Contacts of the helix formed by residues 99 - 104 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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515B ASP* 3.0 43.5 + - - +
518B THR* 5.9 1.8 - - - -
519B LYS* 3.7 45.0 - - + +
97C CYS* 3.8 3.2 + - - -
98C LYS* 1.3 96.5 - - + +
100C TRP* 1.3 68.5 + - - +
101C PRO* 4.1 3.0 - - - +
102C GLU* 3.3 26.2 + - + +
103C CYS* 3.4 12.4 + - - +
108C SER* 5.4 3.4 - - - -
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Residues in contact with TRP 100 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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475B LYS* 4.6 4.7 - - + -
476B GLU* 2.8 29.8 + - - -
515B ASP* 4.1 18.3 + - + +
516B ILE* 5.5 2.7 - - + -
92C VAL* 6.3 1.8 - - + -
97C CYS* 4.0 11.8 + - - -
99C GLN* 1.3 71.6 - - - +
101C PRO* 1.3 95.1 - - + +
102C GLU* 2.5 6.4 + - - -
103C CYS* 3.4 3.6 + - - +
104C ALA* 3.3 29.8 + - + -
115C LEU* 4.6 2.0 - - + -
141C PHE* 3.8 28.9 - + - -
152C LEU* 3.8 10.8 - - + -
153C CYS* 3.5 24.0 - - - -
154C GLU* 3.4 38.7 - - + +
157C LEU* 3.5 33.2 - - + -
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Residues in contact with PRO 101 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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476B GLU* 5.0 8.1 - - + +
479B HIS* 3.8 16.8 - - + +
515B ASP* 4.5 7.2 - - + -
516B ILE* 3.3 39.5 - - + -
520B HIS* 6.0 0.2 - - + -
99C GLN* 4.7 2.5 - - - +
100C TRP* 1.3 116.8 - - + +
102C GLU* 1.3 80.0 + - - +
104C ALA* 3.6 7.3 - - - +
105C LYS* 3.1 27.7 - - + +
152C LEU* 5.3 3.6 - - + +
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Residues in contact with GLU 102 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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479B HIS* 2.7 27.5 + - - -
519B LYS* 4.4 11.4 - - + +
520B HIS* 3.4 15.1 + - - -
99C GLN* 3.3 29.9 - - + +
100C TRP 2.5 6.7 + - - -
101C PRO* 1.3 89.6 - - - +
103C CYS* 1.3 56.7 + - - +
104C ALA 2.9 2.5 - - - -
105C LYS* 2.4 40.7 + - - +
107C MET* 3.1 37.9 - - + -
108C SER* 4.0 8.3 - - - +
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Residues in contact with CYS 103 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97C CYS* 4.1 9.4 - - - -
98C LYS 2.6 31.0 - - - +
99C GLN 3.4 6.1 + - - +
102C GLU* 1.3 77.3 - - - +
104C ALA* 1.3 58.3 + - - +
105C LYS 2.9 6.1 + - - -
106C LYS 3.3 5.0 + - - +
107C MET 4.6 1.1 - - - +
108C SER* 3.0 21.0 + - - -
111C CYS* 3.4 3.4 - - - -
113C CYS* 3.6 9.0 - - - -
115C LEU* 4.4 5.7 - - + +
116C CYS* 3.7 5.0 - - - -
119C ARG* 3.2 21.8 + - - -
175C ZN 2.2 37.9 - - - -
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Residues in contact with ALA 104 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100C TRP* 3.3 40.8 + - + -
101C PRO 3.6 11.9 - - - +
102C GLU 2.7 4.6 + - - -
103C CYS* 1.3 75.0 - - - +
105C LYS* 1.3 57.7 + - - +
115C LEU* 4.2 13.7 - - - +
119C ARG* 3.8 8.6 + - - +
141C PHE* 4.4 5.8 - - + -
142C ASP* 4.5 11.8 - - - +
152C LEU* 3.9 19.2 - - + +
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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