Contacts of the strand formed by residues 4118 - 4123 (chain D) in PDB entry 2H7C
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 TYR4118 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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482D SIA 2.9 47.0 + - + +
4052D GLY* 3.3 23.8 - - - -
4053D ILE 3.2 5.6 - - - +
4054D PRO* 3.6 26.6 - - + +
4055D PHE* 3.5 5.3 - - - -
4058D PRO* 5.0 3.1 - - + +
4084D PRO* 3.7 36.1 - - + -
4085D PRO* 4.5 3.6 - - + -
4115D ASP* 2.7 44.7 + - - -
4116D CYS* 2.9 22.1 + - - +
4117D LEU* 1.3 75.3 - - - +
4119D LEU* 1.3 61.7 + - - +
4168D ILE 4.0 0.2 - - - -
4169D GLN* 3.1 30.0 + - - +
6184F HIS* 5.0 3.8 + - - -
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Residues in contact with LEU4119 (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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4052D GLY 3.5 0.2 + - - -
4053D ILE* 2.9 48.0 + - + +
4055D PHE* 3.9 24.0 - - + -
4118D TYR* 1.3 75.7 - - - +
4120D ASN* 1.3 66.5 + - - +
4121D ILE* 3.6 33.7 - - + -
4149D ALA* 5.7 0.2 - - - -
4166D VAL* 4.1 13.0 - - + -
4167D THR 3.2 13.0 - - - +
4168D ILE* 4.0 15.9 - - + -
4197D ALA* 4.4 9.2 - - + +
4200D TRP* 3.7 28.0 - - + -
4201D VAL* 4.7 0.9 - - + -
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Residues in contact with ASN4120 (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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4050D PHE 3.3 7.4 - - - +
4051D LEU* 3.3 20.9 - - + +
4052D GLY* 2.7 30.8 + - - -
4083D TYR* 4.5 0.4 - - - -
4084D PRO* 3.6 11.0 - - - +
4119D LEU* 1.3 75.5 - - - +
4121D ILE* 1.3 61.2 - - - +
4122D TYR* 4.0 12.6 + - + -
4149D ALA* 4.3 3.8 - - - +
4150D SER* 3.3 35.2 + - - +
4165D VAL 3.8 0.7 - - - +
4166D VAL* 3.3 6.2 - - - +
4167D THR* 2.8 48.6 + - - +
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Residues in contact with ILE4121 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4048D ALA 3.6 0.5 - - - +
4049D ILE* 3.3 5.9 - - - +
4050D PHE* 2.8 47.6 + - + +
4053D ILE* 3.9 11.9 - - + -
4119D LEU* 3.6 15.0 - - + -
4120D ASN* 1.3 78.2 - - - +
4122D TYR* 1.3 71.9 + - - +
4123D THR* 4.4 2.2 - - - +
4164D VAL* 4.0 23.3 - - + -
4165D VAL 3.5 2.7 - - - +
4166D VAL* 4.3 8.1 - - + -
4200D TRP* 3.7 36.6 - - + -
4205D ILE* 4.3 6.1 - - + -
4208D PHE* 4.0 31.0 - - + -
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Residues in contact with TYR4122 (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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4047D VAL* 4.0 6.1 - - + -
4048D ALA 3.7 3.8 - - - -
4049D ILE* 3.8 38.4 - - + -
4051D LEU* 3.9 14.6 - - + +
4083D TYR* 4.5 3.8 + - - -
4104D ARG* 4.1 9.2 + - - -
4120D ASN* 4.0 23.8 + - + +
4121D ILE* 1.3 76.2 - - - +
4123D THR* 1.3 60.6 + - - +
4152D TYR 3.7 13.4 + - - -
4153D ASP* 3.3 21.2 + - - -
4154D GLY* 3.4 32.5 + - - +
4155D LEU* 3.5 13.7 - - - -
4158D ALA* 3.7 9.4 - - + +
4164D VAL* 3.5 2.4 - - - -
4165D VAL* 2.8 46.8 + - + +
4167D THR* 4.3 9.4 - - + -
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Residues in contact with THR4123 (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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4046D PRO 4.6 0.2 - - - +
4047D VAL* 3.7 3.9 - - - +
4048D ALA* 2.9 54.8 + - + +
4050D PHE* 4.3 10.8 - - + -
4121D ILE* 4.6 3.4 - - + -
4122D TYR* 1.3 73.9 - - - +
4124D PRO* 1.3 61.8 - - - +
4125D ALA* 3.2 20.5 + - - +
4127D LEU* 4.4 10.8 - - + -
4164D VAL* 3.6 14.4 - - - +
4208D PHE* 2.7 32.5 + - + +
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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