Contacts of the helix formed by residues 99 - 104 (chain D) in PDB entry 2PKG
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 GLN 99 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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515A ASP* 5.7 4.3 + - - +
519A LYS* 3.4 47.7 - - + +
520A HIS* 5.1 1.9 + - - -
97D CYS* 4.1 2.3 + - - -
98D LYS* 1.3 94.6 - - + +
100D TRP* 1.3 69.4 + - - +
101D PRO* 4.1 5.0 - - - +
102D GLU* 3.3 26.7 + - + +
103D CYS* 3.3 13.5 + - - +
108D SER* 4.5 7.9 - - - +
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Residues in contact with TRP 100 (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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475A LYS* 5.0 3.1 - - - +
476A GLU* 2.8 23.6 + - - -
516A ILE* 5.9 2.9 - - + -
92D VAL* 6.1 2.0 - - + -
97D CYS* 4.0 11.1 - - - -
99D GLN* 1.3 70.5 - - - +
101D PRO* 1.3 96.4 - - + +
102D GLU 2.5 4.5 + - - -
103D CYS* 3.3 6.8 + - - +
104D ALA* 3.4 22.3 + - + -
115D LEU* 4.5 2.2 - - + -
141D PHE* 3.9 23.1 - + - -
152D LEU* 3.7 27.1 - - + -
153D CYS* 3.5 28.9 - - - -
154D GLU* 3.3 40.2 - - + +
157D LEU* 3.3 35.9 - - + -
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Residues in contact with PRO 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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476A GLU* 5.3 8.5 - - + +
479A HIS* 3.5 39.7 - - + +
515A ASP* 6.5 0.7 - - + -
516A ILE* 5.1 14.4 - - + -
520A HIS* 5.4 0.9 - - + +
99D GLN* 4.1 4.7 - - - +
100D TRP* 1.3 117.1 - - + +
102D GLU* 1.3 76.0 + - - +
104D ALA* 3.7 5.5 - - - +
105D LYS* 3.1 29.8 - - - +
152D LEU* 5.3 1.7 - - + +
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Residues in contact with GLU 102 (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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479A HIS* 2.8 30.6 + - + +
520A HIS* 3.1 17.4 + - - -
99D GLN* 3.3 28.2 - - + +
100D TRP 2.5 5.9 + - - -
101D PRO* 1.3 91.7 - - - +
103D CYS* 1.3 57.0 + - - +
104D ALA 2.9 2.2 - - - -
105D LYS* 2.5 30.7 + - - +
107D MET* 3.2 43.9 + - + +
108D SER* 3.8 12.3 - - - +
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Residues in contact with CYS 103 (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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97D CYS* 3.6 15.3 - - - -
98D LYS 2.6 34.5 - - - -
99D GLN 3.3 7.0 + - - +
100D TRP 3.3 1.6 + - - -
102D GLU* 1.3 77.5 - - - +
104D ALA* 1.3 61.4 + - - +
105D LYS 3.0 1.0 + - - -
106D LYS 3.3 4.4 + - - +
108D SER* 3.1 19.6 + - - +
111D CYS* 3.6 3.4 - - - -
113D CYS* 4.3 1.6 - - - -
115D LEU* 4.3 6.0 - - + +
116D CYS* 3.8 6.8 - - - -
119D ARG* 3.2 22.7 + - - -
175D ZN 2.3 35.4 - - - -
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Residues in contact with ALA 104 (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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100D TRP* 3.4 39.9 + - + +
101D PRO 3.7 12.8 - - - +
102D GLU 2.8 3.0 + - - -
103D CYS* 1.3 76.1 - - - +
105D LYS* 1.3 60.1 + - - +
106D LYS 3.7 0.4 - - - -
115D LEU* 4.4 12.2 - - + +
119D ARG* 3.8 9.6 + - - +
141D PHE* 4.5 4.8 - - + -
142D ASP* 4.6 10.9 - - - +
145D ARG* 5.7 0.2 + - - -
152D LEU* 3.8 20.4 - - + +
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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