Contacts of the helix formed by residues 108 - 124 (chain B) in PDB entry 1GKU
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 108 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106B PHE* 3.2 1.3 - - - +
107B PRO* 1.3 85.5 + - - +
109B SER* 1.3 66.7 + - - +
110B LEU* 2.9 26.9 - - + +
111B LEU* 3.2 31.6 + - + +
112B VAL* 3.2 25.6 + - - +
162B THR* 4.0 5.8 - - - -
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Residues in contact with SER 109 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108B THR* 1.3 72.4 - - - +
110B LEU* 1.3 66.9 + - - +
112B VAL* 3.3 13.5 + - - +
113B ILE* 3.4 17.9 + - - +
138B HIS* 2.8 15.1 + - - +
139B GLY* 2.7 33.1 + - - -
140B ARG* 4.6 3.4 + - - +
162B THR* 4.0 13.4 - - - +
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Residues in contact with LEU 110 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108B THR* 2.9 12.8 - - + +
109B SER* 1.3 79.7 - - - +
111B LEU* 1.3 64.1 + - + +
113B ILE* 3.2 20.0 + - + +
114B GLN* 3.2 36.3 + - + +
140B ARG* 5.4 11.7 - - - +
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Residues in contact with LEU 111 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106B PHE* 3.9 26.2 - - + -
107B PRO* 4.0 23.6 - - + -
108B THR* 3.2 31.3 - - + +
109B SER 3.2 0.2 - - - -
110B LEU* 1.3 78.1 - - + +
112B VAL* 1.3 58.8 + - - +
114B GLN* 3.4 23.9 + - - +
115B ALA* 2.9 30.3 + - - +
182B ASP* 4.9 6.3 - - - +
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Residues in contact with VAL 112 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106B PHE* 3.9 15.5 - - + -
108B THR 3.2 16.8 + - - +
109B SER* 3.3 8.2 + - - +
111B LEU* 1.3 76.0 - - - +
113B ILE* 1.3 57.1 + - - +
115B ALA* 3.4 2.4 - - - +
116B ALA* 3.0 27.0 + - - +
136B TYR* 3.9 19.1 - - + -
137B TYR 3.5 17.7 - - - +
138B HIS* 4.6 2.7 - - + -
160B ILE* 3.7 21.1 - - + +
161B THR 3.8 27.1 - - - +
162B THR* 3.9 11.4 - - + -
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Residues in contact with ILE 113 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109B SER 3.4 13.9 - - - +
110B LEU* 3.2 12.5 + - + +
112B VAL* 1.3 74.9 - - - +
114B GLN* 1.3 67.6 + - + +
116B ALA* 3.0 6.8 + - + +
117B GLU* 2.8 46.5 + - + +
136B TYR* 4.1 18.6 - - + +
138B HIS* 2.8 43.5 - - + +
140B ARG* 6.2 3.1 - - - +
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Residues in contact with GLN 114 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110B LEU* 3.2 35.6 + - + +
111B LEU* 3.7 29.1 - - - +
113B ILE* 1.3 78.5 - - + +
115B ALA* 1.3 54.4 + - - +
117B GLU* 3.1 14.1 + - - +
118B THR* 2.6 44.0 + - - +
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Residues in contact with ALA 115 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89B LEU* 4.2 16.4 - - + -
106B PHE* 3.1 41.1 - - + -
111B LEU 2.9 9.9 + - - +
112B VAL 3.4 5.4 - - - +
114B GLN* 1.3 76.0 - - - +
116B ALA* 1.3 58.0 + - - +
118B THR* 3.0 3.7 + - - -
119B ILE* 2.8 33.5 + - - +
160B ILE* 4.0 12.3 - - + -
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Residues in contact with ALA 116 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112B VAL 3.0 14.5 + - - +
113B ILE* 3.4 11.0 - - + +
115B ALA* 1.3 76.1 - - - +
117B GLU* 1.3 62.2 + - + +
119B ILE* 4.1 3.8 - - - +
