Contacts of the helix formed by residues 537 - 544 (chain D) in PDB entry 2FGJ
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 ASP 537 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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535D LEU 4.1 1.2 + - - -
536D ALA* 1.3 72.2 - - - +
538D PRO* 1.3 76.2 - - - +
539D ASN* 3.2 14.5 + - - +
540D TRP* 3.1 38.2 + - + +
541D LEU* 3.3 22.6 + - - +
543D ARG* 5.1 1.2 + - - -
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Residues in contact with PRO 538 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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517D ARG* 3.9 24.5 - - - +
536D ALA 3.9 6.3 - - - +
537D ASP* 1.3 95.9 - - - +
539D ASN* 1.3 57.3 + - + +
541D LEU* 4.2 9.3 - - + +
542D ARG* 3.4 30.5 + - - +
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Residues in contact with ASN 539 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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537D ASP* 3.2 11.0 + - - +
538D PRO* 1.3 79.0 - - + +
540D TRP* 1.3 65.1 + - - +
541D LEU 3.1 1.3 - - - -
542D ARG* 2.9 38.3 + - - +
543D ARG* 3.3 37.5 + - - +
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Residues in contact with TRP 540 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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528D ILE* 3.8 36.8 - - + -
529D ASP* 5.8 2.9 - - + -
531D HIS* 4.6 15.3 - + + -
533D LEU* 4.6 4.3 - - + -
536D ALA* 4.2 21.5 - - + -
537D ASP* 3.1 30.9 + - + +
539D ASN* 1.3 74.7 - - - +
541D LEU* 1.3 91.9 + - + +
543D ARG* 3.4 25.6 + - - +
544D GLN* 3.0 68.7 + - + +
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Residues in contact with LEU 541 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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515D ILE 3.4 23.6 - - - +
516D GLN* 3.3 25.4 - - - +
517D ARG* 3.4 27.6 - - + +
528D ILE* 4.1 10.1 - - + -
533D LEU* 3.8 24.5 - - + +
536D ALA* 5.6 2.5 - - + +
537D ASP 3.3 14.7 + - - +
538D PRO* 4.3 9.6 - - + +
539D ASN 3.1 0.4 - - - -
540D TRP* 1.3 91.3 - - + +
542D ARG* 1.3 65.5 + - + +
544D GLN* 3.1 13.7 + - + +
545D VAL* 3.1 18.0 + - + +
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Residues in contact with ARG 542 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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516D GLN 5.7 3.1 - - - +
518D PHE* 6.5 1.3 - - + -
538D PRO* 3.4 15.4 + - - +
539D ASN* 2.9 49.6 + - - +
541D LEU* 1.3 82.5 - - + +
543D ARG* 1.3 59.0 + - + +
545D VAL* 3.0 20.4 - - - +
622D ASN* 6.0 0.2 + - - -
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Residues in contact with ARG 543 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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537D ASP* 5.1 1.0 + - - -
539D ASN* 3.3 46.1 + - - +
540D TRP* 3.8 26.7 + - - +
541D LEU 3.2 0.2 - - - -
542D ARG* 1.3 76.7 - - + +
544D GLN* 1.3 65.7 + - - +
545D VAL 3.4 0.9 - - - -
622D ASN* 5.6 5.0 + - - +
624D PRO* 3.6 19.6 - - - +
625D LYS 4.4 0.3 + - - -
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Residues in contact with GLN 544 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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528D ILE* 4.5 12.5 - - + +
540D TRP* 3.0 68.5 + - + +
541D LEU* 3.1 14.3 + - + +
543D ARG* 1.3 81.7 - - - +
545D VAL* 1.3 63.4 + - + +
624D PRO* 3.6 0.2 - - - +
625D LYS* 3.0 40.8 + - + +
626D ILE* 2.9 28.5 + - + +
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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