Contacts of the helix formed by residues 551 - 564 (chain A) in PDB entry 4HXG
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 LEU 551 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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500A PHE* 5.5 0.8 - - - -
542A HIS* 3.2 34.5 + - + -
543A SER 5.0 1.8 + - - +
544A LEU* 3.9 25.4 - - + +
546A ASP 4.5 1.6 + - - -
550A PRO* 1.3 72.7 - - - +
552A ASP* 1.3 62.9 + - - +
553A GLN 3.2 0.9 + - - -
554A SER* 3.3 5.6 + - - -
555A LEU* 3.1 38.5 + - + +
570A ILE* 5.3 0.2 - - + -
572A ILE* 4.0 34.3 - - + -
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Residues in contact with ASP 552 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
496A THR* 2.8 36.0 + - - +
500A PHE* 3.5 19.0 - - + -
550A PRO* 3.1 29.7 - - - +
551A LEU* 1.3 73.6 - - - +
553A GLN* 1.3 61.1 + - - +
555A LEU* 4.4 4.5 - - - +
556A MET* 2.8 58.5 + - + +
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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
----------------------------------------------------------
473A ASN* 5.0 1.9 - - - +
490A GLY 3.1 27.8 - - - +
491A ILE* 3.2 10.8 - - + -
492A SER* 2.6 53.6 + - - -
493A TYR* 3.0 20.4 + - - +
496A THR* 2.7 30.2 + - - -
497A SER* 3.3 16.2 - - - +
540A LEU* 5.5 0.2 - - - +
542A HIS* 4.6 2.2 - - + -
549A CYS* 4.4 2.2 - - + -
550A PRO* 3.1 24.9 + - + +
552A ASP* 1.3 83.4 + - - +
554A SER* 1.3 59.9 + - - +
556A MET* 4.6 0.9 - - - -
557A PHE* 3.8 3.5 - - - +
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Residues in contact with SER 554 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
487A SER 5.4 0.3 + - - -
489A ASN 4.3 3.8 + - - -
490A GLY 4.5 3.1 + - - -
540A LEU* 3.3 31.6 - - - +
541A ILE 3.7 6.5 + - - -
542A HIS* 2.4 40.8 + - - +
551A LEU 3.3 4.4 + - - -
553A GLN* 1.3 76.9 - - - +
555A LEU* 1.3 60.8 + - - +
556A MET 3.4 0.2 - - - -
557A PHE* 3.3 2.4 + - - +
558A TYR* 2.9 23.0 + - - +
570A ILE* 4.1 15.5 - - - -
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Residues in contact with LEU 555 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
551A LEU* 3.1 37.5 + - + +
552A ASP* 4.3 3.1 - - - +
554A SER* 1.3 77.0 - - - +
556A MET* 1.3 61.3 + - + +
558A TYR* 3.1 11.3 + - + -
559A HIS* 2.8 62.0 + - + +
570A ILE* 4.0 22.9 - - + -
572A ILE* 4.7 10.5 - - + -
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Residues in contact with MET 556 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
492A SER* 4.7 2.5 - - - +
493A TYR* 4.2 19.5 - - + -
496A THR* 3.9 21.3 - - + +
528A LEU* 4.0 18.4 - - + -
552A ASP* 2.8 59.2 + - + +
553A GLN* 4.5 3.8 - - - +
555A LEU* 1.3 72.0 - - + +
557A PHE* 1.3 63.8 + - - +
559A HIS* 3.4 5.8 + - - +
560A VAL* 3.0 32.5 + - + +
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Residues in contact with PHE 557 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
473A ASN* 3.5 44.9 - - + -
476A LEU* 6.3 0.2 - - + -
477A THR* 4.0 22.9 - - + -
492A SER* 3.8 7.4 + - - +
527A PRO* 4.1 13.9 - - + -
528A LEU* 3.9 21.0 - - + +
531A ALA* 4.0 22.9 - - + -
534A VAL* 4.5 3.8 - - + -
538A LEU* 3.9 17.3 - - + -
540A LEU* 4.3 5.8 - - + -
553A GLN 3.8 13.1 + - - +
554A SER* 3.3 9.3 + - - +
555A LEU 3.2 0.4 - - - -
556A MET* 1.3 80.3 - - - +
558A TYR* 1.3 62.1 + - - +
560A VAL* 3.9 0.4 - - + -
561A LEU* 2.9 50.7 + - + +
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Residues in contact with TYR 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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540A LEU* 3.5 17.4 - - + +
554A SER 2.9 11.7 + - - +
555A LEU* 3.1 9.4 + - + +
557A PHE* 1.3 77.9 - - - +
559A HIS* 1.3 82.4 + + - +
561A LEU* 3.8 3.8 - - - +
562A LYS* 3.1 48.3 + - + +
568A VAL* 3.5 46.3 + - + -
569A TYR* 3.7 9.8 - - - -
570A ILE* 3.8 37.9 - - + -
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Residues in contact with HIS 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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555A LEU* 2.8 49.3 + - + +
556A MET* 3.9 5.4 - - - +
558A TYR* 1.3 91.3 - + - +
560A VAL* 1.3 61.5 + - + +
562A LYS* 3.1 7.9 + - + +
563A ASP* 2.9 28.2 + - - +
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Residues in contact with VAL 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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528A LEU* 3.8 25.1 - - + +
531A ALA* 3.9 23.1 - - + -
556A MET* 3.0 20.8 + - + +
557A PHE 4.0 2.7 - - - +
559A HIS* 1.3 76.0 - - + +
561A LEU* 1.3 62.0 + - - +
563A ASP* 3.2 10.6 + - + +
564A LEU* 3.1 28.3 + - + +
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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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531A ALA* 3.7 35.9 - - + +
534A VAL* 4.2 14.1 - - + -
538A LEU* 3.9 19.7 - - + -
540A LEU* 4.9 0.2 - - + -
557A PHE* 2.9 46.1 + - + +
558A TYR 3.8 4.0 - - - +
560A VAL* 1.3 76.4 - - - +
562A LYS* 1.3 60.9 + - - +
564A LEU* 3.0 10.9 + - - -
565A GLY 3.1 0.2 + - - -
566A LYS* 3.0 40.4 + - + +
568A VAL* 3.9 33.2 - - + -
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Residues in contact with LYS 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 TYR* 3.1 46.0 + - + +
559A HIS* 3.6 8.3 - - + +
561A LEU* 1.3 73.0 - - - +
563A ASP* 1.3 64.7 + - - +
565A GLY* 3.0 14.9 + - - +
566A LYS 4.1 13.7 + - - +
567A GLU* 5.4 1.0 - - - +
568A VAL* 3.4 29.8 + - + +
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Residues in contact with ASP 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 HIS 2.9 13.0 + - - +
560A VAL* 3.3 15.9 - - + +
561A LEU 3.2 0.4 - - - -
562A LYS* 1.3 77.7 - - - +
564A LEU* 1.3 62.9 + - + +
565A GLY 3.6 0.5 + - - -
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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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531A ALA* 3.6 18.2 - - + +
532A LYS* 3.6 36.3 - - + +
560A VAL* 3.1 21.5 + - + +
561A LEU* 3.0 9.2 + - - +
563A ASP* 1.3 82.8 - - + +
565A GLY* 1.3 58.6 + - - +
566A LYS* 3.3 21.3 + - + +
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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
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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