Contacts of the helix formed by residues 558 - 574 (chain A) in PDB entry 3G4G
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 ALA 558 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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341A LEU* 6.2 0.2 - - + -
547A TRP* 4.9 4.0 - - + -
550A TRP* 4.1 13.0 - - + +
551A ALA* 3.9 30.2 + - + +
554A VAL* 3.9 12.4 - - + +
556A PRO 3.2 0.6 - - - -
557A ASP* 1.3 77.7 - - - +
559A GLN* 1.3 59.4 + - - +
560A ASP 3.4 2.0 - - - -
561A ILE* 3.3 22.8 + - + +
562A LEU* 3.0 28.2 + - - +
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Residues in contact with GLN 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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551A ALA* 5.4 4.0 - - - +
555A HIS* 5.6 5.7 - - - -
556A PRO* 3.3 23.4 + - + +
557A ASP 3.5 1.4 - - - -
558A ALA* 1.3 77.6 - - - +
560A ASP* 1.3 55.0 + - - +
562A LEU* 3.1 21.1 + - - +
563A ASP* 2.5 74.1 + - - +
566A GLU* 5.5 1.2 + - - -
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Residues in contact with ASP 560 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
557A ASP 5.2 1.5 + - - +
558A ALA 3.4 0.2 - - - -
559A GLN* 1.3 75.8 - - - +
561A ILE* 1.3 66.1 + - + +
563A ASP* 3.2 15.3 + - - +
564A THR* 2.9 28.7 + - - +
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Residues in contact with ILE 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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268A TRP* 3.7 47.6 - - + +
340A VAL* 5.8 2.5 - - + -
341A LEU* 4.2 9.4 - - + -
489A THR* 3.6 33.4 - - + +
547A TRP* 3.9 30.3 - - + -
557A ASP 4.9 3.1 - - - +
558A ALA* 3.3 23.2 + - + +
559A GLN 3.3 0.2 - - - -
560A ASP* 1.3 77.0 - - + +
562A LEU* 1.3 60.0 + - - +
564A THR* 3.2 7.9 + - - -
565A LEU* 3.1 24.9 + - - +
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Residues in contact with LEU 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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544A HIS* 4.1 19.7 - - + +
547A TRP* 3.8 38.6 - - + +
548A GLU* 3.8 15.3 - - + +
551A ALA* 4.2 17.9 - - + -
558A ALA 3.0 16.8 + - - +
559A GLN* 3.1 22.9 + - - +
561A ILE* 1.3 75.5 - - + +
563A ASP* 1.3 65.1 + - - +
565A LEU* 3.5 6.8 + - + +
566A GLU* 3.1 40.6 + - - +
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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
----------------------------------------------------------
559A GLN* 2.5 63.6 + - - +
560A ASP* 3.2 15.3 + - - +
562A LEU* 1.3 71.6 - - - +
564A THR* 1.3 64.5 + - - +
566A GLU* 3.3 13.1 + - - +
567A ASP* 3.0 32.3 + - - +
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Residues in contact with THR 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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268A TRP* 5.9 0.9 - - - -
489A THR 3.7 13.0 + - - +
490A LYS 3.6 15.5 - - - +
491A PRO* 4.1 8.5 - - + -
492A LEU 5.3 0.2 - - - +
560A ASP 2.9 15.4 + - - -
561A ILE* 3.2 8.3 + - - -
563A ASP* 1.3 78.1 - - - +
565A LEU* 1.3 56.8 + - - +
567A ASP* 3.3 8.6 + - + +
568A ASN* 2.8 52.7 + - - +
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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
----------------------------------------------------------
488A PRO* 3.4 45.1 + - + +
489A THR* 3.8 9.2 - - + +
539A ILE* 4.0 14.3 - - + +
543A VAL* 3.6 17.3 - - + -
544A HIS* 3.7 44.6 - - + -
547A TRP* 4.3 7.0 - - + -
561A ILE 3.1 12.7 + - - +
562A LEU* 3.6 17.3 - - + +
564A THR* 1.3 76.4 - - - +
566A GLU* 1.3 57.4 + - - +
568A ASN* 3.3 2.6 + - - +
569A ARG* 2.9 27.2 + - - +
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Residues in contact with GLU 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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539A ILE* 6.0 0.2 - - - -
