Contacts of the helix formed by residues 97 - 101 (chain D) in PDB entry 1DGH
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 ALA 97 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95D SER* 3.2 17.4 + - - +
96D LYS* 1.3 81.2 - - - +
98D LYS* 1.3 65.3 + - - +
99D VAL* 4.0 11.9 - - + -
100D PHE* 3.0 29.0 + - + +
101D GLU* 3.3 7.8 + - - -
340D PRO* 4.6 5.2 - - + -
341D PRO 3.2 21.7 + - - +
342D GLY* 3.8 0.2 - - - -
343D ILE* 4.0 14.1 - - + -
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Residues in contact with LYS 98 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96D LYS 3.3 4.8 + - - +
97D ALA* 1.3 72.4 - - - +
99D VAL* 1.3 63.1 + - - +
100D PHE 3.0 2.2 + - - -
101D GLU* 3.0 30.1 + - - +
105D LYS* 3.0 23.5 + - - +
138D THR* 5.5 1.3 - - - +
139D GLU* 3.9 39.9 + - + +
140D ASP* 3.7 43.4 + - + +
340D PRO* 5.8 1.2 - - - +
341D PRO 4.6 1.0 + - - -
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Residues in contact with VAL 99 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85D PHE* 3.7 27.5 - - + -
87D VAL* 3.2 18.4 - - - +
97D ALA* 4.0 9.6 - - + -
98D LYS* 1.3 77.3 - - - +
100D PHE* 1.3 86.2 + - + +
105D LYS* 4.6 5.5 - - - +
107D THR* 3.8 22.2 + - - +
136D PHE* 4.1 16.6 - - + -
138D THR* 3.9 23.5 - - + -
139D GLU* 4.8 1.3 + - - -
143D TRP* 3.9 13.9 - - + -
340D PRO* 5.3 2.7 - - + +
343D ILE* 4.6 1.6 - - + -
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Residues in contact with PHE 100 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85D PHE* 4.0 23.8 - + - -
87D VAL* 3.8 17.2 - - + +
89D HIS 5.2 1.0 - - - +
90D ASP* 5.8 0.7 - - - -
91D ILE* 3.8 33.4 + - + -
92D THR* 4.0 11.1 - - + +
95D SER* 3.9 19.7 - - - +
97D ALA* 3.0 18.2 + - + +
98D LYS 3.0 0.8 - - - -
99D VAL* 1.3 93.9 - - + +
101D GLU* 1.3 65.3 + - - +
102D HIS* 2.9 6.5 + - - -
143D TRP* 3.7 31.2 - + - -
222D LEU* 4.9 4.5 - - + -
234D PHE* 4.6 8.1 - + - -
279D PHE* 4.8 4.5 - + - -
281D ILE* 6.0 0.2 - - + -
313D VAL* 4.1 17.9 - - + -
343D ILE* 3.9 15.7 - - + -
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Residues in contact with GLU 101 (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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90D ASP* 5.1 1.4 - - - +
92D THR* 3.8 20.3 - - - +
96D LYS 5.5 2.7 - - - +
97D ALA 3.3 5.7 + - - +
98D LYS* 3.0 42.2 + - - +
99D VAL 3.6 0.2 - - - -
100D PHE* 1.3 76.4 - - - +
102D HIS* 1.3 77.3 + - + +
105D LYS* 2.8 29.2 + - + +
139D GLU* 4.1 3.5 - - - +
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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