Contacts of the helix formed by residues 104 - 116 (chain C) in PDB entry 3RKR
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 LYS 104 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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60A HIS* 5.4 13.6 - - - -
120B TYR* 3.1 6.5 + - - -
124B ARG* 4.6 6.1 - - - +
102C THR 3.7 4.9 + - - +
103C MET* 1.3 69.3 - - - +
105C PRO* 1.3 75.9 - - + +
106C ALA* 4.1 9.9 - - + +
107C GLU* 2.9 47.2 + - + +
108C TRP 2.9 10.4 + - - -
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Residues in contact with PRO 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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67B SER* 5.2 10.5 - - - +
117B LYS* 5.0 9.4 - - - +
120B TYR* 3.0 17.7 - - + +
121B LEU* 3.9 15.3 - - + -
124B ARG* 3.6 32.8 - - - +
104C LYS* 1.3 85.1 - - + +
106C ALA* 1.3 57.1 + - - +
108C TRP* 3.3 5.3 + - + +
109C ASP* 2.9 35.7 + - - +
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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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104C LYS* 3.0 8.7 + - + +
105C PRO* 1.3 79.1 - - - +
107C GLU* 1.3 58.2 - - + +
109C ASP* 3.3 11.1 + - - +
110C ALA* 2.9 29.6 + - - +
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Residues in contact with GLU 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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95C TRP* 3.1 39.7 + - + +
102C THR 4.5 1.0 - - - +
103C MET* 3.6 13.5 - - + +
104C LYS* 2.9 51.3 + - + +
106C ALA* 1.3 76.2 - - + +
108C TRP* 1.3 65.5 + - - +
110C ALA* 3.4 7.1 + - - +
111C LEU* 3.2 23.9 + - - +
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Residues in contact with TRP 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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112B ILE* 5.7 2.9 - - + +
116B LEU* 3.7 36.1 - - + -
117B LYS* 3.5 42.0 - - + +
120B TYR* 3.5 42.2 - + + +
166B LEU* 3.7 29.2 - - + -
100C LEU* 4.6 0.4 - - + -
103C MET* 3.7 15.7 - - - +
104C LYS 2.9 8.1 + - - +
105C PRO 3.4 7.0 - - - +
107C GLU* 1.3 77.2 - - - +
109C ASP* 1.3 80.2 + - - +
111C LEU* 3.7 1.4 - - - +
112C ILE* 3.0 52.9 + - + +
155C ALA* 3.7 24.0 - - + -
158C ALA* 5.0 1.6 - - + -
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Residues in contact with ASP 109 (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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117B LYS* 2.8 30.7 + - - +
105C PRO* 2.9 24.3 + - - +
106C ALA* 3.6 11.3 - - - +
107C GLU 3.3 0.2 - - - -
108C TRP* 1.3 83.5 - - - +
110C ALA* 1.3 57.9 + - - +
112C ILE* 4.3 2.2 - - - +
113C ALA* 2.9 33.1 + - - +
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Residues in contact with ALA 110 (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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65C SER* 5.0 6.0 - - - -
93C VAL* 4.3 4.4 - - + +
106C ALA 2.9 16.5 + - - +
107C GLU* 3.9 7.0 - - - +
108C TRP 3.3 0.2 - - - -
109C ASP* 1.3 77.7 - - - +
111C LEU* 1.3 62.6 + - - +
113C ALA* 3.8 4.4 - - - +
114C VAL* 3.4 27.4 + - - +
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Residues in contact with LEU 111 (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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93C VAL* 3.7 17.9 - - + +
94C GLY 4.0 7.0 - - - +
95C TRP* 3.8 37.0 - - + +
103C MET* 4.4 7.9 - - + -
107C GLU 3.2 15.9 + - - +
108C TRP 3.7 3.4 - - - +
109C ASP 3.2 0.4 - - - -
110C ALA* 1.3 75.6 - - - +
112C ILE* 1.3 66.5 + - + +
113C ALA 3.4 0.2 + - - -
114C VAL* 3.5 0.9 + - - -
115C ASN* 2.9 42.5 + - - +
155C ALA* 3.7 13.7 - - + +
156C TYR* 4.0 17.7 - - + +
159C SER* 3.5 32.3 - - - +
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Residues in contact with ILE 112 (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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108B TRP* 5.7 1.8 - - + +
112B ILE* 4.7 17.3 - - + -
116B LEU* 4.4 11.4 - - + -
108C TRP* 3.0 60.3 + - + +
109C ASP* 4.3 2.2 - - - +
111C LEU* 1.3 82.4 - - + +
113C ALA* 1.3 62.9 + - - +
116C LEU* 2.9 39.2 + - + +
117C LYS* 3.0 14.5 + - + +
155C ALA* 4.3 6.3 - - + +
158C ALA* 5.2 0.4 - - + -
159C SER* 4.0 25.4 - - - +
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Residues in contact with ALA 113 (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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64C LEU 4.0 4.4 - - - +
65C SER* 3.9 28.7 - - - +
109C ASP 2.9 19.9 + - - +
110C ALA* 3.8 5.2 - - - +
111C LEU 3.2 0.2 - - - -
112C ILE* 1.3 77.9 - - - +
114C VAL* 1.3 57.6 + - - +
117C LYS* 3.6 16.7 - - + +
118C ALA* 2.9 30.0 + - - +
121C LEU* 5.7 0.2 - - - +
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Residues in contact with VAL 114 (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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63C ASP* 5.6 0.4 - - - +
64C LEU* 4.3 18.2 - - + +
65C SER* 4.1 24.0 - - - +
91C ALA* 4.2 10.0 - - + +
92C GLY* 4.1 16.6 - - - +
93C VAL* 4.3 20.2 - - + -
110C ALA 3.4 16.6 + - - +
111C LEU 4.2 1.3 - - - +
113C ALA* 1.3 77.2 - - - +
115C ASN* 1.3 74.5 + - - +
118C ALA* 3.5 9.7 - - - +
119C PRO* 3.4 17.2 - - - +
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Residues in contact with ASN 115 (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 ALA 5.2 2.9 - - - -
92C GLY* 3.3 7.4 - - - -
93C VAL* 2.8 46.0 + - - +
111C LEU* 2.9 30.4 + - - +
114C VAL* 1.3 72.7 - - - +
116C LEU* 1.3 58.6 + - - +
119C PRO* 3.7 13.0 - - - +
156C TYR* 3.9 3.0 - - - -
159C SER* 3.0 37.8 + - - +
160C LYS* 3.8 23.3 + - - +
163C LEU* 4.1 12.6 - - - +
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Residues in contact with LEU 116 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108B TRP* 3.9 21.0 - - + -
112B ILE* 4.4 8.3 - - + -
116B LEU* 3.9 26.9 - - + -
158B ALA* 4.3 7.6 - - + +
112C ILE* 2.9 26.9 + - + +
114C VAL 3.5 0.2 - - - -
115C ASN* 1.3 78.6 - - - +
117C LYS* 1.3 70.3 + - - +
118C ALA 3.5 0.7 - - - -
119C PRO* 3.4 8.2 - - - +
120C TYR 3.7 6.6 + - - -
159C SER* 4.0 15.9 - - - +
162C GLY* 3.5 14.4 - - - +
163C LEU* 3.5 34.1 - - + +
166C LEU* 4.0 14.9 - - + +
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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