Contacts of the helix formed by residues 481 - 493 (chain A) in PDB entry 6FD3
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 481 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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479A ASN 3.8 3.6 + - - -
480A GLU* 1.3 75.2 + - - +
482A PRO* 1.3 77.6 - - + +
483A LEU* 4.5 3.4 - - + +
484A ARG* 3.0 17.1 + - + +
485A ALA* 3.0 18.5 + - - +
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Residues in contact with PRO 482 (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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441A PRO* 3.9 23.4 - - + +
442A TYR* 3.8 21.3 - - + +
480A GLU 3.5 0.4 - - - +
481A ASN* 1.3 86.1 - - + +
483A LEU* 1.3 61.0 + - + +
485A ALA* 3.2 6.7 + - + +
486A LEU* 2.9 34.9 + - + +
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Residues in contact with LEU 483 (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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481A ASN* 3.3 4.0 - - + +
482A PRO* 1.3 81.3 - - + +
484A ARG* 1.3 61.1 + - - +
486A LEU* 3.4 23.0 + - + +
487A TYR* 3.2 21.0 + - - +
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Residues in contact with ARG 484 (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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480A GLU* 3.5 31.1 + - + +
481A ASN* 3.0 19.5 + - + +
483A LEU* 1.3 76.7 - - - +
485A ALA* 1.3 67.2 + - - +
487A TYR* 3.1 36.1 + - - +
488A LEU* 2.9 43.8 + - + +
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Residues in contact with ALA 485 (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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441A PRO* 4.9 3.6 - - + -
442A TYR* 3.5 39.0 - - + -
477A TYR* 4.1 17.0 - - + +
480A GLU* 4.2 1.7 - - + +
481A ASN 3.0 8.6 + - - +
482A PRO* 3.5 7.4 - - + +
484A ARG* 1.3 78.2 - - - +
486A LEU* 1.3 56.8 + - - +
488A LEU* 3.1 8.8 + - - +
489A ILE* 2.8 37.7 + - + +
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Residues in contact with LEU 486 (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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437A MET* 4.1 21.1 - - + -
441A PRO* 3.8 22.7 - - + +
444A MET* 3.8 19.3 - - + -
449A VAL* 3.6 38.9 - - + +
482A PRO* 2.9 21.1 + - + +
483A LEU* 3.7 28.3 - - + +
484A ARG 3.2 0.4 - - - -
485A ALA* 1.3 75.1 - - - +
487A TYR* 1.3 61.9 + - - +
489A ILE* 3.3 4.1 + - - -
490A ALA* 3.0 23.0 + - - +
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Residues in contact with TYR 487 (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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483A LEU 3.2 9.7 + - - +
484A ARG* 3.1 39.0 + - - +
486A LEU* 1.3 78.1 - - - +
488A LEU* 1.3 70.4 + - + +
490A ALA* 3.2 7.2 + - + +
491A THR* 2.9 61.6 + - + +
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Residues in contact with LEU 488 (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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477A TYR* 3.7 40.8 - - + -
480A GLU* 4.2 14.6 - - + +
484A ARG* 2.9 57.8 + - + +
485A ALA 3.5 6.3 - - - +
487A TYR* 1.3 84.8 - - + +
489A ILE* 1.3 58.2 + - - +
491A THR* 3.7 4.5 - - - +
492A ASN* 2.8 49.1 + - - +
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Residues in contact with ILE 489 (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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441A PRO 3.2 29.2 - - - +
442A TYR* 4.3 12.8 - - - +
444A MET 3.6 24.5 - - - +
446A PRO* 4.0 19.8 - - + +
449A VAL* 4.0 21.5 - - + -
461A TRP* 4.6 9.2 - - + +
477A TYR* 3.9 19.1 - - + -
485A ALA 2.8 25.0 + - - +
486A LEU* 3.7 4.7 - - - +
488A LEU* 1.3 75.9 - - - +
490A ALA* 1.3 63.9 + - - +
491A THR 3.3 0.5 + - - -
492A ASN* 5.2 0.2 - - - -
493A GLY* 3.3 23.3 + - - +
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Residues in contact with ALA 490 (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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446A PRO* 5.1 3.4 - - - -
449A VAL* 3.9 8.0 - - + +
450A THR* 3.8 28.0 - - + +
486A LEU 3.0 14.1 + - - +
487A TYR* 3.2 13.2 + - + +
489A ILE* 1.3 79.0 - - - +
491A THR* 1.3 62.4 + - + +
493A GLY 4.5 1.7 + - - -
517A MET* 4.9 9.2 - - - +
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Residues in contact with THR 491 (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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487A TYR* 2.9 59.9 + - + +
488A LEU* 3.5 7.1 + - - +
490A ALA* 1.3 82.6 - - + +
492A ASN* 1.3 71.0 + - - +
493A GLY 3.4 1.3 - - - -
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Residues in contact with ASN 492 (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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477A TYR* 2.9 36.0 + - - +
488A LEU* 2.8 32.4 + - - +
491A THR* 1.3 84.3 + - - +
493A GLY* 1.3 66.1 + - - +
494A THR 3.3 10.5 + - - +
495A PRO* 5.5 1.8 - - + -
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Residues in contact with GLY 493 (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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461A TRP* 3.5 8.8 - - - -
477A TYR* 5.2 0.9 + - - -
489A ILE* 3.3 16.1 + - - +
490A ALA 4.5 0.6 + - - -
491A THR 3.4 2.6 - - - -
492A ASN* 1.3 80.3 - - - +
494A THR* 1.3 63.7 + - - -
495A PRO* 3.1 10.6 - - - +
517A MET* 3.2 36.3 - - - -
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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