Contacts of the helix formed by residues 441 - 453 (chain D) in PDB entry 4R0C
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 TYR 441 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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133D VAL* 4.0 4.7 + - + +
134D ASP* 2.6 32.4 + - - -
137D TYR* 3.6 59.7 - + + -
138D VAL* 4.2 4.8 - - + +
439D MET* 3.0 23.7 + - + -
440D PRO* 1.3 87.9 - - + +
442D PHE* 1.3 64.3 + - - +
443D VAL 3.1 3.4 - - - -
444D LEU* 2.9 44.3 + - + +
445D VAL* 3.1 13.5 + - + +
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Residues in contact with PHE 442 (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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163D PHE* 4.7 12.1 - + - -
434D ILE 4.7 8.1 - - - -
436D THR 3.4 22.2 - - - +
437D PRO* 3.6 20.6 - - + +
439D MET* 3.1 25.8 + - + +
441D TYR* 1.3 77.9 - - - +
443D VAL* 1.3 63.6 + - + +
445D VAL* 4.0 5.0 - - - +
446D LEU* 3.2 25.7 + - + +
458D ILE* 3.6 51.8 - - + -
461D LEU* 3.9 27.4 - - + -
462D ILE* 3.9 21.5 - - + -
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Residues in contact with VAL 443 (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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437D PRO 5.2 1.0 + - - +
439D MET 4.6 0.6 + - - -
440D PRO 4.4 11.8 + - - +
441D TYR 3.1 1.2 - - - -
442D PHE* 1.3 83.6 - - + +
444D LEU* 1.3 70.8 + - + +
446D LEU* 3.6 14.5 - - + +
447D GLY* 3.2 18.2 + - - -
450D ARG* 6.2 0.4 - - - +
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Residues in contact with LEU 444 (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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138D VAL* 3.8 19.5 - - + -
440D PRO 5.2 0.9 - - - +
441D TYR* 2.9 42.5 + - + +
443D VAL* 1.3 87.8 - - + +
445D VAL* 1.3 57.1 + - + +
447D GLY* 3.4 3.3 + - - -
448D PHE* 3.1 56.6 + - + -
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Residues in contact with VAL 445 (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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137D TYR* 4.5 6.3 - - + -
141D ILE* 4.0 17.3 - - + -
159D ILE* 4.5 14.1 - - + +
163D PHE* 3.6 56.1 - - + -
441D TYR* 3.1 14.9 + - + +
442D PHE 4.1 3.8 - - - +
443D VAL 3.3 0.2 - - - -
444D LEU* 1.3 74.7 - - + +
446D LEU* 1.3 66.1 - - - +
447D GLY 3.1 1.6 - - - -
448D PHE* 2.9 13.7 + - + +
449D ALA* 2.9 21.1 + - - +
461D LEU* 3.9 13.2 - - + -
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Residues in contact with LEU 446 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
442D PHE* 3.2 21.3 + - + +
443D VAL* 3.6 15.3 - - + +
445D VAL* 1.3 77.9 - - - +
447D GLY* 1.3 51.6 + - - +
449D ALA* 3.1 7.7 + - + +
450D ARG* 2.8 69.1 + - + +
456D THR* 3.6 21.5 - - - +
457D GLY 3.4 22.0 - - - +
458D ILE* 4.0 28.7 - - + +
461D LEU* 3.6 19.4 - - + +
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Residues in contact with GLY 447 (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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443D VAL 3.2 10.7 + - - -
444D LEU* 3.6 6.1 - - - -
445D VAL 3.1 0.8 - - - -
446D LEU* 1.3 79.4 - - - +
448D PHE* 1.3 61.4 + - - +
450D ARG* 3.1 20.3 + - - +
451D ARG* 3.4 11.6 + - - +
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Residues in contact with PHE 448 (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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137D TYR* 3.5 23.8 - - + -
138D VAL* 4.2 15.5 - - + -
141D ILE* 4.0 20.0 - - + -
142D PRO* 4.0 27.8 - - + -
159D ILE* 3.4 21.5 - - + +
444D LEU* 3.1 54.0 + - + -
445D VAL* 2.9 19.3 + - + +
447D GLY* 1.3 75.2 - - - +
449D ALA* 1.3 61.8 + - - +
451D ARG* 3.6 16.0 + - - +
452D TYR* 3.8 5.0 - - - -
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Residues in contact with ALA 449 (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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156D ILE* 4.4 18.2 - - + +
159D ILE* 3.7 22.4 - - + +
445D VAL 2.9 11.8 + - - +
446D LEU* 3.5 11.9 - - + +
448D PHE* 1.3 73.0 - - - +
450D ARG* 1.3 55.4 + - - +
451D ARG 3.0 10.7 + - - -
452D TYR* 3.1 8.1 + - - +
453D GLN* 3.1 20.6 + - - +
456D THR* 4.3 12.3 - - - +
461D LEU* 5.1 11.9 - - + -
464D LEU* 6.2 0.2 - - + -
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Residues in contact with ARG 450 (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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443D VAL* 6.2 0.4 - - - +
446D LEU* 2.8 49.3 + - + +
447D GLY* 3.1 11.5 + - - +
449D ALA* 1.3 69.0 - - - +
451D ARG* 1.3 64.1 + - - +
452D TYR 3.4 0.2 - - - -
453D GLN 3.6 8.7 - - - -
454D PRO* 3.1 44.0 + - + +
455D GLU 4.6 1.6 + - - -
456D THR* 2.5 46.0 + - - +
457D GLY* 3.6 10.9 - - - -
458D ILE* 5.8 0.4 - - - +
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Residues in contact with ARG 451 (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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146D LEU* 4.5 9.1 - - - +
240D ASP* 3.7 26.4 + - - +
242D SER* 3.3 25.5 + - - -
447D GLY 3.4 8.4 + - - +
448D PHE* 3.6 13.2 - - - +
449D ALA 3.0 0.8 + - - -
450D ARG* 1.3 79.9 - - - +
452D TYR* 1.3 86.8 + - + +
454D PRO* 4.8 2.4 - - - +
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Residues in contact with TYR 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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142D PRO* 4.3 5.6 + - + -
145D GLY* 3.7 11.0 - - - -
146D LEU* 3.2 37.0 + - + +
149D GLN* 3.5 26.7 - - + -
155D PRO* 3.5 39.0 - - + -
156D ILE* 4.8 4.9 - - + -
159D ILE* 4.1 16.6 - - + -
236D ASN* 4.2 16.9 + - - +
239D ALA* 6.0 0.2 - - + -
448D PHE 3.8 16.4 - - - -
449D ALA 3.1 5.7 + - - +
451D ARG* 1.3 103.4 + - + +
453D GLN* 1.3 70.6 + - + +
454D PRO* 4.0 5.1 - - - +
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Residues in contact with GLN 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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155D PRO* 6.0 1.2 - - - +
156D ILE* 3.8 25.2 - - + +
233D ALA* 3.5 29.7 - - - +
449D ALA 3.1 5.0 + - - +
450D ARG* 3.6 4.3 - - - -
452D TYR* 1.3 84.7 - - - +
454D PRO* 1.3 61.9 - - - +
455D GLU* 3.1 35.3 + - + +
456D THR* 2.8 38.5 + - + -
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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