Contacts of the helix formed by residues 122 - 135 (chain B) in PDB entry 6JKG
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 TYR 122 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118B TYR* 2.7 65.1 + + + +
121B ASN* 1.3 74.1 - - + +
123B ILE* 1.3 76.4 + - + +
124B GLY 3.3 1.3 - - - -
125B THR* 3.0 4.4 + - - -
126B LYS* 2.8 69.5 + - + +
175B THR* 5.4 2.2 - - - +
178B LEU* 3.9 47.9 - - + +
179B GLN* 4.6 1.8 - - - -
182B ALA* 4.5 7.0 - - + -
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Residues in contact with ILE 123 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86B CYS* 4.3 19.1 - - + +
118B TYR* 3.2 25.0 + - + +
119B ARG* 3.2 27.8 + - + +
122B TYR* 1.3 92.9 - - + +
124B GLY* 1.3 62.3 + - - +
126B LYS* 3.4 10.1 + - + +
127B ASN* 3.2 19.1 + - - +
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Residues in contact with GLY 124 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85B LEU* 3.6 24.1 - - - +
86B CYS* 4.1 13.9 - - - -
103B HIS* 5.3 0.4 - - - -
119B ARG 2.7 20.3 + - - -
120B VAL 4.1 2.7 - - - -
123B ILE* 1.3 72.2 - - - +
125B THR* 1.3 60.6 + - - +
127B ASN* 3.4 3.3 + - - +
128B VAL* 2.8 32.6 + - - +
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Residues in contact with THR 125 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103B HIS* 3.0 26.3 - - - +
120B VAL 3.9 1.9 + - - -
121B ASN 2.8 26.4 + - - -
122B TYR* 3.0 5.7 + - - -
124B GLY* 1.3 75.8 - - - +
126B LYS* 1.3 54.2 + - - +
128B VAL* 3.0 9.3 + - + +
129B ILE* 2.7 45.7 + - + +
140B LEU* 5.9 0.4 - - + -
179B GLN* 3.2 16.9 + - + +
182B ALA* 4.9 2.5 - - + -
183B VAL* 3.6 30.5 - - + -
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Residues in contact with LYS 126 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122B TYR* 2.8 55.9 + - + +
123B ILE* 3.7 12.6 - - + +
124B GLY 3.4 0.2 - - - -
125B THR* 1.3 75.5 - - - +
127B ASN* 1.3 56.8 + - - +
129B ILE* 3.3 11.4 + - + +
130B GLU* 2.8 27.8 + - - +
182B ALA* 4.7 14.6 - - + -
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Residues in contact with ASN 127 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85B LEU 2.5 26.8 + - - +
86B CYS 3.4 16.4 + - - +
87B SER 3.3 19.6 + - - -
88B ARG* 3.3 13.6 + - - +
91B LEU* 3.4 13.9 - - - +
123B ILE* 3.2 12.6 + - + +
124B GLY 3.7 5.6 - - - +
125B THR 3.1 0.6 - - - -
126B LYS* 1.3 74.5 - - - +
128B VAL* 1.3 64.3 + - - +
129B ILE 3.1 1.3 - - - -
130B GLU* 3.5 12.2 - - - +
131B THR* 2.9 40.4 + - - +
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Residues in contact with VAL 128 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43B ILE* 5.1 11.7 - - + -
85B LEU* 4.8 12.6 - - + -
91B LEU* 3.9 19.5 - - + -
95B LEU* 4.8 1.3 - - + +
101B VAL* 5.0 5.6 - - + -
103B HIS* 4.2 27.8 - - + +
124B GLY 2.8 25.2 + - - +
125B THR* 3.0 10.1 + - + +
127B ASN* 1.3 71.9 - - - +
129B ILE* 1.3 57.8 + - - +
131B THR* 4.3 0.3 + - - -
132B CYS* 3.0 33.5 + - - +
140B LEU* 4.1 30.5 - - + -
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Residues in contact with ILE 129 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125B THR* 2.7 38.7 + - + +
126B LYS* 3.5 12.1 - - + +
128B VAL* 1.3 72.6 - - - +
130B GLU* 1.3 65.4 + - - +
132B CYS* 3.4 5.0 + - - +
133B LYS* 3.2 33.8 + - + +
140B LEU* 4.2 19.1 - - + -
182B ALA* 3.9 33.7 - - + +
183B VAL* 4.0 5.2 - - - +
186B ALA* 3.7 24.0 - - + -
193B PHE* 4.3 9.4 - - + -
195B THR* 6.3 0.4 - - + -
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Residues in contact with GLU 130 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88B ARG* 4.1 14.6 - - - -
126B LYS 2.8 17.4 + - - +
127B ASN* 3.1 21.7 + - - +
129B ILE* 1.3 81.0 - - - +
131B THR* 1.3 57.7 + - - +
133B LYS* 3.5 8.5 + - - +
134B GLU* 3.4 38.4 + - + +
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Residues in contact with THR 131 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88B ARG* 3.5 23.8 - - + +
91B LEU* 3.1 16.2 - - - +
92B TYR* 4.8 11.6 - - + -
95B LEU* 3.1 21.9 - - - +
127B ASN* 2.9 30.6 + - - +
130B GLU* 1.3 75.2 - - - +
132B CYS* 1.3 60.3 + - - +
133B LYS 3.2 0.9 - - - -
134B GLU* 3.5 22.3 - - - +
135B ALA* 3.1 29.8 + - - +
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Residues in contact with CYS 132 (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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95B LEU* 3.8 8.7 - - - +
101B VAL* 3.4 39.0 - - - -
128B VAL* 3.0 29.2 + - - +
129B ILE 3.4 1.1 + - - +
131B THR* 1.3 76.6 + - - +
133B LYS* 1.3 59.9 + - - +
136B GLY 3.6 0.9 + - - -
137B VAL* 3.0 42.1 + - + +
140B LEU* 4.1 17.0 - - - -
193B PHE* 3.6 22.0 - - + -
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Residues in contact with LYS 133 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129B ILE* 3.2 22.4 + - + +
130B GLU* 3.6 8.5 - - - +
131B THR 3.2 0.4 - - - -
132B CYS* 1.3 75.6 - - - +
134B GLU* 1.3 67.0 + - + +
136B GLY* 3.0 14.4 + - - -
137B VAL 5.1 1.3 - - - +
186B ALA* 5.7 1.3 + - + -
188B ASP* 4.0 14.8 + - - +
191B LYS* 3.4 36.9 - - - +
193B PHE* 4.1 33.1 - - + -
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Residues in contact with GLU 134 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88B ARG* 3.4 30.8 + - - -
92B TYR* 4.4 18.2 - - + +
96B LYS* 4.8 5.0 + - - -
130B GLU* 3.4 29.3 + - + +
131B THR* 3.5 26.1 - - - +
132B CYS 3.5 0.2 - - - -
133B LYS* 1.3 78.8 - - + +
135B ALA* 1.3 57.8 + - - +
136B GLY* 2.9 7.3 + - - -
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Residues in contact with ALA 135 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92B TYR* 3.8 17.5 - - + -
95B LEU* 3.6 29.7 - - + +
96B LYS* 3.6 37.6 + - - +
97B GLY 4.3 2.9 + - - -
98B VAL 4.5 1.4 - - - +
131B THR 3.1 17.5 + - - +
133B LYS 3.3 0.2 - - - -
134B GLU* 1.3 76.3 - - - +
136B GLY* 1.3 61.0 + - - +
137B VAL* 3.1 7.1 + - + +
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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
------------------------------------------------------------
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