Contacts of the strand formed by residues 478 - 484 (chain D) in PDB entry 3GXM
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 478 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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56D ILE* 3.7 4.6 - - - +
57D GLN 3.4 8.3 - - - -
58D ALA* 4.9 4.0 - - - -
472D ILE 3.7 0.9 - - - +
473D LYS* 3.8 3.2 - - - +
474D ASP* 2.8 39.5 + - - +
475D PRO* 4.6 1.8 + - - +
476D ALA 4.0 0.2 - - - -
477D VAL* 1.3 76.7 - - - +
479D PHE* 1.3 72.8 + - - -
480D LEU* 5.1 0.7 - - - +
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Residues in contact with PHE 479 (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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55D PRO 3.9 0.7 - - - +
56D ILE* 3.2 7.0 - - - +
57D GLN* 2.8 41.7 + - - +
58D ALA 3.6 17.7 - - - -
59D ASN* 3.6 19.3 - - - +
60D HIS* 3.5 28.0 - + + -
66D LEU* 4.1 13.0 - - + -
471D THR* 3.6 23.6 - - + -
472D ILE 3.6 2.7 - - - -
473D LYS* 3.8 45.3 - - + -
478D GLY* 1.3 79.3 - - - -
480D LEU* 1.3 62.9 - - - +
481D GLU* 3.9 12.3 - - - +
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Residues in contact with LEU 480 (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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37D PHE* 3.5 39.0 - - + -
55D PRO 4.4 0.2 - - - -
56D ILE* 3.4 39.5 - - + -
470D LEU 4.1 0.2 - - - +
471D THR* 3.2 6.8 - - - -
472D ILE* 3.1 45.5 + - + +
474D ASP* 5.8 0.9 - - + -
477D VAL* 5.3 1.1 - - + -
478D GLY 5.1 1.6 - - - +
479D PHE* 1.3 75.8 - - - +
481D GLU* 1.3 63.1 + - - +
482D THR* 3.8 5.1 + - + +
492D TYR* 4.0 19.1 - - + -
494D TRP* 3.8 33.9 - - + -
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Residues in contact with GLU 481 (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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37D PHE* 4.4 14.8 - - - -
55D PRO 4.8 1.0 + - - -
57D GLN* 3.5 43.0 + - - +
59D ASN 4.1 4.6 - - - +
60D HIS* 3.2 28.9 - - + +
61D THR 5.1 0.7 + - - +
470D LEU 4.1 1.1 - - - +
471D THR* 3.5 18.4 - - - +
479D PHE* 3.9 13.2 + - - +
480D LEU* 1.3 69.7 - - - +
482D THR* 1.3 62.1 + - - +
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Residues in contact with THR 482 (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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37D PHE* 5.4 4.2 - - - -
39D ARG* 3.8 11.0 + - - +
469D PRO* 3.7 2.4 - - - +
470D LEU* 2.8 61.2 + - + +
472D ILE* 5.0 3.1 - - + -
480D LEU* 4.6 6.3 - - + +
481D GLU* 1.3 78.2 - - - +
483D ILE* 1.3 74.8 + - - +
492D TYR* 2.6 44.4 + - + +
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Residues in contact with ILE 483 (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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39D ARG* 3.8 7.6 + - - +
467D ASP* 4.1 22.2 - - + +
468D VAL 3.4 11.7 - - - +
469D PRO* 4.5 11.9 - - + -
482D THR* 1.3 84.9 + - - +
484D SER* 1.3 69.7 + - - +
485D PRO* 3.3 16.6 - - + +
490D HIS* 3.3 14.6 - - - -
492D TYR* 4.7 0.2 - - - -
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Residues in contact with SER 484 (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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444D LEU* 3.9 8.4 - - - +
460D VAL* 3.6 19.9 + - - +
461D LEU 4.7 0.2 - - - -
462D ASN* 3.0 28.6 + - - +
468D VAL 2.6 41.3 + - - -
470D LEU* 3.7 21.6 - - - +
482D THR 4.3 0.2 - - - -
483D ILE* 1.3 72.3 - - - +
485D PRO* 1.3 59.0 - - - +
488D SER* 3.9 4.3 + - - -
490D HIS* 4.4 7.6 + - - -
492D TYR* 5.7 0.7 - - - -
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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