Contacts of the strand formed by residues 451 - 456 (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 PHE 451 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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444D GLU* 3.5 44.6 - - + -
445D VAL* 4.6 1.0 - - - +
446D ASP* 3.1 53.5 + - + +
449D GLY 3.5 1.7 - - - -
450D LYS* 1.3 84.3 - - + +
452D VAL* 1.3 71.3 + - - +
453D ARG* 3.7 31.4 - - + -
471D ARG* 5.1 0.5 + - - -
496D THR* 3.8 8.3 - - + -
497D ILE 3.3 13.2 - - - +
498D TRP* 3.4 35.2 - + + -
520D TRP* 3.7 5.6 - - - +
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Residues in contact with VAL 452 (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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442D VAL* 4.3 4.3 - - + -
444D GLU 3.5 9.2 - - - +
445D VAL* 4.7 2.9 - - + -
451D PHE* 1.3 77.1 - - - +
453D ARG* 1.3 62.7 + - - +
454D LEU* 4.0 22.0 - - + -
469D ILE* 4.5 9.9 - - + -
471D ARG* 3.6 16.4 - - - +
496D THR* 3.4 2.1 - - - +
497D ILE* 2.9 32.2 + - + +
520D TRP* 3.5 40.4 - - + -
528D THR* 3.9 25.1 - - + +
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Residues in contact with ARG 453 (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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442D VAL* 3.7 2.4 - - - +
443D GLU* 2.9 31.7 + - + +
444D GLU* 2.8 46.1 + - + +
451D PHE* 3.7 37.2 - - + -
452D VAL* 1.3 73.9 - - - +
454D LEU* 1.3 63.5 + - - +
494D VAL* 4.1 14.8 - - + +
495D VAL 3.6 4.0 - - - -
496D THR* 2.9 41.8 + - - +
498D TRP* 3.8 16.1 - - - -
511D ASP* 5.4 0.8 + - - -
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Residues in contact with LEU 454 (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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440D VAL* 3.9 7.4 - - + -
441D ALA 3.3 6.3 - - - +
442D VAL* 3.8 29.2 - - + -
443D GLU* 4.7 0.9 - - - -
452D VAL* 4.0 14.1 - - + -
453D ARG* 1.3 80.6 - - - +
455D ARG* 1.3 59.9 + - - +
464D MET* 3.7 18.4 - - + -
469D ILE* 4.2 6.1 - - + -
483D PHE* 3.5 31.0 - - + -
489D LEU* 4.4 0.8 - - - +
493D GLN 4.0 0.2 - - - +
494D VAL* 3.2 6.9 - - - +
495D VAL* 2.9 40.6 + - + +
497D ILE* 4.2 11.4 - - + -
530D LEU* 3.8 19.1 - - + -
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Residues in contact with ARG 455 (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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443B GLU* 4.2 1.6 - - - +
455B ARG* 3.4 38.5 - - - +
456B ASN 4.5 0.6 + - - -
457B LYS* 3.7 28.9 + - - +
492B GLY* 4.0 11.9 + - - -
440D VAL* 3.4 3.7 - - - -
441D ALA* 2.9 36.2 + - + +
443D GLU* 2.7 49.1 + - + +
454D LEU* 1.3 75.9 - - - +
456D ASN* 1.3 69.4 + - - +
457D LYS* 3.2 15.5 + - + +
492D GLY 3.0 26.2 + - - -
493D GLN* 3.5 4.0 - - - +
494D VAL* 3.2 25.3 - - + +
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Residues in contact with ASN 456 (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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439D ARG* 3.4 11.9 - - - +
440D VAL* 4.2 3.1 - - + +
455D ARG* 1.3 71.4 - - - +
457D LYS* 1.3 57.0 + - - +
458D SER* 2.8 27.4 + - - +
460D GLU 2.8 21.9 + - - +
462D GLN* 3.6 12.5 - - - +
489D LEU* 3.0 38.8 + - + +
490D LYS 3.4 19.5 + - - +
491D ALA* 3.8 2.5 - - - -
492D GLY* 2.8 34.0 + - - -
493D GLN 3.0 8.5 + - - -
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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