Contacts of the helix formed by residues 538 - 549 (chain A) in PDB entry 4E9F
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 GLY 538 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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532A ILE* 3.9 12.3 - - - -
537A ILE* 1.3 73.1 - - - +
539A LYS* 1.3 66.2 + - - -
540A TYR 3.3 3.3 + - - -
541A GLY 3.5 0.3 + - - -
542A ASN* 3.0 23.4 + - - +
9C C 2.9 31.0 + - - -
10C A 4.4 4.3 - - - -
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Residues in contact with LYS 539 (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 ILE* 3.9 14.1 - - + +
538A GLY* 1.3 70.8 - - - -
540A TYR* 1.3 58.3 + - - +
542A ASN* 3.8 2.1 - - - +
543A ASP* 2.8 69.1 + - - +
557A HIS* 2.9 25.6 + - - +
559A GLU* 3.7 29.8 - - + +
9C C 3.2 5.4 + - - +
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Residues in contact with TYR 540 (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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449A GLN* 3.1 24.6 + - - -
463A THR* 3.6 34.5 - - - -
466A LEU* 3.5 12.0 - - + +
467A ASN* 4.7 0.2 - - - -
539A LYS* 1.3 73.9 - - - +
541A GLY* 1.3 57.5 + - - +
543A ASP* 3.8 5.1 - - - +
544A SER* 2.9 41.1 + - - -
560A ASP* 3.5 38.9 + - + -
562A LYS* 5.6 0.7 - - - -
563A LEU* 4.0 9.6 - - + -
7C 3DR 3.0 37.3 - - + -
8C G 3.6 20.2 - - - +
9C C 2.9 20.5 + - - +
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Residues in contact with GLY 541 (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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460A LEU* 3.5 6.7 - - - +
463A THR* 3.7 28.7 - - - -
537A ILE* 3.8 14.4 - - - -
540A TYR* 1.3 75.8 - - - +
542A ASN* 1.3 57.0 + - - +
544A SER* 3.3 2.9 + - - -
545A TYR* 3.0 28.6 + - - +
9C C 3.1 15.5 + - - -
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Residues in contact with ASN 542 (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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530A TYR* 3.4 9.5 - - - +
531A PRO* 3.2 20.7 - - - +
532A ILE* 3.1 48.6 + - + +
537A ILE* 3.7 1.8 - - - +
538A GLY 3.0 19.6 + - - +
539A LYS* 3.8 4.3 - - - +
541A GLY* 1.3 74.6 - - - +
543A ASP* 1.4 63.1 + - - +
545A TYR* 3.3 2.3 + - - +
546A ARG* 3.0 57.3 + - - +
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Residues in contact with ASP 543 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
539A LYS* 2.8 63.5 + - - +
540A TYR* 3.8 2.6 - - - +
542A ASN* 1.4 74.3 + - - +
544A SER* 1.3 62.2 + - - +
546A ARG* 3.3 10.5 + - - +
547A ILE* 3.1 29.5 + - - +
556A VAL* 3.7 25.7 - - + +
557A HIS 4.9 0.5 + - - -
558A PRO* 3.4 12.9 - - + +
559A GLU 4.3 0.9 + - - -
563A LEU* 3.7 20.8 - - + +
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Residues in contact with SER 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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449A GLN* 3.0 30.8 + - - -
459A LEU* 3.9 17.0 - - - -
463A THR* 3.8 6.8 - - - +
540A TYR* 2.9 20.8 + - - -
541A GLY 3.4 9.2 - - - -
542A ASN 3.2 0.2 - - - -
543A ASP* 1.3 77.6 - - - +
545A TYR* 1.3 54.8 + - - +
547A ILE 3.4 0.5 + - - -
548A PHE* 2.9 37.3 + - - +
563A LEU* 3.7 16.6 - - - +
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Residues in contact with TYR 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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456A PRO* 4.0 16.6 - - + +
459A LEU* 4.2 2.4 - - - +
460A LEU* 4.3 9.4 - - + -
528A TRP* 3.8 30.0 - + - -
529A LYS 4.1 13.4 + - - -
530A TYR* 4.2 4.5 - + - -
531A PRO* 3.4 32.3 - - + -
541A GLY 3.0 16.6 + - - +
542A ASN 3.5 4.5 - - - +
544A SER* 1.3 75.1 - - - +
546A ARG* 1.3 67.0 + - + +
549A CYS* 2.8 59.1 + - + +
550A VAL* 3.3 39.5 + - + +
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Residues in contact with ARG 546 (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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530A TYR* 4.0 25.0 - - + -
542A ASN* 3.0 39.9 + - - +
543A ASP* 4.0 7.9 + - - +
544A SER 3.3 0.2 - - - -
545A TYR* 1.3 77.0 - - + +
547A ILE* 1.4 58.9 + - - +
550A VAL* 3.1 21.1 - - - +
552A GLU* 2.8 46.4 + - + +
553A TRP 3.3 5.0 + - - -
555A GLN* 3.3 44.7 + - - +
556A VAL* 3.6 25.1 - - + +
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Residues in contact with ILE 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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438A TRP* 2.8 34.2 + - + -
440A PRO* 4.2 0.7 - - - +
543A ASP 3.1 20.5 + - - +
546A ARG* 1.4 78.0 - - - +
548A PHE* 1.3 66.8 + - + +
550A VAL 3.7 0.9 - - - +
553A TRP* 4.1 12.8 - - + +
556A VAL* 3.8 29.2 - - + -
558A PRO* 4.2 7.9 - - + -
563A LEU* 3.9 26.9 - - + +
566A TYR* 3.7 31.4 - - + -
567A HIS* 4.2 13.2 - - + -
570A LEU* 4.1 11.9 - - + -
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Residues in contact with PHE 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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438A TRP* 3.6 3.2 - - - +
440A PRO* 3.3 42.0 - - + +
447A LEU* 4.2 6.3 - - + -
449A GLN* 3.6 36.1 - - + -
450A GLU* 3.7 22.0 - - + -
453A PHE* 3.5 13.7 - - + +
459A LEU* 3.8 15.9 - - + -
544A SER 2.9 26.9 + - - +
547A ILE* 1.3 91.5 - - + +
549A CYS* 1.3 59.9 + - - +
550A VAL 3.6 0.4 - - - -
563A LEU* 3.9 20.6 - - + -
566A TYR* 3.5 45.1 - + - -
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Residues in contact with CYS 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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438A TRP* 4.4 4.4 - - - +
453A PHE* 3.7 22.0 - - - +
456A PRO* 3.9 24.5 - - + -
459A LEU* 4.0 23.8 - - - -
545A TYR* 2.8 48.2 + - + +
548A PHE* 1.3 72.5 - - - +
550A VAL* 1.3 66.1 + - - +
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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