Contacts of the helix formed by residues 542 - 565 (chain A) in PDB entry 5MQF
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 ASN 542 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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656 G 3.5 13.4 - - - +
666 C 3.3 22.8 + - - +
540A PHE 3.5 1.6 - - - -
541A GLY* 1.3 79.5 - - - +
543A ALA* 1.3 61.5 + - - +
544A PHE 3.4 0.4 - - - -
545A HIS* 3.5 1.4 + - - +
546A LEU* 2.9 27.4 + - - +
594A TYR* 4.1 6.5 - - - +
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Residues in contact with ALA 543 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
666 C 2.9 38.2 + - - +
542A ASN* 1.3 71.1 - - - +
544A PHE* 1.3 60.4 + - - +
546A LEU* 3.1 7.4 + - - +
547A CYS* 2.9 28.6 + - - +
651A TRP* 5.5 7.4 - - + +
652A LEU* 5.9 3.1 - - + -
655A LEU* 4.9 13.2 - - + -
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Residues in contact with PHE 544 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
656 G 5.6 0.6 + - - +
666 C 4.6 0.6 + - - -
507A LEU* 6.3 3.1 - - + -
540A PHE* 3.3 36.0 - - + +
542A ASN 4.3 0.8 - - - +
543A ALA* 1.3 78.7 - - - +
545A HIS* 1.3 58.6 + - - +
547A CYS* 3.6 7.6 + - - +
548A ARG* 2.9 26.5 + - - +
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Residues in contact with HIS 545 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
540A PHE 3.7 4.9 + - - +
541A GLY* 3.2 32.5 - - - +
542A ASN 3.5 2.6 + - - +
543A ALA 3.2 0.6 - - - -
544A PHE* 1.3 75.5 - - - +
546A LEU* 1.3 60.9 + - - +
548A ARG* 3.2 9.4 + - - +
549A GLU* 2.9 26.5 + - - +
591A MET 5.2 1.7 - - - +
593A ARG* 5.7 4.0 - - + -
594A TYR* 4.4 9.2 - - + +
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Residues in contact with LEU 546 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
542A ASN 2.9 18.7 + - - +
543A ALA* 3.1 8.7 + - - +
545A HIS* 1.3 74.2 - - - +
547A CYS* 1.3 59.9 + - - +
549A GLU* 3.0 6.2 + - - +
550A VAL* 2.9 28.5 + - - +
594A TYR* 3.7 20.6 - - + +
648A LEU* 5.7 9.6 - - + -
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Residues in contact with CYS 547 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
543A ALA 2.9 16.0 + - - +
544A PHE* 4.0 7.2 - - - +
546A LEU* 1.3 75.2 - - - +
548A ARG* 1.3 55.8 + - - +
549A GLU 3.3 0.2 - - - -
550A VAL* 4.3 6.2 - - - +
551A LEU* 2.9 32.1 + - - +
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Residues in contact with ARG 548 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
522A PHE* 3.5 24.2 - - + +
544A PHE 2.9 19.3 + - - +
545A HIS* 3.4 11.2 - - - +
546A LEU 3.1 0.4 - - - -
547A CYS* 1.3 77.9 - - - +
549A GLU* 1.3 50.8 + - - +
551A LEU* 4.6 3.4 - - - -
552A ARG* 2.7 36.1 + - - +
590A GLY 4.8 2.6 - - - +
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Residues in contact with GLU 549 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
545A HIS 2.9 12.4 + - - +
546A LEU* 3.0 10.7 + - - +
548A ARG* 1.3 76.3 - - - +
550A VAL* 1.3 61.1 + - - +
552A ARG* 3.0 6.3 + - - +
553A LEU* 2.9 31.0 + - - +
590A GLY 4.1 6.0 + - - +
591A MET* 3.6 36.3 - - + +
594A TYR* 5.3 3.6 - - + -
595A LYS* 6.0 1.8 - - + +
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Residues in contact with VAL 550 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99A VAL* 5.8 8.5 - - + -
546A LEU 2.9 15.0 + - - +
547A CYS* 4.3 6.3 - - - +
549A GLU* 1.3 76.7 - - - +
551A LEU* 1.3 57.6 + - - +
553A LEU* 4.3 2.5 - - - +
554A THR* 2.8 32.0 + - - -
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Residues in contact with LEU 551 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
500A GLY* 5.4 12.8 - - - -
522A PHE* 4.7 5.4 - - + +
547A CYS 2.9 21.6 + - - +
548A ARG* 3.8 4.3 - - - +
550A VAL* 1.3 75.1 - - - +
552A ARG* 1.3 59.7 + - - +
554A THR* 3.9 7.2 - - - -
555A LYS* 2.9 36.0 + - + +
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Residues in contact with ARG 552 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
521A ASN 5.3 0.7 - - - +
522A PHE* 3.7 17.7 - - + -
548A ARG 2.7 23.8 + - - +
549A GLU* 3.0 11.3 + - - +
551A LEU* 1.3 75.6 - - - +
553A LEU* 1.3 53.7 + - - +
555A LYS* 4.7 0.4 - - - +
556A LEU* 2.6 37.3 + - - +
589A THR* 5.9 1.8 - - - -
590A GLY* 4.3 24.0 - - - +
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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
----------------------------------------------------------
549A GLU 2.9 13.8 + - - +
550A VAL* 4.5 2.2 - - - +
552A ARG* 1.3 74.5 - - - +
554A THR* 1.3 66.4 + - - +
556A LEU* 3.3 6.2 - - - +
557A VAL* 2.9 27.0 + - - +
589A THR* 5.7 2.9 - - - -
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Residues in contact with THR 554 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98A ALA* 5.8 3.6 - - - -
