Contacts of the strand formed by residues 468 - 473 (chain D) in PDB entry 3GEF
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 GLN 468 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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466D ASN 4.1 1.7 - - - +
467D TRP* 1.3 75.0 - - - +
469D ILE* 1.3 65.1 + - - +
470D LYS* 3.8 19.3 - - - +
480D THR* 3.3 22.9 - - + +
481D TYR 3.2 9.9 - - - +
482D TRP* 3.4 46.4 - - + -
483D PHE* 4.7 0.7 - - - -
530D LEU* 3.5 7.4 - - - +
531D ILE* 2.8 65.4 + - + +
532D ASN 4.4 4.3 - - - +
535D GLY* 5.0 3.1 - - - -
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Residues in contact with ILE 469 (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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452D VAL* 4.5 6.3 - - + -
454D LEU* 4.2 8.5 - - + -
468D GLN* 1.3 77.9 - - - +
470D LYS* 1.3 62.6 + - - +
471D ARG 4.0 0.2 + - - -
479D LEU 3.7 1.2 - - - +
480D THR* 3.4 4.9 - - - +
481D TYR* 2.9 39.7 + - + +
483D PHE* 3.7 20.6 - - + -
497D ILE* 3.6 34.3 - - + -
520D TRP* 3.5 34.0 - - + -
528D THR* 3.6 26.2 - - + -
529D ALA 3.3 6.7 - - - +
530D LEU* 4.0 8.7 - - + -
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Residues in contact with LYS 470 (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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468D GLN* 3.8 24.2 - - - +
469D ILE* 1.3 76.1 - - - +
471D ARG* 1.3 59.4 + - - +
472D GLN* 4.2 0.4 + - - -
478D LEU* 4.0 26.9 - - + +
479D LEU 3.5 4.3 - - - -
480D THR* 4.0 13.9 - - - +
527D ARG 3.5 3.1 - - - +
528D THR* 3.5 0.7 - - - -
529D ALA* 2.9 41.5 + - + +
531D ILE* 3.9 30.4 - - + +
535D GLY 5.8 1.2 + - - -
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Residues in contact with ARG 471 (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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445D VAL* 3.6 23.0 - - - +
446D ASP 4.2 7.7 + - - -
449D GLY* 4.5 0.2 - - - -
451D PHE 5.1 0.6 + - - -
452D VAL* 3.6 12.7 - - - +
469D ILE 4.0 0.2 - - - -
470D LYS* 1.3 73.2 - - - +
472D GLN* 1.3 58.8 + - - +
473D ASN* 2.8 24.3 + - - +
478D LEU* 3.3 4.2 - - - +
479D LEU* 2.9 44.8 + - + +
520D TRP* 3.3 62.3 + - + +
521D GLY 2.8 26.7 + - - -
526D LEU* 3.9 13.0 - - - +
527D ARG 3.3 9.6 - - - +
528D THR* 3.1 28.8 + - - +
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Residues in contact with GLN 472 (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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470D LYS 4.1 0.8 - - - +
471D ARG* 1.3 72.7 - - - +
473D ASN* 1.3 74.6 + - - +
474D GLY 3.0 27.3 + - - +
475D ASP 4.0 0.6 - - - -
476D ASP 2.8 29.3 + - - +
477D PRO 4.6 0.6 - - - -
478D LEU* 3.9 27.1 + - + +
525D SER* 3.8 1.7 + - - +
527D ARG* 2.9 44.9 + - + +
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Residues in contact with ASN 473 (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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471D ARG* 2.8 31.2 + - - +
472D GLN* 1.3 73.4 - - - +
474D GLY* 1.3 67.7 + - - +
475D ASP 3.0 0.2 + - - -
476D ASP* 2.9 40.9 + - + +
477D PRO 5.4 1.2 + - - -
479D LEU* 4.2 15.2 - - - +
520D TRP 2.9 23.6 + - - -
521D GLY* 3.6 10.8 - - - -
522D CSD 4.9 4.9 - - - +
525D SER 3.4 3.8 - - - -
526D LEU* 3.1 24.3 - - + +
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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