Contacts of the strand formed by residues 451 - 456 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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444C GLU* 3.1 45.1 - - + -
445C VAL* 4.6 0.9 - - - +
446C ASP* 3.1 62.8 + - + +
449C GLY 3.5 1.9 - - - -
450C LYS* 1.3 82.1 - - + +
452C VAL* 1.3 76.3 + - - +
453C ARG* 4.1 11.7 - - + -
496C THR* 3.5 30.3 - - + -
497C ILE 3.3 9.4 - - - +
498C TRP* 3.6 27.4 - + + -
520C TRP* 3.5 7.0 - - - +
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Residues in contact with VAL 452 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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442C VAL* 4.3 4.7 - - + -
444C GLU 3.5 9.0 - - - +
445C VAL* 4.5 4.0 - - + -
451C PHE* 1.3 82.6 - - - +
453C ARG* 1.3 62.7 + - - +
454C LEU* 4.0 21.8 - - + -
469C ILE* 4.4 9.4 - - + -
471C ARG* 3.9 17.0 - - - +
496C THR* 3.3 1.2 - - - -
497C ILE* 2.9 33.8 + - + +
520C TRP* 3.5 37.2 - - + -
528C THR* 4.0 23.8 - - + -
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Residues in contact with ARG 453 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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457A LYS* 3.9 29.7 + - - +
442C VAL* 3.8 1.0 - - - +
443C GLU* 2.9 54.3 + - + +
444C GLU* 2.5 59.6 + - + +
451C PHE* 4.1 11.1 - - + -
452C VAL* 1.3 75.4 - - - +
454C LEU* 1.3 74.8 + - - +
494C VAL* 3.8 21.5 - - + +
495C VAL 3.3 10.1 - - - +
496C THR* 3.7 18.2 - - - +
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Residues in contact with LEU 454 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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440C VAL* 3.9 8.1 - - + -
441C ALA 3.3 7.0 - - - +
442C VAL* 3.9 28.3 - - + -
443C GLU* 4.6 0.4 - - - -
452C VAL* 4.0 14.4 - - + -
453C ARG* 1.3 83.0 - - - +
455C ARG* 1.3 60.5 + - - +
464C MET* 3.8 17.5 - - + -
469C ILE* 4.2 7.9 - - + -
483C PHE* 3.7 30.3 - - + -
489C LEU* 4.5 1.7 - - + +
493C GLN 3.9 0.2 - - - +
494C VAL* 3.1 27.0 - - - +
495C VAL* 2.9 25.9 + - + +
497C ILE* 4.2 6.7 - - + -
530C LEU* 3.8 18.4 - - + -
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Residues in contact with ARG 455 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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443A GLU* 4.2 4.3 - - - +
455A ARG* 3.7 28.3 - - - +
456A ASN 4.4 0.2 + - - -
457A LYS* 3.3 31.3 + - - +
492A GLY* 4.1 13.7 + - - -
440C VAL* 3.3 5.6 - - - -
441C ALA* 2.9 36.5 + - + +
443C GLU* 2.7 50.1 + - + +
454C LEU* 1.3 75.5 - - - +
456C ASN* 1.3 68.1 + - - +
457C LYS* 3.3 14.6 + - + +
489C LEU* 4.2 0.2 - - - -
492C GLY 2.9 29.2 + - - -
493C GLN* 3.5 3.9 - - - +
494C VAL* 3.2 20.6 - - + +
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Residues in contact with ASN 456 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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439C ARG* 3.4 12.6 - - - +
440C VAL* 4.3 3.1 - - + -
455C ARG* 1.3 72.3 - - - +
457C LYS* 1.3 57.3 + - - +
458C SER* 2.8 26.7 + - - +
460C GLU 2.8 23.1 + - - -
462C GLN* 3.5 11.9 - - - +
489C LEU* 3.0 38.0 + - + +
490C LYS 3.3 20.8 + - - +
491C ALA* 3.7 2.7 - - - -
492C GLY* 2.9 33.0 + - - +
493C GLN 2.9 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