Contacts of the helix formed by residues 554 - 569 (chain A) in PDB entry 4RG7
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 LYS 554 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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549A LEU* 3.1 29.9 + - + +
552A LEU* 4.9 7.6 - - + +
553A GLN* 1.3 74.6 - - - +
555A ASP* 1.3 69.0 + - - +
556A VAL* 3.5 3.8 + - + -
557A ALA* 4.2 9.2 - - + +
558A LEU* 3.3 22.7 + - - +
585A LEU* 6.0 1.5 - - - +
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Residues in contact with ASP 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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553A GLN 3.6 6.0 + - - +
554A LYS* 1.3 75.1 - - - +
556A VAL* 1.3 80.6 + - - +
558A LEU* 3.9 2.5 - - - +
559A SER* 2.9 24.6 + - - -
582A CYS* 4.9 1.9 - - - -
585A LEU* 5.2 13.5 - - + -
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Residues in contact with VAL 556 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
554A LYS* 5.4 2.7 - - + -
555A ASP* 1.3 88.9 + - - +
557A ALA* 1.3 61.0 + - + +
559A SER* 3.4 7.2 - - - -
560A VAL* 2.8 51.5 + - + +
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Residues in contact with ALA 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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545A TYR* 5.4 2.7 - - - +
549A LEU* 3.7 29.4 - - + +
554A LYS* 3.6 11.8 + - + +
555A ASP 3.3 0.6 - - - -
556A VAL* 1.3 85.5 - - + +
558A LEU* 1.3 57.7 + - - +
560A VAL* 3.4 8.3 + - - +
561A LEU* 2.9 28.1 + - - +
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Residues in contact with LEU 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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546A SER* 3.2 48.5 - - - +
549A LEU* 3.9 15.2 - - + +
550A TRP* 4.2 15.5 - - + +
554A LYS 3.3 14.9 + - - +
555A ASP* 4.0 2.5 - - - +
557A ALA* 1.3 77.3 - - - +
559A SER* 1.3 61.0 + - - +
561A LEU* 3.7 5.9 - - + +
562A SER* 2.9 32.6 + - - -
578A ALA* 4.2 8.7 - - + +
581A ASN* 3.3 29.2 - - - +
582A CYS* 3.5 15.9 - - + -
585A LEU* 4.3 8.7 - - + -
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Residues in contact with SER 559 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
555A ASP 2.9 18.4 + - - -
556A VAL* 3.4 9.4 - - - +
558A LEU* 1.3 77.1 - - - +
560A VAL* 1.3 57.5 + - - +
562A SER* 2.6 17.4 + - - -
563A LYS* 3.0 15.4 + - - +
582A CYS* 3.5 20.6 - - - -
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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
----------------------------------------------------------
532A ARG* 5.3 2.7 - - - +
556A VAL* 2.8 37.0 + - + +
557A ALA* 3.6 7.6 - - - +
558A LEU 3.3 0.2 - - - -
559A SER* 1.3 72.4 - - - +
561A LEU* 1.3 63.0 + - - +
563A LYS* 3.5 4.6 + - - +
564A ASP* 2.9 50.6 + - - +
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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
----------------------------------------------------------
532A ARG* 4.7 9.9 - - - +
542A MET* 6.4 0.2 - - + -
545A TYR* 5.2 11.2 - - + -
546A SER* 5.9 2.0 - - - -
549A LEU* 4.5 10.3 - - + -
557A ALA 2.9 17.9 + - - +
558A LEU* 3.7 12.3 - - + +
559A SER 3.3 0.2 - - - -
560A VAL* 1.3 75.5 - - - +
562A SER* 1.3 55.6 + - - +
564A ASP* 3.1 5.8 + - - +
565A LEU* 2.8 50.4 + - + +
578A ALA* 5.5 1.8 - - + -
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Residues in contact with SER 562 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
558A LEU 2.9 14.8 + - - -
559A SER* 2.6 25.5 + - - -
561A LEU* 1.3 75.5 - - - +
563A LYS* 1.3 59.2 + - - +
565A LEU* 4.6 0.9 - - - -
566A THR* 2.8 37.7 + - - +
578A ALA* 4.1 16.0 - - - +
579A ALA* 3.6 32.5 - - - +
582A CYS* 4.0 7.9 - - - -
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Residues in contact with LYS 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 SER 3.0 13.8 + - - +
560A VAL* 3.6 7.6 - - - +
562A SER* 1.3 82.9 + - - +
564A ASP* 1.3 62.4 + - - +
566A THR* 3.0 5.6 + - - -
567A ASP* 2.9 44.2 + - - +
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Residues in contact with ASP 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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532A ARG* 3.1 40.3 + - - +
560A VAL* 2.9 30.1 + - - +
561A LEU 3.6 1.8 - - - +
563A LYS* 1.3 79.2 - - - +
565A LEU* 1.3 63.3 + - + +
567A ASP* 3.8 8.5 - - - +
568A MET* 3.4 20.8 + - - +
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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
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532A ARG* 5.1 15.0 - - - +
538A ARG 4.3 6.3 - - - +
539A VAL* 4.0 24.9 - - + +
542A MET* 3.7 34.5 - - + +
546A SER* 5.7 0.2 - - - -
561A LEU* 2.8 30.4 + - + +
562A SER 3.9 2.2 - - - +
564A ASP* 1.3 74.1 - - + +
566A THR* 1.3 63.4 + - - +
567A ASP 3.2 1.6 - - - -
568A MET* 3.2 4.1 + - + +
569A ASP* 3.0 21.3 + - - +
574A GLU 4.4 2.7 - - - +
575A ALA* 3.4 28.9 - - + +
578A ALA* 3.7 26.9 - - + -
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Residues in contact with THR 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 SER 2.8 27.3 + - - +
563A LYS* 3.0 12.0 + - - -
565A LEU* 1.3 73.3 - - - +
567A ASP* 1.3 66.5 + - - +
568A MET 3.2 0.9 + - - -
569A ASP 3.7 7.2 + - - -
570A LYS* 3.9 17.0 + - - +
575A ALA* 4.0 15.7 - - + +
576A TRP* 4.7 21.3 - - + -
579A ALA* 4.0 24.9 - - + -
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Residues in contact with ASP 567 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
563A LYS* 2.9 32.0 + - - +
564A ASP* 3.8 10.9 + - - +
566A THR* 1.3 82.6 + - - +
568A MET* 1.3 59.3 + - - +
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Residues in contact with MET 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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536A ASN 6.0 1.8 - - - +
537A TYR* 6.3 1.1 - - - -
539A VAL* 5.0 6.3 - - + -
564A ASP 3.4 14.5 + - - +
565A LEU* 3.2 6.1 + - + +
566A THR 3.1 1.2 - - - -
567A ASP* 1.3 81.6 - - - +
569A ASP* 1.3 62.2 + - + +
570A LYS 4.2 0.4 - - - -
55B TYR* 3.6 40.9 - - + +
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Residues in contact with ASP 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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539A VAL* 4.5 4.5 - - + -
565A LEU 3.0 9.8 + - - +
566A THR 3.7 1.0 + - - -
568A MET* 1.3 79.6 - - + +
570A LYS* 1.3 58.7 + - - +
571A ASN* 2.9 29.4 + - - +
572A SER* 2.4 41.8 + - - +
575A ALA* 3.6 13.2 - - - +
52B GLY 5.6 1.2 - - - +
53B LYS* 5.1 3.3 - - - +
55B TYR* 2.9 37.3 + - + +
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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