120B ARG* 3.3 22.7 + - - +
131B GLU* 5.6 1.2 - - - +
134B ILE* 4.9 8.3 - - + +
136B TYR* 3.9 33.7 - - + -
160B ILE* 4.0 13.2 - - + +
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Residues in contact with GLU 117 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113B ILE* 2.8 39.7 + - + +
114B GLN* 3.6 15.2 - - - +
116B ALA* 1.3 71.6 - - + +
118B THR* 1.3 61.7 + - - +
120B ARG* 3.3 7.3 + - - +
121B LYS* 3.0 47.0 + - - +
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Residues in contact with THR 118 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89B LEU* 4.1 15.2 - - + +
114B GLN* 2.6 26.3 + - - +
115B ALA 3.4 4.5 - - - -
117B GLU* 1.3 71.7 - - - +
119B ILE* 1.3 67.0 + - - +
121B LYS* 2.9 16.6 + - + +
122B TYR* 2.9 55.3 + - + +
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Residues in contact with ILE 119 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89B LEU* 3.5 48.7 - - + +
92B SER* 4.9 2.9 - - - +
93B LEU* 4.2 23.9 - - + +
104B VAL* 5.2 0.4 - - + -
115B ALA 2.8 18.4 + - - +
116B ALA* 4.1 5.6 - - - +
118B THR* 1.3 72.7 - - - +
120B ARG* 1.3 59.4 + - - +
122B TYR* 3.3 10.5 + - - +
123B ALA* 3.0 24.8 + - + +
128B VAL* 5.6 2.2 - - + -
134B ILE* 5.2 13.5 - - + -
158B ILE* 4.2 24.9 - - + -
160B ILE* 3.8 21.5 - - + -
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Residues in contact with ARG 120 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116B ALA 3.3 12.0 + - - +
117B GLU* 3.5 10.8 - - - +
118B THR 3.1 0.6 - - - -
119B ILE* 1.3 78.4 - - - +
121B LYS* 1.3 66.4 + - + +
123B ALA* 3.3 10.5 + - - +
124B GLU* 3.2 29.6 + - - +
128B VAL* 4.0 22.5 - - - +
130B THR* 5.0 6.1 - - - +
131B GLU* 3.7 47.2 + - - +
134B ILE* 5.4 3.6 - - - -
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Residues in contact with LYS 121 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117B GLU* 3.0 32.8 + - - +
118B THR* 2.9 17.8 + - + +
120B ARG* 1.3 75.0 - - + +
122B TYR* 1.3 62.2 + - + +
124B GLU* 2.7 35.4 - - - +
125B LYS* 3.2 14.2 + - - +
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Residues in contact with TYR 122 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49B PHE* 6.0 0.5 - - - -
53B CYS* 3.3 41.8 - - - -
54B VAL* 3.6 24.9 - - + +
86B SER* 3.4 30.6 + - - -
89B LEU* 3.9 27.8 - - + -
90B ALA* 4.1 7.9 - - + -
93B LEU* 3.7 11.4 - - + +
118B THR* 2.9 39.4 + - + +
119B ILE* 3.5 13.9 - - - +
121B LYS* 1.3 74.4 - - + +
123B ALA* 1.3 55.8 + - - +
124B GLU 2.7 15.6 + - - -
125B LYS* 3.2 25.7 + - - +
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Residues in contact with ALA 123 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93B LEU* 3.9 8.5 - - + +
119B ILE 3.0 13.1 + - - +
120B ARG* 3.3 17.5 + - - +
122B TYR* 1.3 75.9 - - - +
124B GLU* 1.3 50.6 + - - +
125B LYS 2.5 16.2 + - - -
126B ALA* 3.1 1.4 + - - -
127B GLY* 2.6 33.5 + - - +
128B VAL* 3.3 35.4 - - + +
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Residues in contact with GLU 124 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120B ARG* 3.2 23.3 + - - +
121B LYS* 2.7 25.9 + - - +
122B TYR 2.7 1.4 + - - -
123B ALA* 1.3 72.8 - - - +
125B LYS* 1.3 77.6 + - + +
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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