Contacts of the helix formed by residues 99 - 108 (chain C) in PDB entry 2CKJ
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 HIS 99 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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91C ILE* 3.4 31.9 - - + +
92C GLY* 4.1 0.8 - - - -
97C ARG 3.6 2.0 + - - -
98C LEU* 1.3 73.4 - - - +
100C PRO* 1.3 76.4 - - + +
101C VAL* 2.7 45.8 + - + +
102C GLN* 2.5 42.2 + - - +
103C GLU 2.9 8.7 + - - -
125C TYR* 3.7 15.2 - + - -
128C LEU* 5.7 1.3 - - + -
204C LEU* 3.8 12.2 - - + +
209C GLU* 2.8 40.2 + - - -
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Residues in contact with PRO 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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98C LEU 3.6 4.2 - - - +
99C HIS* 1.3 90.5 - - + +
101C VAL* 1.3 60.9 + - - +
102C GLN 3.0 0.2 - - - -
103C GLU* 3.7 12.3 - - + +
104C ARG* 3.3 37.3 + - - +
163C PHE* 3.8 5.7 - - + -
202C THR* 3.6 28.0 - - - +
204C LEU* 3.5 40.2 - - + +
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Residues in contact with VAL 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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91C ILE* 5.3 1.1 - - + -
99C HIS* 2.7 32.7 + - + +
100C PRO* 1.3 72.4 - - - +
102C GLN* 1.3 63.7 + - - +
105C ILE* 3.9 19.1 + - - +
121C VAL* 3.9 23.2 - - + +
124C MET* 3.7 28.5 - - + -
125C TYR* 4.5 13.5 - - + +
128C LEU* 4.0 25.6 - - + -
160C PHE* 4.0 14.4 - - + -
163C PHE* 4.2 11.0 - - + -
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Residues in contact with GLN 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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88C VAL* 4.0 13.3 + - - +
91C ILE* 3.9 19.4 - - + +
92C GLY* 3.4 30.6 + - - +
98C LEU* 3.8 12.0 - - + +
99C HIS* 2.5 31.0 + - - +
101C VAL* 1.3 82.8 - - - +
103C GLU* 1.3 60.7 + - - +
105C ILE* 3.4 19.9 - - - +
106C ALA* 3.6 4.0 + - - +
121C VAL* 4.1 12.1 - - + -
587C ALA* 3.2 38.2 + - + +
588C SER* 3.6 11.4 - - - +
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Residues in contact with GLU 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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98C LEU* 3.8 31.8 - - + +
99C HIS 2.9 8.1 + - - +
100C PRO* 3.6 15.7 + - + +
102C GLN* 1.3 77.6 - - - +
104C ARG* 1.3 70.3 + - + +
106C ALA* 3.4 4.2 + - - +
107C LYS* 3.3 54.2 + - + +
201C PHE* 3.8 3.5 - - + -
202C THR* 2.7 48.6 + - - +
584C ASP* 5.2 0.6 - - - +
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Residues in contact with ARG 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 PRO* 3.3 15.2 + - - +
101C VAL 4.9 0.7 - - - +
103C GLU* 1.3 77.8 - - + +
105C ILE* 1.3 61.7 + - - +
106C ALA 3.1 1.9 + - - -
107C LYS 3.7 0.4 + - - +
108C SER* 2.9 28.9 + - - -
159C GLY* 4.7 2.2 - - - +
160C PHE* 5.0 5.4 - - + -
162C THR* 2.6 44.5 + - + -
163C PHE* 3.4 48.3 - - + -
201C PHE* 3.2 50.0 + - + +
202C THR 3.1 27.3 + - - -
203C PRO* 3.7 19.4 + - - +
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Residues in contact with ILE 105 (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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101C VAL 3.9 8.9 + - - +
102C GLN* 3.4 14.5 + - - +
104C ARG* 1.3 78.9 - - - +
106C ALA* 1.3 63.9 + - - +
108C SER* 3.6 6.7 + - - -
110C GLY* 3.3 49.9 + - - +
111C SER* 4.9 0.9 - - - +
117C THR* 3.9 24.0 - - + +
120C ILE* 5.1 9.6 - - + -
121C VAL* 4.8 8.7 - - + -
156C ILE* 4.4 17.3 - - + -
159C GLY* 5.7 1.1 - - - -
160C PHE* 3.8 33.1 - - + -
587C ALA* 4.2 13.7 - - + -
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Residues in contact with ALA 106 (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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98C LEU* 5.9 0.2 - - + -
102C GLN 3.6 8.3 + - - +
103C GLU* 3.4 7.0 + - - +
104C ARG 3.1 0.6 - - - -
105C ILE* 1.3 82.4 - - - +
107C LYS* 1.3 57.6 + - - +
108C SER 3.2 6.0 + - - -
109C HIS* 3.9 8.0 + - - -
110C GLY 4.8 0.8 + - - +
111C SER* 5.2 2.7 - - - -
579C PRO* 4.5 8.1 - - - +
583C ALA* 3.6 40.4 - - + +
584C ASP* 3.6 24.6 - - - +
587C ALA* 4.3 5.2 - - + -
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Residues in contact with LYS 107 (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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103C GLU* 3.3 47.3 + - + +
104C ARG 3.7 1.1 + - - +
105C ILE 3.6 0.2 - - - -
106C ALA* 1.3 72.6 - - - +
108C SER* 1.3 57.4 + - - +
109C HIS* 3.4 12.3 + - - -
196C PHE* 3.4 20.6 - - + +
200C GLU* 3.5 46.9 + - - +
201C PHE* 4.2 20.2 - - + +
202C THR* 6.2 0.8 - - - +
579C PRO* 5.2 11.6 - - + +
584C ASP* 5.3 6.7 - - - +
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Residues in contact with SER 108 (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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104C ARG 2.9 21.1 + - - -
105C ILE* 3.6 8.8 + - - +
106C ALA 3.2 0.4 - - - -
107C LYS* 1.3 77.7 - - - +
109C HIS* 1.3 73.8 + - - +
110C GLY* 4.5 1.4 + - - -
154C ARG* 4.6 2.6 + - - -
155C PRO* 3.6 16.8 + - - +
159C GLY* 3.8 17.0 - - - -
196C PHE* 3.7 43.2 - - - -
201C PHE* 4.6 2.0 - - - -
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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