Contacts of the helix formed by residues 508 - 516 (chain B) in PDB entry 3RFU
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 ASN 508 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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492B GLY 5.0 2.4 + - - -
493B LYS* 3.3 26.9 + - - +
507B GLY* 1.3 76.4 - - - +
509B ALA* 1.3 67.9 + - - +
510B ARG* 3.5 18.2 - - - +
511B LEU* 2.9 31.9 + - - +
512B MET* 3.3 9.4 + - - +
537B MET* 4.1 15.1 - - + +
538B PHE* 3.5 4.9 - - - -
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Residues in contact with ALA 509 (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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508B ASN* 1.3 76.3 - - - +
510B ARG* 1.3 62.2 + - - +
512B MET* 3.1 8.9 + - - +
513B GLN* 3.0 22.0 + - - +
523B PHE* 4.3 16.0 - - + -
538B PHE* 3.4 27.7 - - + -
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Residues in contact with ARG 510 (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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493B LYS* 4.9 5.9 - - + +
508B ASN* 3.1 19.6 - - - +
509B ALA* 1.3 78.9 - - - +
511B LEU* 1.3 57.0 + - - +
513B GLN* 2.8 75.7 + - - +
514B GLU* 3.0 45.7 + - - +
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Residues in contact with LEU 511 (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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490B PRO* 4.4 17.5 - - + -
493B LYS* 3.6 15.3 - - + +
494B GLY* 3.8 5.2 - - - -
495B VAL 3.9 3.8 - - - +
496B VAL* 5.6 1.8 - - + -
505B ALA* 4.1 6.5 - - + -
506B ILE 3.3 46.0 - - - +
507B GLY 3.5 0.4 - - - +
508B ASN* 2.9 25.4 + - - +
510B ARG* 1.3 76.6 - - - +
512B MET* 1.3 62.4 + - + +
514B GLU* 3.4 16.1 + - - +
515B HIS* 3.0 53.5 + - + +
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Residues in contact with MET 512 (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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505B ALA* 3.6 25.4 - - + +
507B GLY 4.5 0.2 - - - +
508B ASN 3.7 7.2 - - - +
509B ALA* 3.1 8.5 + - - +
510B ARG 3.1 0.4 - - - -
511B LEU* 1.3 96.6 - - + +
513B GLN* 1.3 60.7 + - - +
514B GLU 3.1 2.0 - - - -
515B HIS 5.1 0.7 - - - +
516B GLY* 2.8 34.9 + - - +
517B GLY* 3.8 2.0 + - - +
523B PHE* 4.7 9.6 - - + -
538B PHE* 3.3 44.0 - - + +
539B MET 3.9 1.8 - - - +
540B ALA* 3.6 32.1 - - + -
545B THR* 3.8 19.1 - - - +
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Residues in contact with GLN 513 (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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509B ALA* 3.0 13.1 + - - +
510B ARG* 2.8 44.1 + - - +
512B MET* 1.3 79.7 - - - +
514B GLU* 1.3 56.8 + - - +
516B GLY 4.8 1.8 - - - +
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Residues in contact with GLU 514 (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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493B LYS* 2.9 39.3 + - - -
510B ARG* 3.0 59.4 + - - +
511B LEU* 3.5 16.8 + - - +
512B MET 3.1 0.2 - - - -
513B GLN* 1.3 80.7 - - - +
515B HIS* 1.3 77.5 + - + +
516B GLY 3.8 1.1 - - - -
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Residues in contact with HIS 515 (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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488B GLU* 5.2 8.6 + - - -
496B VAL* 3.9 29.9 - - + +
503B HIS 4.9 3.0 - - - +
505B ALA* 3.9 19.5 - - + -
511B LEU* 3.0 40.4 + - + +
512B MET* 3.8 2.9 - - + -
514B GLU* 1.3 97.0 + - + +
516B GLY* 1.3 54.2 - - - +
540B ALA* 3.8 14.6 - - - +
543B GLY* 3.8 16.4 + - - -
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Residues in contact with GLY 516 (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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512B MET* 2.8 22.2 + - - +
513B GLN 5.3 1.7 - - - +
514B GLU 3.8 1.0 - - - -
515B HIS* 1.3 76.3 - - - +
517B GLY* 1.3 57.6 + - - -
540B ALA* 4.2 8.1 - - - -
543B GLY* 3.0 24.4 - - - +
544B LYS* 3.8 3.4 - - - -
545B THR* 4.7 0.2 - - - -
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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