Contacts of the strand formed by residues 4041 - 4047 (chain D) in PDB entry 1D1Z
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 TYR4041 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4007D TYR* 3.6 27.6 + + - -
4031D LEU* 4.2 16.6 - - + -
4032D ARG 3.3 12.1 - - - +
4033D ASP* 3.4 25.8 - - - -
4034D SER 3.9 0.4 - - - +
4039D GLY* 4.0 15.5 - - - -
4040D VAL* 1.3 84.2 - - - +
4042D CYS* 1.3 66.4 - - - +
4055D ARG* 3.4 6.1 - - - -
4056D VAL* 2.8 43.8 + - + +
4057D SER* 5.2 0.4 - - - -
4058D GLN* 5.6 2.1 + - - -
4064D TRP* 3.7 37.4 - + - -
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Residues in contact with CYS4042 (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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4031D LEU* 3.4 7.3 - - - -
4032D ARG* 2.7 49.5 + - + -
4034D SER* 3.8 23.3 - - - -
4041D TYR* 1.3 79.4 - - - +
4043D LEU* 1.3 61.5 + - - +
4044D CYS* 3.7 5.3 - - - -
4053D THR* 3.6 22.7 - - + -
4054D TYR 3.5 3.6 - - - -
4055D ARG* 4.1 10.3 - - - -
5004D SO4 3.7 25.8 - - - -
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Residues in contact with LEU4043 (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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4029D TYR* 4.1 23.3 - - + -
4030D LEU 3.6 14.6 - - - +
4031D LEU* 3.8 8.3 - - + +
4041D TYR 4.2 0.4 - - - -
4042D CYS* 1.3 69.6 - - - +
4044D CYS* 1.3 58.1 + - - +
4045D VAL* 4.2 7.4 - - + -
4052D TYR 3.6 1.6 - - - +
4053D THR* 3.5 1.9 - - - -
4054D TYR* 2.8 55.8 + - + +
4056D VAL* 3.8 15.7 - - + +
4066D ALA* 5.0 3.4 - - + -
4083D LEU* 4.7 16.4 - - + -
4084D ILE* 4.1 15.3 - - + -
4087D PHE* 5.0 5.4 - - + -
4094D ILE* 4.9 8.1 - - + -
4098D LEU* 4.2 23.6 - - + -
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Residues in contact with CYS4044 (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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4016D GLY* 6.1 1.1 - - - -
4017D GLU* 5.9 2.5 - - + -
4020D LEU* 3.6 20.6 - - + +
4029D TYR* 3.1 6.8 - - - +
4030D LEU* 2.9 39.9 + - + +
4032D ARG* 3.4 37.9 - - - -
4042D CYS* 3.7 21.3 - - - -
4043D LEU* 1.3 73.4 - - - +
4045D VAL* 1.3 63.5 + - - +
4051D ILE* 4.1 9.2 - - + -
4052D TYR 3.3 4.3 - - - -
4053D THR* 4.0 8.5 - - - -
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Residues in contact with VAL4045 (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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4020D LEU* 4.2 0.4 - - - +
4027D GLY* 4.1 7.4 - - - -
4028D SER 3.4 10.1 - - - +
4043D LEU* 4.2 10.3 - - + -
4044D CYS* 1.3 79.4 - - - +
4046D LEU* 1.3 72.8 + - - +
4050D TYR 3.6 0.5 - - - +
4051D ILE* 3.4 5.6 - - - +
4052D TYR* 2.8 44.4 + - + +
4054D TYR* 4.2 20.4 - - + -
4094D ILE* 4.5 3.6 - - + -
4095D VAL* 5.2 3.1 - - + -
4096D ILE* 3.9 23.8 - - + +
4098D LEU* 3.6 31.0 - - + -
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Residues in contact with LEU4046 (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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4020D LEU* 3.4 24.1 - - + +
4021D LEU* 3.8 22.2 - - + -
4023D THR* 3.9 0.4 - - - +
4024D GLY* 3.8 11.0 - - - -
4025D LEU 3.5 36.3 - - - +
4026D ASP* 3.5 1.4 - - - +
4027D GLY* 2.9 27.4 + - - -
4028D SER* 2.9 15.9 + - - +
4045D VAL* 1.3 75.8 - - - +
4047D TYR* 1.3 65.7 + - - +
4048D HIS 5.0 0.2 - - - +
4049D GLY* 3.8 10.8 - - - +
4050D TYR 3.4 16.8 - - - +
4051D ILE* 3.3 27.7 - - + +
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Residues in contact with TYR4047 (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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4026D ASP* 3.6 12.8 - - - -
4046D LEU* 1.3 76.3 - - - +
4048D HIS* 1.3 107.2 + + + +
4049D GLY 3.2 1.1 - - - -
4050D TYR* 2.8 22.6 + - - +
4052D TYR* 3.7 25.2 + - + -
4095D VAL* 3.6 44.6 - - + -
4096D ILE* 3.7 37.6 - - + +
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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