Contacts of the helix formed by residues 109 - 119 (chain I) in PDB entry 6AHU
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 THR 109 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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82I SER 3.9 15.6 + - - -
108I LYS* 1.3 80.3 + - - +
110I GLU* 1.3 58.2 + - + +
111I LYS* 3.7 24.5 - - + +
112I LEU* 3.0 17.4 + - - +
113I PHE* 2.6 34.3 + - - +
135I PHE* 3.8 2.7 - - - -
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Residues in contact with GLU 110 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109I THR* 1.3 72.1 - - + +
111I LYS* 1.3 73.0 + - + +
113I PHE* 3.6 13.3 - - + +
114I HIS* 3.2 21.0 + - - +
135I PHE* 3.8 12.3 - - + -
136I TYR* 4.4 22.8 + - - +
138I LYS* 5.4 13.8 - - + +
141I PRO* 6.0 1.0 - - - +
268L GLU* 5.5 4.1 - - - +
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Residues in contact with LYS 111 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109I THR* 3.2 13.7 - - + +
110I GLU* 1.3 84.7 - - + +
112I LEU* 1.3 62.2 + - - +
114I HIS* 3.5 13.2 + - - +
115I ILE* 3.7 15.8 + - - +
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Residues in contact with LEU 112 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81I VAL* 3.7 33.7 - - + +
82I SER 4.3 9.0 - - - +
83I ASP 3.8 14.6 - - - +
84I PRO* 3.8 23.3 - - + -
87I CYS* 4.5 6.7 - - + -
105I VAL* 5.9 3.1 - - + -
107I PRO* 3.8 25.8 - - + -
108I LYS 4.7 1.8 - - - +
109I THR* 3.0 18.6 + - - +
111I LYS* 1.3 77.4 - - - +
113I PHE* 1.3 60.7 + - - +
114I HIS 3.2 0.4 - - - -
115I ILE* 3.3 23.5 - - + +
116I ALA* 3.1 25.7 + - + +
120I LEU* 6.0 1.3 - - + -
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Residues in contact with PHE 113 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107I PRO* 3.6 23.6 - - + -
109I THR 2.6 18.6 + - - +
110I GLU* 3.8 10.1 - - + +
111I LYS 3.3 0.4 - - - -
112I LEU* 1.3 74.3 - - - +
114I HIS* 1.3 60.7 + - - +
116I ALA* 3.5 5.2 + - + +
117I CYS* 3.3 43.6 + - - -
125I VAL* 4.0 23.6 - - + -
127I ILE* 5.1 3.6 - - + -
135I PHE* 3.6 28.0 - + + -
136I TYR 5.9 0.9 - - - -
137I PHE* 4.8 11.0 - + - -
138I LYS* 5.2 4.5 - - + -
141I PRO* 4.0 20.0 - - + -
142I ILE* 3.7 28.9 - - + -
152I PHE* 3.8 7.4 - + - -
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Residues in contact with HIS 114 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110I GLU 3.2 16.4 + - - +
111I LYS* 3.7 8.3 - - - +
112I LEU 3.2 0.6 - - - -
113I PHE* 1.3 78.8 - - - +
115I ILE* 1.3 68.3 + - - +
117I CYS* 3.4 3.5 + - - +
118I THR* 3.3 37.2 + - + -
119I HIS* 5.4 4.0 - - - -
138I LYS* 5.7 4.5 - - + -
140I PRO 5.8 0.4 - - - -
141I PRO* 4.3 27.7 - - + +
232L GLU* 2.6 36.0 + - - -
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Residues in contact with ILE 115 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84I PRO* 6.4 1.1 - - + -
87I CYS* 3.9 28.9 - - + -
91I ARG* 5.1 6.7 - - - +
111I LYS 3.7 13.2 - - - +
112I LEU* 3.3 30.5 - - + +
114I HIS* 1.3 81.0 - - + +
116I ALA* 1.3 56.7 + - - +
119I HIS* 2.9 36.8 + - + +
120I LEU* 2.6 35.6 + - + +
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Residues in contact with ALA 116 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105I VAL* 4.7 12.1 - - + -
107I PRO* 5.0 9.9 - - + -
112I LEU* 3.1 21.3 + - + +
113I PHE* 3.7 11.7 - - + +
114I HIS 3.2 0.6 - - - -
115I ILE* 1.3 79.8 - - + +
117I CYS* 1.3 62.8 + - - +
120I LEU* 3.4 39.6 - - + +
122I VAL* 4.2 4.7 - - - +
125I VAL* 5.5 4.0 - - + -
150I LEU* 3.8 12.3 - - - +
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Residues in contact with CYS 117 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113I PHE* 3.3 46.0 + - - +
114I HIS 3.4 4.0 + - - +
115I ILE 3.3 0.2 - - - -
116I ALA* 1.3 79.3 - - - +
118I THR* 1.3 61.8 + - - +
125I VAL* 5.2 1.1 - - - -
141I PRO* 3.4 31.2 - - + +
144I VAL* 4.1 9.5 - - + +
145I ALA* 4.1 17.7 - - + +
148I ARG* 3.3 20.9 + - - -
150I LEU* 3.7 14.0 - - - +
152I PHE* 4.4 3.1 - - - -
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Residues in contact with THR 118 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114I HIS* 3.3 29.6 + - + -
116I ALA 3.4 0.2 - - - -
117I CYS* 1.3 80.3 + - - +
119I HIS* 1.3 84.2 + - + +
141I PRO* 5.8 1.2 - - - +
144I VAL* 3.9 23.8 - - + +
148I ARG* 3.0 22.1 + - - +
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Residues in contact with HIS 119 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91I ARG* 3.4 25.7 + - - +
114I HIS* 5.4 6.1 - - - -
115I ILE* 2.9 34.4 + - + +
118I THR* 1.3 95.9 + - + +
120I LEU* 1.3 65.7 + - - +
121I ASP* 3.5 13.7 + - - +
148I ARG* 4.5 0.4 - - - -
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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