544A HIS* 2.8 39.0 + - + +
559A GLN* 5.5 0.5 + - - -
562A LEU* 3.1 29.3 + - - +
563A ASP* 3.8 15.2 - - - +
564A THR 3.3 0.2 - - - -
565A LEU* 1.3 76.7 - - - +
567A ASP* 1.3 63.3 + - - +
569A ARG* 3.4 8.2 + - - +
570A GLU* 3.0 30.5 + - - +
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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 ASP* 3.0 24.7 + - - +
564A THR* 3.6 7.7 - - + +
566A GLU* 1.3 78.4 - - - +
568A ASN* 1.3 59.0 + - - +
570A GLU* 3.2 10.1 + - - +
571A TRP* 3.0 26.5 + - - +
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Residues in contact with ASN 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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488A PRO 2.7 26.4 + - - +
490A LYS 2.7 28.9 + - - -
492A LEU* 3.6 26.0 + - + +
495A TYR* 3.8 20.5 - - + -
539A ILE* 4.5 2.5 - - + -
564A THR* 2.8 25.7 + - - +
565A LEU 3.6 2.5 - - - +
566A GLU 3.2 0.2 - - - -
567A ASP* 1.3 75.4 - - - +
569A ARG* 1.3 66.4 + - - +
571A TRP* 3.3 6.7 + - - +
572A TYR* 3.1 28.1 + - - -
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Residues in contact with ARG 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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536A VAL* 3.3 24.6 - - + +
539A ILE* 3.6 33.4 - - + +
540A ASP* 2.8 41.5 + - - +
565A LEU 2.9 16.0 + - - +
566A GLU* 3.5 9.0 - - + +
568A ASN* 1.3 76.7 - - - +
570A GLU* 1.3 75.7 + - - +
572A TYR* 3.4 3.7 + - - +
573A GLN* 2.9 59.0 + - - +
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Residues in contact with GLU 570 (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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566A GLU 3.0 14.3 + - - +
567A ASP* 3.2 15.9 - - - +
568A ASN 3.1 0.2 - - - -
569A ARG* 1.3 104.3 + - - +
571A TRP* 1.3 60.8 + - - +
573A GLN* 3.4 14.2 + - - +
574A SER* 3.2 21.7 + - - -
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Residues in contact with TRP 571 (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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492A LEU* 3.9 32.7 - - + +
496A ARG* 3.2 53.8 - - - -
567A ASP 3.0 12.7 + - - +
568A ASN* 3.3 8.7 + - - +
570A GLU* 1.3 74.5 - - - +
572A TYR* 1.3 112.2 + + - +
574A SER* 2.6 28.9 + - - -
575A THR* 3.4 29.8 + - + -
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Residues in contact with TYR 572 (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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492A LEU* 4.7 2.5 - - + -
495A TYR* 3.3 42.4 - + - -
496A ARG* 3.9 15.2 - - - +
499A THR* 3.1 27.9 + - - +
531A VAL* 4.5 9.2 - - + -
532A GLU* 3.9 32.2 - - + +
535A GLN* 3.8 23.1 - - + -
536A VAL* 4.0 13.9 - - + +
539A ILE* 5.4 0.9 - - + -
568A ASN 3.1 14.8 + - - +
569A ARG* 3.9 4.5 - - - +
571A TRP* 1.3 110.7 - + - +
573A GLN* 1.3 62.5 + - - +
575A THR* 3.1 15.8 + - + +
576A ILE* 3.3 13.5 + - - +
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Residues in contact with GLN 573 (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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533A LYS* 5.6 1.2 + - - -
536A VAL* 3.6 15.5 - - + +
569A ARG* 2.9 51.9 + - - +
570A GLU* 3.4 17.5 + - - +
572A TYR* 1.3 76.3 - - - +
574A SER* 1.3 58.3 + - - +
575A THR 3.0 5.1 + - - -
576A ILE* 3.2 41.9 + - - +
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Residues in contact with SER 574 (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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570A GLU 3.2 9.0 + - - -
571A TRP* 2.6 30.2 + - - -
573A GLN* 1.3 79.0 - - - +
575A THR* 1.3 61.3 + - - +
576A ILE 3.4 2.9 - - - +
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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