Contacts of the helix formed by residues 543 - 553 (chain A) in PDB entry 3GTL
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 543 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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542A GLU* 1.3 75.7 - - - +
544A ASP* 1.3 65.7 + - - +
546A VAL* 2.9 16.3 + - + +
547A LEU* 3.2 51.6 + - + +
560A ILE* 5.6 1.1 - - + -
570A PRO* 4.4 8.8 + - + +
572A TRP* 4.0 32.1 - - + -
79H TRP* 4.9 10.8 - - + -
81H PRO* 4.9 23.1 - - + -
82H PRO* 6.0 2.0 - - + -
51K LEU* 5.3 10.5 - - + -
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Residues in contact with ASP 544 (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 GLU* 3.3 26.0 - - - +
543A LEU* 1.3 75.8 - - - +
545A GLN* 1.3 72.6 + - - +
547A LEU* 3.8 11.8 + - - +
548A ASN* 3.5 18.6 + - - -
1079B LYS* 4.8 12.0 + - - -
47K ARG* 3.1 29.6 + - - +
51K LEU* 5.2 4.3 - - + -
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Residues in contact with GLN 545 (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 PHE 5.5 0.6 + - - -
541A ILE* 3.4 32.9 - - + +
542A GLU* 3.9 7.4 + - - +
543A LEU 3.3 0.2 - - - -
544A ASP* 1.3 80.5 + - - +
546A VAL* 1.3 56.0 + - - +
547A LEU 2.6 17.2 + - - -
548A ASN* 2.7 20.8 + - - +
549A MET* 3.0 27.0 + - + +
655A PHE* 4.3 13.8 - - + -
656A TRP* 4.0 19.9 + - - +
659A HIS* 4.5 20.6 - - + +
1079B LYS* 5.0 15.7 - - - +
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Residues in contact with VAL 546 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
541A ILE* 3.2 42.8 - - + +
542A GLU 3.3 6.3 - - - +
543A LEU* 2.9 11.8 + - + +
545A GLN* 1.3 74.6 - - - +
547A LEU* 1.3 58.7 + - + +
549A MET* 3.9 7.9 - - - +
550A LEU* 3.1 44.7 + - + +
560A ILE* 5.0 2.5 - - + -
572A TRP* 3.9 38.1 - - + +
577A ILE* 4.0 14.0 - - + +
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Residues in contact with LEU 547 (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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543A LEU* 3.2 48.7 - - + +
544A ASP* 4.2 7.9 - - - +
545A GLN 2.6 5.5 + - - -
546A VAL* 1.3 75.5 - - + +
548A ASN* 1.3 66.0 + - - +
550A LEU* 3.5 2.6 + - - +
551A TYR* 2.9 24.6 + - - +
560A ILE* 3.5 21.3 - - + -
51K LEU* 4.3 19.5 - - + -
57K LEU 4.9 8.5 - - - +
58K PHE* 3.5 34.5 - - + -
59K ALA 3.7 20.4 - - - +
60K ALA* 3.6 4.0 - - - +
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Residues in contact with ASN 548 (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 ASP 3.5 10.9 + - - -
545A GLN* 2.7 12.1 + - - +
547A LEU* 1.3 71.8 - - - +
549A MET* 1.3 52.3 + - - +
551A TYR* 2.8 5.6 + - - +
552A TRP* 2.6 39.5 + - + +
655A PHE* 4.0 23.8 - - + -
47K ARG* 3.1 33.8 - - - +
60K ALA* 3.9 5.4 - - - -
61K TYR* 2.6 53.1 + - - +
62K LYS* 6.0 0.5 - - - +
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Residues in contact with MET 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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541A ILE* 3.6 16.6 - - + -
545A GLN* 3.0 36.4 + - + +
546A VAL* 3.9 5.4 - - - +
548A ASN* 1.3 73.6 - - - +
550A LEU* 1.3 66.0 - - - +
552A TRP* 2.7 30.8 + - - +
553A VAL* 3.3 5.5 + - - +
577A ILE* 3.6 33.0 - - + -
652A VAL* 4.1 23.5 - - + +
655A PHE* 3.9 13.5 - - + -
656A TRP* 3.5 45.1 - - + -
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Residues in contact with LEU 550 (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 VAL* 3.1 34.9 + - + +
547A LEU* 3.6 5.4 - - - +
549A MET* 1.3 79.0 - - - +
551A TYR* 1.3 63.3 + - - +
553A VAL* 3.4 17.2 + - - +
556A TRP* 3.4 52.0 - - + +
560A ILE* 3.9 20.2 - - + -
561A PRO* 3.8 21.5 - - + -
577A ILE* 4.1 10.5 - - + +
580A VAL* 3.7 34.3 - - + -
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Residues in contact with TYR 551 (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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547A LEU 2.9 12.5 + - - +
548A ASN* 2.8 12.6 + - - +
550A LEU* 1.3 74.3 - - - +
552A TRP* 1.3 63.8 + - - +
553A VAL 3.3 8.4 + - - +
554A PRO* 4.9 0.2 - - - +
556A TRP* 4.3 10.8 - + - -
24K ASP* 5.6 0.7 - - - -
32K VAL* 3.1 28.8 - - - +
58K PHE* 3.8 6.7 - + + -
60K ALA* 3.5 34.8 - - + -
61K TYR* 4.4 3.1 - - - -
62K LYS* 3.0 39.6 + - + +
72K LYS* 4.1 15.0 + - - +
74K ARG* 3.6 38.9 - - + +
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Residues in contact with TRP 552 (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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358A ASN* 4.1 20.6 - - - -
548A ASN* 2.6 22.7 + - + -
549A MET* 2.7 16.7 + - - +
551A TYR* 1.3 74.4 - - - +
553A VAL* 1.3 56.8 + - - +
554A PRO* 3.5 3.5 - - - +
651A LYS* 3.7 50.7 - - + +
652A VAL* 5.2 2.0 - - - +
655A PHE* 2.8 50.5 - + + -
61K TYR 5.2 0.8 + - - -
62K LYS* 3.8 41.9 + - + +
63K VAL* 3.7 30.5 - - + -
64K GLU* 4.2 13.2 - - + -
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Residues in contact with VAL 553 (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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549A MET 3.3 3.6 + - - +
550A LEU 3.5 12.1 - - - +
551A TYR* 3.3 10.1 - - - +
552A TRP* 1.3 75.9 - - - +
554A PRO* 1.3 67.0 - - + +
555A ASP* 3.2 14.3 + - + +
556A TRP* 3.5 22.3 + - + +
580A VAL* 4.4 18.6 - - + +
581A ALA* 4.7 7.0 - - + +
648A ASN* 3.8 33.2 - - + +
651A LYS* 5.1 0.9 - - + -
652A VAL* 3.4 31.2 - - + +
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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