Contacts of the strand formed by residues 468 - 473 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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466B ASN 4.2 1.9 - - - +
467B TRP* 1.4 74.0 - - - +
469B ILE* 1.3 63.5 + - - +
470B LYS* 3.2 28.9 + - + +
480B THR* 4.0 11.5 - - + +
481B TYR 3.2 10.5 - - - +
482B TRP* 3.2 44.1 - - + -
530B LEU* 3.4 8.2 - - - +
531B ILE* 2.7 62.9 + - + +
532B ASN 4.0 6.3 - - - +
533B SER 5.9 0.3 - - - -
535B GLY* 4.7 4.9 + - - -
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Residues in contact with ILE 469 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
442B VAL* 6.3 0.7 - - + -
452B VAL* 4.5 8.7 - - + -
454B LEU* 4.3 9.9 - - + -
468B GLN* 1.3 78.1 - - - +
470B LYS* 1.3 62.7 + - - +
471B ARG 4.1 0.2 + - - -
479B LEU 3.9 0.5 - - - +
480B THR* 3.5 3.3 - - - -
481B TYR* 3.0 40.9 + - + +
483B PHE* 3.9 15.0 - - + -
497B ILE* 3.9 32.3 - - + -
520B TRP* 3.4 34.5 - - + -
528B THR* 3.6 24.5 - - + -
529B ALA 3.1 6.7 - - - +
530B LEU* 3.9 14.6 - - + -
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Residues in contact with LYS 470 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
468B GLN* 3.2 26.3 + - - +
469B ILE* 1.3 73.7 - - - +
471B ARG* 1.3 60.3 + - - +
472B GLN 4.2 0.2 - - - -
478B LEU* 4.0 23.3 - - + -
479B LEU 3.4 4.0 - - - -
480B THR* 3.9 19.3 - - + +
527B ARG 3.5 1.4 - - - +
528B THR* 3.4 4.9 - - - +
529B ALA* 2.8 41.2 + - + +
531B ILE* 3.7 31.9 - - + +
535B GLY* 5.5 2.4 + - - -
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Residues in contact with ARG 471 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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445B VAL* 3.8 23.1 - - - +
446B ASP 5.2 2.8 + - - -
452B VAL* 3.9 4.8 - - - +
469B ILE 4.1 0.4 + - - -
470B LYS* 1.3 73.9 - - - +
472B GLN* 1.3 64.9 + - - +
473B ASN* 2.6 26.7 + - - +
477B PRO 4.6 0.7 - - - +
478B LEU* 3.6 4.9 - - - +
479B LEU* 2.9 46.0 + - + +
520B TRP* 3.5 59.5 + - + +
521B GLY 3.3 25.3 + - - -
526B LEU* 4.2 17.7 - - - +
527B ARG 3.2 16.2 - - - -
528B THR* 2.9 20.5 + - - +
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Residues in contact with GLN 472 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
470B LYS 4.2 0.4 - - - -
471B ARG* 1.3 73.6 - - - +
473B ASN* 1.3 77.2 + - - +
474B GLY 2.8 28.8 + - - +
475B ASP* 3.6 1.8 - - - -
476B ASP 2.7 29.8 + - - +
477B PRO 4.8 0.2 - - - -
478B LEU* 4.3 20.8 + - + +
526B LEU* 3.4 4.9 - - - -
527B ARG* 2.9 49.3 + - + +
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Residues in contact with ASN 473 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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471B ARG* 2.6 35.9 + - - +
472B GLN* 1.3 74.9 - - - +
474B GLY* 1.3 67.7 + - - +
475B ASP 3.0 0.2 + - - -
476B ASP* 2.8 43.7 + - + +
477B PRO 5.4 1.4 + - - +
479B LEU* 3.9 13.9 - - - +
520B TRP 2.6 24.8 + - - -
521B GLY* 3.5 13.9 - - - -
522B CSD 5.1 4.5 - - - +
525B SER 4.1 2.7 - - - -
526B LEU* 3.1 16.8 - - + +
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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