Contacts of the helix formed by residues 4162 - 4169 (chain D) in PDB entry 6X34
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 ALA4162 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4054D LEU* 5.1 10.3 - - + -
4058D ASP* 4.1 5.8 - - - +
4138D VAL* 5.7 9.4 - - + -
4142D LEU* 5.7 8.5 - - + -
4158D PHE 3.2 17.2 + - - +
4159D LEU* 3.4 8.0 + - - +
4160D GLU 3.2 0.8 - - - -
4161D LEU* 1.3 76.4 - - - +
4163D GLU* 1.3 62.1 + - - +
4164D SER 3.2 2.5 - - - -
4165D ILE* 3.3 20.8 + - + +
4166D LEU* 3.4 16.4 + - + +
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Residues in contact with GLU4163 (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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4159D LEU 3.2 5.6 + - - +
4160D GLU* 3.3 19.7 + - - +
4161D LEU 3.4 1.6 - - - -
4162D ALA* 1.3 78.1 - - - +
4164D SER* 1.3 60.8 + - - +
4166D LEU* 3.4 27.7 - - + +
4167D GLU* 3.4 13.3 + - - +
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Residues in contact with SER4164 (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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4058D ASP* 3.9 28.4 + - - -
4061D LEU* 3.3 20.3 - - - +
4162D ALA 3.2 0.8 - - - -
4163D GLU* 1.3 78.6 - - - +
4165D ILE* 1.3 63.4 + - - +
4167D GLU* 3.6 5.5 + - - +
4168D TYR* 3.5 12.3 + - - +
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Residues in contact with ILE4165 (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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4057D PHE* 6.0 4.3 - - + -
4058D ASP* 3.9 13.7 + - - +
4061D LEU* 4.0 10.5 - - + -
4135D GLY* 4.9 12.3 - - - +
4138D VAL* 5.8 8.3 - - + -
4139D ALA* 4.5 6.2 - - + +
4162D ALA* 3.3 16.8 + - + +
4164D SER* 1.3 79.5 - - - +
4166D LEU* 1.3 61.2 + - - +
4168D TYR* 3.4 4.5 + - - +
4169D PHE* 3.3 22.7 + - - +
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Residues in contact with LEU4166 (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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4139D ALA* 4.6 18.1 - - + +
4142D LEU* 6.0 8.1 - - + -
4159D LEU* 4.0 16.8 - - + +
4162D ALA* 3.4 17.3 + - + +
4163D GLU* 3.4 22.7 - - + +
4165D ILE* 1.3 76.3 - - - +
4167D GLU* 1.3 71.3 + - + +
4169D PHE 3.7 1.3 - - - +
4170D ARG* 3.1 25.2 + - + +
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Residues in contact with GLU4167 (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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4163D GLU 3.4 16.9 + - - +
4164D SER* 3.9 7.0 - - - +
4165D ILE 3.3 1.0 - - - -
4166D LEU* 1.3 86.2 - - + +
4168D TYR* 1.3 60.7 + - - +
4170D ARG* 3.7 15.1 - - - +
4171D PRO* 4.3 3.3 - - - +
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Residues in contact with TYR4168 (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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4061D LEU* 3.6 46.9 - - + -
4064D LYS* 4.9 19.9 + - + +
4132D ARG* 6.3 4.3 - - + -
4135D GLY 6.6 0.4 - - - -
4164D SER 3.5 2.6 + - - +
4165D ILE 3.4 4.4 + - - +
4166D LEU 3.3 0.6 - - - -
4167D GLU* 1.3 78.5 - - - +
4169D PHE* 1.3 61.4 + - + +
4170D ARG 3.2 4.7 + - - -
4171D PRO* 3.6 12.3 - - - +
4172D TYR* 3.9 23.3 + + - -
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Residues in contact with PHE4169 (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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4135D GLY 4.6 2.7 - - - +
4136D PHE* 4.5 17.7 - - + +
4139D ALA* 3.8 28.3 - - + -
4165D ILE 3.3 9.4 + - - +
4166D LEU 3.7 2.7 - - - +
4167D GLU 3.5 0.2 - - - -
4168D TYR* 1.3 81.2 - - + +
4170D ARG* 1.3 63.1 + - - +
4171D PRO* 3.6 0.7 - - - -
4172D TYR* 3.7 13.8 + - + -
4173D LEU* 3.4 26.6 + - + +
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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