Contacts of the strand formed by residues 469 - 473 (chain B) in PDB entry 4QGC
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 ILE 469 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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438B ALA* 3.4 34.5 - - + +
439B HIS* 3.9 11.7 - - + -
442B ALA* 3.7 16.6 - - + -
450B ILE* 3.4 13.0 - - + +
452B ALA* 3.9 22.0 - - + -
463B ALA* 3.8 28.1 - - + +
466B TYR* 3.4 30.2 + - + +
467B ARG 3.3 1.0 - - - -
468B GLY* 1.3 78.4 - - - +
470B PHE* 1.3 61.2 + - - +
471B PRO* 3.1 13.4 - - - +
1004B GOL 3.2 21.7 + - - -
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Residues in contact with PHE 470 (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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106B ARG* 3.3 42.2 - - - -
449B PRO* 5.2 4.5 - - + -
450B ILE 2.7 16.6 + - - +
451B ILE* 3.6 10.0 - - + +
452B ALA 3.4 15.1 + - - -
468B GLY 3.8 1.6 + - - +
469B ILE* 1.3 71.6 - - - +
471B PRO* 1.3 67.7 - - - +
472B VAL* 3.6 2.8 + - + -
496B VAL* 3.6 28.0 - - + -
500B ARG* 3.8 28.5 - - + -
502B PHE* 3.9 33.2 - + + -
1004B GOL 4.0 13.0 - - - -
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Residues in contact with PRO 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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106B ARG* 2.9 36.2 + - - +
107B PRO* 4.0 5.9 - - + +
452B ALA* 3.7 12.1 - - + +
460B ALA* 3.1 36.1 - - + +
463B ALA* 3.7 17.0 - - + -
464B HIS* 3.4 23.3 - - + +
469B ILE* 3.1 15.2 - - + +
470B PHE* 1.3 83.2 - - - +
472B VAL* 1.3 58.7 + - - +
1004B GOL 3.7 7.9 - - - -
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Residues in contact with VAL 472 (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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103B ILE 5.3 1.6 - - - +
105B TYR 5.4 2.2 - - - +
106B ARG* 4.1 9.9 - - - +
107B PRO* 5.2 0.9 - - - -
451B ILE* 4.4 6.7 - - + -
452B ALA 2.9 10.0 + - - +
453B VAL* 4.0 20.0 - - + -
454B THR* 3.0 28.6 + - - +
460B ALA* 5.0 1.5 - - - +
470B PHE* 4.2 7.6 - - + +
471B PRO* 1.3 78.6 - - - +
473B LEU* 1.3 59.7 + - - +
492B PHE* 3.4 32.3 - - + -
493B ALA* 5.2 0.9 - - - -
496B VAL* 3.6 38.8 - - + -
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Residues in contact with LEU 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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102B PRO* 4.7 7.6 + - - +
105B TYR* 4.1 37.0 + - + +
107B PRO* 4.8 3.7 - - + +
454B THR* 3.5 15.9 - - + +
455B ARG* 3.7 23.8 - - - +
456B ASN 4.1 3.4 - - - +
457B PRO* 4.0 30.1 - - + -
460B ALA* 4.5 10.5 - - + -
472B VAL* 1.3 71.8 - - - +
474B CYS* 1.3 65.3 + - - +
475B LYS* 3.6 33.7 + - + +
492B PHE* 3.5 15.7 - - - -
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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