Contacts of the strand formed by residues 469 - 473 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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438D ALA* 3.5 35.9 - - + +
439D HIS* 4.0 9.9 - - + -
442D ALA* 3.7 17.3 - - + -
450D ILE* 3.4 16.8 - - + +
452D ALA* 4.0 17.0 - - + -
463D ALA* 3.7 30.4 - - + +
466D TYR* 3.4 32.2 + - + +
467D ARG 3.2 1.2 - - - -
468D GLY* 1.3 78.3 - - - +
470D PHE* 1.3 60.4 + - - +
471D PRO* 3.2 11.4 - - - +
1004D GOL 3.6 18.1 + - - -
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Residues in contact with PHE 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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43D ARG 5.9 0.2 - - - -
106D ARG* 3.3 35.0 - - - -
449D PRO* 5.1 4.3 - - + -
450D ILE 2.7 16.6 + - - +
451D ILE* 3.5 10.3 - - + +
452D ALA 3.3 15.6 + - - -
468D GLY 3.7 2.6 + - - +
469D ILE* 1.3 70.6 - - - +
471D PRO* 1.3 67.1 - - - +
472D VAL* 3.6 1.9 + - + -
496D VAL* 3.9 24.5 - - + -
500D ARG* 3.7 29.8 - - + -
502D PHE* 3.9 31.6 - + + -
1004D GOL 3.5 31.9 - - - +
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Residues in contact with PRO 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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106D ARG* 2.7 42.3 + - - +
107D PRO* 3.9 7.5 - - + +
452D ALA* 3.7 11.0 - - + +
454D THR* 6.1 0.2 - - + -
460D ALA* 3.1 35.2 - - - +
463D ALA* 3.7 16.6 - - + -
464D HIS* 3.5 24.0 - - + +
469D ILE* 3.2 16.1 - - + +
470D PHE* 1.3 83.4 - - - +
472D VAL* 1.3 59.0 + - - +
1004D GOL 3.8 6.3 - - - +
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Residues in contact with VAL 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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102D PRO 5.4 2.9 - - - +
103D ILE 5.5 0.7 - - - +
105D TYR 5.6 0.9 - - - +
106D ARG* 4.1 9.9 - - - +
451D ILE* 4.4 11.9 - - + -
452D ALA 2.7 13.8 + - - +
453D VAL* 4.0 21.3 - - + -
454D THR* 3.0 31.8 + - - +
460D ALA* 4.9 1.8 - - - +
470D PHE* 4.7 2.0 - - + +
471D PRO* 1.3 78.2 - - - +
473D LEU* 1.3 62.1 + - - +
492D PHE* 3.4 29.6 - - + -
493D ALA* 5.2 0.9 - - - -
496D VAL* 3.7 39.7 - - + -
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Residues in contact with LEU 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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102D PRO* 4.8 6.4 + - - +
105D TYR* 4.1 34.1 + - + +
107D PRO* 5.6 5.1 - - + +
454D THR* 3.4 11.9 - - - +
455D ARG* 3.8 20.6 - - - +
456D ASN 4.1 2.9 - - - +
457D PRO* 3.8 33.9 - - + -
460D ALA* 4.4 11.2 - - + -
472D VAL* 1.3 73.6 - - - +
474D CYS* 1.3 65.5 + - - +
475D LYS* 3.7 37.3 + - + +
492D PHE* 3.6 15.5 - - - -
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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