Contacts of the helix formed by residues 105 - 118 (chain A) in PDB entry 2FK8
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 SER 105 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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103A THR* 3.1 3.6 + - - +
104A LEU* 1.3 77.6 - - - +
106A LYS* 1.3 58.9 + - - +
107A ASN* 3.4 9.0 + - - +
108A GLN* 2.9 47.1 + - - +
109A HIS* 3.0 23.9 + - - +
129A LEU* 3.4 7.8 - - - +
302A SAM 3.7 3.7 + - - -
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Residues in contact with LYS 106 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104A LEU 3.9 1.4 + - - -
105A SER* 1.3 72.1 + - - +
107A ASN* 1.3 58.3 + - - +
109A HIS* 3.4 5.3 + - - +
110A ALA* 3.1 27.4 + - - +
129A LEU* 3.7 24.6 - - + +
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Residues in contact with ASN 107 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27A VAL 4.5 10.9 + - - -
28A SER* 4.6 3.8 - - - +
29A ASP* 3.6 37.7 + - - +
105A SER* 3.6 7.3 + - - +
106A LYS* 1.3 75.4 - - - +
108A GLN* 1.3 64.9 + - - +
110A ALA* 3.2 7.2 + - - +
111A ARG* 3.1 22.9 + - - +
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Residues in contact with GLN 108 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83A GLY* 3.3 26.2 - - - +
84A TRP* 3.5 51.8 - - + -
103A THR* 2.7 24.0 + - + +
105A SER* 2.9 26.6 + - - +
107A ASN* 1.3 71.4 - - + +
109A HIS* 1.3 66.0 + - - +
111A ARG* 4.0 0.5 - - - +
112A CYS* 2.9 29.8 + - - -
302A SAM 2.4 41.9 + - - -
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Residues in contact with HIS 109 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103A THR* 3.9 10.7 - - + +
105A SER 3.0 15.0 + - - +
106A LYS* 3.5 10.2 + - - +
107A ASN 3.2 0.2 - - - -
108A GLN* 1.3 76.9 - - - +
110A ALA* 1.3 64.7 + - - +
112A CYS* 3.7 1.7 - - - +
113A GLU* 3.0 56.1 + - - +
127A VAL* 3.1 42.4 + - + +
128A LEU* 3.8 1.8 - - - -
129A LEU* 3.6 37.2 + - + +
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Residues in contact with ALA 110 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106A LYS 3.1 14.0 + - - +
107A ASN* 3.2 8.9 + - - +
109A HIS* 1.3 79.2 + - - +
111A ARG* 1.3 64.1 + - - +
113A GLU* 3.3 23.6 + - - +
114A GLN* 3.1 24.4 + - - +
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Residues in contact with ARG 111 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29A ASP* 5.0 2.5 - - - +
38A PRO 4.8 5.1 + - - -
39A THR 5.2 1.4 + - - -
40A ARG* 3.5 51.4 - - - +
84A TRP* 3.8 38.2 + - + +
107A ASN 3.1 16.6 + - - +
108A GLN 4.0 2.9 - - - +
110A ALA* 1.3 75.7 - - - +
112A CYS* 1.3 59.5 + - - +
114A GLN* 3.0 15.3 + - + +
115A VAL* 2.9 36.5 + - + +
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Residues in contact with CYS 112 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82A CYS* 4.0 8.7 - - - -
83A GLY 3.2 27.4 - - - -
84A TRP 3.6 1.3 - - - -
85A GLY* 3.4 24.2 - - - -
88A MET* 4.0 13.7 - - + -
108A GLN 2.9 18.6 + - - +
109A HIS 3.7 0.4 - - - +
111A ARG* 1.3 74.6 - - - +
113A GLU* 1.3 60.2 + - - +
115A VAL* 4.3 6.3 - - - -
116A LEU* 2.8 35.3 + - - +
127A VAL* 3.7 22.2 - - + -
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Residues in contact with GLU 113 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109A HIS* 3.0 40.9 + - + +
110A ALA* 3.5 16.7 - - - +
112A CYS* 1.3 76.2 - - - +
114A GLN* 1.3 58.4 + - + +
116A LEU* 4.0 2.8 - - - +
117A ALA* 2.9 34.6 + - - +
127A VAL* 3.7 18.6 - - + +
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Residues in contact with GLN 114 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110A ALA* 3.1 25.5 + - - +
111A ARG* 3.0 12.9 + - + +
113A GLU* 1.3 76.9 - - + +
115A VAL* 1.3 62.7 + - + +
117A ALA* 4.2 3.3 - - - +
118A SER* 2.9 29.6 + - - -
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Residues in contact with VAL 115 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84A TRP 3.7 16.4 - - - +
85A GLY* 4.0 14.6 - - - +
89A ARG* 3.7 52.2 + - + +
111A ARG* 2.9 30.9 + - + +
112A CYS* 3.7 9.0 - - - +
114A GLN* 1.3 75.1 - - + +
116A LEU* 1.3 66.8 + - + +
118A SER* 3.3 15.5 + - - -
119A ILE* 3.4 13.2 - - - +
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Residues in contact with LEU 116 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85A GLY* 4.9 3.1 - - - +
88A MET* 3.7 48.0 - - + -
89A ARG 4.5 2.7 - - - +
99A VAL* 4.2 11.4 - - + -
112A CYS* 2.8 23.2 + - - +
113A GLU* 4.2 2.5 - - - +
115A VAL* 1.3 75.2 - - + +
117A ALA* 1.3 62.1 + - - +
118A SER 3.2 0.9 + - - -
119A ILE* 3.3 25.4 + - + +
125A ARG* 2.9 38.0 + - + +
126A GLN 4.0 20.4 - - - +
127A VAL* 4.0 20.6 - - + +
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Residues in contact with ALA 117 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113A GLU 2.9 19.6 + - - +
114A GLN* 4.3 3.8 - - - +
116A LEU* 1.3 77.7 - - - +
118A SER* 1.3 58.7 + - - +
119A ILE 4.1 1.6 - - - +
125A ARG* 3.1 17.2 + - - +
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Residues in contact with SER 118 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89A ARG* 5.5 2.6 + - - -
114A GLN 2.9 18.4 + - - -
115A VAL* 3.3 7.8 + - - -
116A LEU 3.1 0.2 - - - -
117A ALA* 1.3 78.3 - - - +
119A ILE* 1.3 64.1 + - - +
120A ASP* 3.6 2.3 + - - +
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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