99A VAL* 6.3 2.7 - - - -
102A LEU* 5.2 16.5 - - - +
550A VAL 2.8 24.2 + - - -
551A LEU* 3.9 4.9 - - - -
553A LEU* 1.3 78.8 - - - +
555A LYS* 1.3 58.0 + - - +
557A VAL* 4.1 1.3 - - - +
558A VAL* 2.9 30.1 + - - +
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Residues in contact with LYS 555 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
497A CYS* 4.9 17.0 - - + +
520A TYR 4.5 16.2 - - - +
522A PHE* 6.4 0.2 - - + -
551A LEU* 2.9 25.9 + - + +
552A ARG* 4.7 0.4 - - - +
554A THR* 1.3 74.5 - - - +
556A LEU* 1.3 57.5 + - - +
558A VAL* 3.5 9.1 - - - +
559A ASP* 2.9 31.9 + - - +
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Residues in contact with LEU 556 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
552A ARG 2.6 25.5 + - - +
553A LEU* 3.3 10.1 - - - +
554A THR 3.1 0.2 - - - -
555A LYS* 1.3 77.2 - - - +
557A VAL* 1.3 59.2 + - - +
559A ASP* 3.8 2.4 - - - +
560A SER* 2.9 27.6 + - - -
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Residues in contact with VAL 557 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
553A LEU 2.9 16.9 + - - +
554A THR* 4.3 1.3 - - - +
556A LEU* 1.3 71.8 - - - +
558A VAL* 1.3 60.5 + - - +
560A SER* 3.4 8.3 - - - -
561A HIS* 2.9 30.8 + - - +
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Residues in contact with VAL 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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489A TRP 6.1 1.1 - - - -
493A GLY* 4.5 23.8 - - - +
494A LEU* 5.9 0.2 - - - -
497A CYS* 5.2 5.6 - - + -
554A THR 2.9 20.6 + - - +
555A LYS* 3.5 11.0 - - - +
557A VAL* 1.3 78.3 - - - +
559A ASP* 1.3 59.6 + - - +
561A HIS* 3.2 4.1 + - - +
562A VAL* 2.9 26.9 + - - +
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Residues in contact with ASP 559 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168A PRO* 4.5 20.4 - - + +
555A LYS 2.9 20.6 + - - +
556A LEU* 4.1 2.0 - - - +
558A VAL* 1.3 72.4 - - - +
560A SER* 1.3 58.2 + - - +
562A VAL* 3.7 9.5 - - - +
563A GLN* 2.9 29.8 + - - +
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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
----------------------------------------------------------
168A PRO* 5.4 5.6 - - - +
556A LEU 2.9 19.2 + - - -
557A VAL* 3.4 11.2 - - - -
558A VAL 3.1 0.2 - - - -
559A ASP* 1.3 77.2 - - - +
561A HIS* 1.3 56.7 + - - +
563A GLN* 3.3 6.2 + - - +
564A TYR* 2.9 26.6 + - - +
578A LEU* 6.6 0.4 - - - -
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Residues in contact with HIS 561 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
489A TRP* 5.8 9.9 - - + -
490A VAL* 6.0 1.1 - - - -
557A VAL 2.9 16.9 + - - +
558A VAL* 3.8 3.8 - - - +
560A SER* 1.3 73.4 - - - +
562A VAL* 1.3 59.8 + - - +
564A TYR* 3.4 9.6 - - + +
565A ARG* 2.9 31.2 + - - +
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Residues in contact with VAL 562 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
490A VAL* 5.0 19.1 - - + +
494A LEU* 6.4 2.0 - - + -
558A VAL 2.9 17.0 + - - +
559A ASP* 3.7 10.3 - - - +
560A SER 3.2 0.2 - - - -
561A HIS* 1.3 77.9 - - - +
563A GLN* 1.3 56.8 + - - +
565A ARG* 4.9 3.1 - - - -
566A LEU* 2.9 35.5 + - + +
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Residues in contact with GLN 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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168A PRO* 4.4 18.4 - - + -
559A ASP 2.9 18.4 + - - +
560A SER* 3.7 4.9 - - - +
562A VAL* 1.3 73.7 - - - +
564A TYR* 1.3 57.9 + - - +
566A LEU 2.8 14.9 - - - +
568A ASN* 2.7 33.7 + - + +
570A ASP* 5.3 0.9 - - - -
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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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187A PRO* 4.5 5.0 - - - +
560A SER 2.9 15.1 + - - +
561A HIS* 3.4 13.2 - - + +
562A VAL 3.3 0.2 - - - -
563A GLN* 1.3 78.9 - - - +
565A ARG* 1.3 65.7 + - - +
568A ASN 3.7 8.0 - - - +
569A VAL* 4.6 1.9 - - - -
570A ASP* 4.0 20.1 + - + -
571A ALA 5.2 1.4 + - - +
574A LEU* 3.6 28.7 - - + -
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Residues in contact with ARG 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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182A ILE* 5.8 3.4 - - + -
187A PRO* 3.2 43.3 - - + +
490A VAL* 5.4 10.1 - - + -
561A HIS 2.9 19.7 + - - +
562A VAL* 4.2 3.1 - - - +
564A TYR* 1.3 77.0 - - - +
566A LEU* 1.3 62.5 + - + +
567A GLY 4.3 2.1 + - - +
569A VAL* 6.0 0.3 - - - -
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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) + - + + + + + -
------------------------------------------------------------
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