Contacts of the helix formed by residues 165 - 170 (chain D) in PDB entry 1D1T
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 PRO 165 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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163D ALA 3.3 9.9 - - - +
164D ALA* 1.4 78.9 - - + +
166D PRO* 1.3 70.5 - - + +
167D GLU* 3.2 22.0 - - - +
168D LYS* 3.0 17.7 + - + +
169D VAL* 3.0 23.5 + - + +
335D PHE* 4.2 14.1 - - + -
336D LEU* 4.0 14.8 - - + -
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Residues in contact with PRO 166 (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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41D LEU* 4.0 33.2 - - + -
42D ALA* 3.5 6.8 - - + +
70D THR* 3.0 48.6 + - + +
88D LYS* 4.1 8.7 - - - +
164D ALA 2.8 14.3 - - - +
165D PRO* 1.3 79.3 - - + +
167D GLU* 1.3 66.7 + - + +
168D LYS 3.0 5.1 + - - -
169D VAL* 4.0 0.4 - - + -
170D CYS* 3.3 12.6 + - - +
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Residues in contact with GLU 167 (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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42D ALA* 3.7 16.8 - - + -
165D PRO* 3.7 10.8 - - - +
166D PRO* 1.3 89.9 - - + +
168D LYS* 1.3 82.9 + - + +
170D CYS* 4.1 4.0 - - - -
346D ILE* 3.5 16.1 - - - +
349D VAL* 5.1 13.0 - - + +
371D VAL* 3.8 21.5 - - + +
373D THR* 4.5 10.8 - - + -
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Residues in contact with LYS 168 (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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165D PRO* 3.0 16.6 + - + +
166D PRO 3.0 0.2 - - - -
167D GLU* 1.3 107.1 - - + +
169D VAL* 1.3 59.3 + - - +
170D CYS* 3.0 9.8 + - - -
171D LEU* 3.2 17.7 + - - +
335D PHE* 4.1 28.5 - - + -
342D LEU* 3.4 17.9 - - + +
343D ASP* 3.1 38.6 + - - +
346D ILE* 3.9 12.8 - - + -
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Residues in contact with VAL 169 (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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70D THR* 3.6 22.9 - - + +
90D ILE* 3.5 6.3 - - + +
160D ILE* 4.0 7.6 - - + -
164D ALA* 3.8 29.6 - - + -
165D PRO 3.0 21.8 + - - +
168D LYS* 1.3 69.9 - - - +
170D CYS* 1.3 64.4 + - - +
171D LEU 3.1 2.7 - - - -
172D ILE* 2.9 36.2 + - + +
332D VAL* 4.5 12.8 - - + -
335D PHE* 3.4 35.9 - - + -
342D LEU* 4.2 0.7 - - - -
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Residues in contact with CYS 170 (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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42D ALA* 3.8 5.6 - - - +
44D GLY 4.3 7.6 - - - -
68D GLU* 3.1 16.3 - - - +
69D ALA* 3.7 24.6 + - - +
70D THR* 3.0 23.4 + - - +
166D PRO 3.3 12.7 + - - +
167D GLU 4.1 6.5 - - - -
168D LYS 3.0 2.2 + - - -
169D VAL* 1.3 77.5 - - - +
171D LEU* 1.3 64.1 + - - +
173D GLY* 2.8 19.8 + - - -
371D VAL* 3.6 36.6 - - - -
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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