VAL* 3.9 11.1 - - + +
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Residues in contact with CYS 552 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
542A ILE* 3.5 32.7 - - - +
543A MET* 3.1 11.2 - - - -
544A GLY* 3.0 42.0 - - - -
548A HIS 3.2 11.7 + - - -
549A TYR* 3.1 12.3 + - + +
551A THR* 1.3 77.4 - - - +
553A LEU* 1.3 58.4 + - + +
556A ALA* 2.9 32.1 + - - +
569A GLY* 3.9 9.2 - - - -
570A ILE 4.4 3.6 - - - +
592A ILE* 4.1 5.4 - - - -
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Residues in contact with LEU 553 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378A TYR* 5.1 6.5 - - + +
379A HIS* 3.4 36.2 - - + +
382A VAL* 4.6 14.4 - - + -
549A TYR* 3.1 54.3 + - + +
550A ALA* 3.8 5.2 - - - +
552A CYS* 1.3 75.4 - - - +
554A GLU* 1.3 58.6 + - - +
556A ALA* 3.4 4.2 + - - +
557A LEU* 3.0 23.2 + - - +
569A GLY* 4.3 19.7 - - - +
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Residues in contact with GLU 554 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376A THR* 2.8 32.8 + - - +
379A HIS* 2.9 28.8 + - + +
474A SER 3.8 1.9 - - - +
478A TYR* 4.1 18.0 - - + +
550A ALA 2.8 21.7 + - - +
551A THR 4.1 1.8 - - - +
553A LEU* 1.3 71.0 - - - +
555A GLY* 1.3 61.3 + - - +
557A LEU* 3.2 2.3 + - - +
558A LYS* 2.7 62.1 + - + +
650A VAL* 3.8 22.4 - - + -
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Residues in contact with GLY 555 (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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542A ILE* 4.0 11.0 - - - -
551A THR 2.9 17.6 + - - -
552A CYS 4.0 0.2 - - - -
554A GLU* 1.3 74.3 - - - +
556A ALA* 1.3 66.2 + - - +
558A LYS* 3.2 8.2 + - - +
559A ILE* 3.0 30.1 + - - +
650A VAL* 4.7 7.3 - - - +
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Residues in contact with ALA 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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542A ILE* 3.7 9.4 - - + +
552A CYS 2.9 20.3 + - - +
553A LEU* 3.6 4.9 - - - +
555A GLY* 1.3 75.2 - - - +
557A LEU* 1.3 62.7 + - - +
560A LYS* 3.0 16.3 + - - +
567A SER* 2.6 28.3 + - - +
568A GLU* 3.7 14.1 - - - +
569A GLY* 3.4 24.5 - - - +
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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
----------------------------------------------------------
375A GLY* 4.4 7.4 - - - -
376A THR* 3.7 31.9 - - - +
379A HIS* 3.7 19.3 - - + -
553A LEU 3.0 17.9 + - - +
554A GLU 3.6 4.7 - - - +
555A GLY 3.2 0.4 - - - -
556A ALA* 1.3 74.5 - - - +
558A LYS* 1.3 64.1 + - - +
560A LYS* 3.3 17.9 + - + +
561A GLU* 2.8 45.1 + - + +
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Residues in contact with LYS 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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325A MET* 5.1 6.3 - - + -
376A THR* 3.1 16.6 + - - -
473A ALA* 3.8 20.2 - - + -
474A SER 2.7 35.1 + - - +
475A THR* 4.6 8.1 - - + +
554A GLU* 2.7 41.4 + - + +
555A GLY* 3.2 10.5 + - - +
557A LEU* 1.3 79.1 - - - +
559A ILE* 1.3 59.8 + - + +
561A GLU* 3.2 15.9 + - - +
562A ILE* 2.8 39.5 + - + +
650A VAL* 6.2 1.1 - - + -
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Residues in contact with ILE 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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534A LEU* 6.3 2.5 - - + -
540A VAL* 4.6 7.2 - - + -
542A ILE* 3.9 22.4 - - + -
555A GLY* 3.0 16.3 + - - +
558A LYS* 1.3 77.7 - - + +
560A LYS* 1.3 57.0 + - - +
563A THR* 2.9 43.4 + - - +
564A TYR 3.2 2.8 + - - -
565A MET* 3.3 35.0 + - + -
567A SER* 3.1 20.4 - - - +
590A ILE* 5.4 7.0 - - + -
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Residues in contact with LYS 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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556A ALA* 3.0 17.7 + - - +
557A LEU* 3.6 19.7 - - + +
559A ILE* 1.3 76.8 - - - +
561A GLU* 1.3 62.4 + - - +
564A TYR* 3.1 24.5 + - - +
565A MET 3.5 19.1 - - - +
566A HIS* 4.5 15.0 + - + -
567A SER* 2.7 33.5 + - - +
568A GLU* 4.4 6.9 - - - +
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Residues in contact with GLU 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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472A VAL* 3.9 17.3 - - + +
473A ALA* 3.5 27.4 - - - +
474A SER 4.9 0.2 + - - -
557A LEU* 2.8 31.8 + - + +
558A LYS* 3.9 14.6 + - - +
560A LYS* 1.3 74.4 - - - +
562A ILE* 1.3 65.0 + - + +
564A TYR* 3.1 22.2 + - - -
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Residues in contact with ILE 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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325A MET* 3.8 38.6 - - + -
472A VAL* 3.6 30.7 - - + -
473A ALA* 3.8 20.0 - - + -
558A LYS* 2.8 18.8 + - + +
559A ILE* 5.3 0.2 - - - -
561A GLU* 1.3 88.5 - - + +
563A THR* 1.3 65.8 + - - +
564A TYR* 3.6 16.3 + - - -
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Residues in contact with THR 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 ILE* 2.9 30.0 + - - +
562A ILE* 1.3 80.4 - - - +
564A TYR* 1.3 74.6 + - - +
565A MET* 4.1 22.8 - - + +
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Residues in contact with TYR 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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559A ILE 3.2 0.4 + - - -
560A LYS* 3.1 19.5 + - - -
561A GLU* 3.1 24.7 + - - -
562A ILE* 4.0 12.3 + - - -
563A THR* 1.3 82.3 - - - +
565A MET* 1.3 59.4 + - - +
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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