Contacts of the helix formed by residues 537 - 544 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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535B LEU 4.0 0.2 + - - -
536B ALA* 1.3 72.4 - - - +
538B PRO* 1.3 67.6 - - - +
539B ASN* 2.7 25.4 + - - +
540B TRP* 2.7 43.3 + - + +
541B LEU* 3.0 25.3 + - - +
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Residues in contact with PRO 538 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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517B ARG* 4.0 33.0 - - - +
536B ALA 3.9 3.4 - - - +
537B ASP* 1.3 86.5 - - - +
539B ASN* 1.3 67.1 + - - +
541B LEU* 3.3 8.7 + - + +
542B ARG* 3.1 34.0 + - - +
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Residues in contact with ASN 539 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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537B ASP* 2.7 21.9 + - - +
538B PRO* 1.3 76.5 - - - +
540B TRP* 1.3 60.6 + - - +
542B ARG* 3.5 15.7 + - - +
543B ARG* 3.2 33.9 + - - +
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Residues in contact with TRP 540 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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528B ILE* 4.4 18.8 - - + -
529B ASP* 6.2 1.1 - - + -
531B HIS* 4.4 29.2 - + + -
533B LEU* 4.9 5.6 - - + -
536B ALA* 3.7 30.5 - - + -
537B ASP* 2.7 31.0 + - + +
539B ASN* 1.3 73.8 - - - +
541B LEU* 1.3 93.2 + - + +
543B ARG* 3.3 34.7 + - - +
544B GLN* 3.2 61.4 + - + +
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Residues in contact with LEU 541 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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515B ILE 3.4 20.2 - - - +
516B GLN* 3.3 16.4 - - - +
517B ARG* 3.3 44.2 - - + +
528B ILE* 3.9 20.0 - - + -
533B LEU* 4.2 16.2 - - + +
536B ALA* 5.3 3.1 - - + -
537B ASP 3.0 12.3 + - - +
538B PRO* 3.6 9.6 - - + +
539B ASN 3.3 0.2 - - - -
540B TRP* 1.3 88.4 - - + +
542B ARG* 1.3 61.1 + - + +
544B GLN* 2.9 26.8 + - + +
545B VAL* 3.3 9.5 + - + +
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Residues in contact with ARG 542 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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516B GLN 5.9 2.9 - - - +
538B PRO 3.1 20.0 + - - +
539B ASN* 3.5 14.7 + - - +
540B TRP 3.4 0.2 - - - -
541B LEU* 1.3 77.7 - - + +
543B ARG* 1.3 60.7 + - + +
544B GLN 3.4 0.7 + - - -
545B VAL* 3.4 18.3 - - - +
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Residues in contact with ARG 543 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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539B ASN* 3.2 20.0 + - - +
540B TRP* 3.4 42.2 - - - +
541B LEU 3.1 0.2 - - - -
542B ARG* 1.3 76.5 - - - +
544B GLN* 1.3 64.2 + - - +
545B VAL 3.6 0.7 - - - -
622B ASN 5.7 0.3 - - - +
623B ASN 5.0 1.2 - - - +
624B PRO* 4.2 13.5 - - - +
625B LYS* 4.7 1.2 + - - +
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Residues in contact with GLN 544 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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528B ILE* 4.5 16.0 - - + +
540B TRP* 3.2 62.3 + - + +
541B LEU* 2.9 19.0 + - + +
543B ARG* 1.3 83.3 - - - +
545B VAL* 1.3 63.4 + - + +
624B PRO* 3.5 1.7 - - - +
625B LYS* 3.1 40.3 + - + +
626B ILE* 3.0 31.1 + - + +
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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