Contacts of the helix formed by residues 122 - 135 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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117A PHE 4.0 0.2 + - - -
118A TYR* 3.4 47.4 + + + +
120A VAL 3.4 0.2 - - - -
121A ASN* 1.3 77.6 - - + +
123A ILE* 1.3 95.6 + - + +
125A THR* 2.9 16.2 + - - -
126A LYS* 3.0 34.3 + - + +
175A THR* 5.1 2.2 - - - +
178A LEU* 3.7 46.9 - - + -
179A GLN* 4.9 3.4 - - - +
182A ALA* 5.1 7.4 - - + -
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Residues in contact with ILE 123 (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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86A CYS* 4.8 12.8 - - + +
118A TYR* 4.1 24.0 - - + +
119A ARG* 3.3 12.2 + - - +
122A TYR* 1.3 109.3 - - + +
124A GLY* 1.3 65.7 + - - +
126A LYS* 3.1 26.1 + - + +
127A ASN* 3.0 20.2 + - + +
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Residues in contact with GLY 124 (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 LEU* 4.0 8.4 - - - +
86A CYS* 4.0 26.0 - - - -
119A ARG 2.9 13.1 + - - -
120A VAL 3.7 10.5 - - - -
122A TYR 3.3 0.2 - - - -
123A ILE* 1.3 75.2 - - - +
125A THR* 1.3 50.3 + - - +
127A ASN* 3.0 7.4 + - - +
128A VAL* 2.8 38.6 + - - +
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Residues in contact with THR 125 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85A LEU* 5.2 0.2 - - - +
103A HIS* 3.9 16.1 + - + -
120A VAL 3.6 4.5 + - - -
121A ASN 2.2 31.4 + - - +
122A TYR* 2.9 5.0 + - - -
124A GLY* 1.3 71.2 - - - +
126A LYS* 1.3 54.8 + - - +
128A VAL* 2.9 15.5 + - + +
129A ILE* 2.6 39.9 + - + +
140A LEU* 5.9 0.4 - - + -
179A GLN* 3.3 20.6 + - + +
182A ALA* 5.3 2.5 - - + -
183A VAL* 3.5 31.6 - - + -
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Residues in contact with LYS 126 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A ARG* 5.0 0.2 - - - -
122A TYR* 3.0 41.5 + - + +
123A ILE* 3.3 26.6 - - + +
125A THR* 1.3 74.2 - - - +
127A ASN* 1.3 58.0 + - - +
129A ILE* 3.0 14.7 + - + +
130A GLU* 3.0 41.7 + - - +
182A ALA* 5.1 10.7 - - + +
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Residues in contact with ASN 127 (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 LEU 3.0 10.4 - - - +
86A CYS* 3.0 36.5 + - + +
87A SER 3.2 10.0 - - - +
88A ARG* 3.0 46.5 - - - +
91A LEU* 3.7 3.2 - - - +
123A ILE* 3.0 10.7 + - + +
124A GLY 3.0 12.4 + - - +
126A LYS* 1.3 72.5 - - - +
128A VAL* 1.3 55.9 + - - +
131A THR* 2.7 39.9 + - - +
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Residues in contact with VAL 128 (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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43A ILE* 3.9 23.3 - - + -
85A LEU* 3.6 27.8 - - + -
91A LEU* 4.0 3.1 - - + -
95A LEU* 5.5 0.2 - - + -
101A VAL* 4.7 3.8 - - + -
103A HIS* 4.1 15.9 - - + +
124A GLY 2.8 24.2 + - - +
125A THR* 2.9 19.3 + - + +
127A ASN* 1.3 73.6 - - - +
129A ILE* 1.3 59.6 + - - +
131A THR* 2.9 18.0 + - - +
132A CYS* 2.9 30.8 + - - -
140A LEU* 4.3 14.6 - - + -
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Residues in contact with ILE 129 (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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125A THR 2.6 19.6 + - - +
126A LYS* 3.0 14.8 + - + +
128A VAL* 1.3 72.9 - - - +
130A GLU* 1.3 71.3 + - + +
132A CYS* 3.3 8.4 + - - +
133A LYS* 3.1 34.2 + - + +
140A LEU* 4.6 16.6 - - + -
182A ALA* 3.7 43.1 - - + +
183A VAL* 3.8 13.2 - - + +
186A ALA* 4.2 21.3 - - + -
193A PHE* 4.4 3.6 - - + -
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Residues in contact with GLU 130 (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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88A ARG* 3.0 40.3 + - - +
126A LYS* 3.0 23.1 + - - +
129A ILE* 1.3 80.1 - - + +
131A THR* 1.3 55.0 + - - +
133A LYS* 2.8 12.2 + - + +
134A GLU* 2.4 42.2 + - + +
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Residues in contact with THR 131 (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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88A ARG* 3.9 30.5 - - + +
91A LEU* 3.3 15.6 - - + +
92A TYR* 4.7 9.6 - - + +
95A LEU* 3.3 22.8 - - - +
127A ASN* 2.7 40.0 + - - +
128A VAL 2.9 11.4 + - - -
130A GLU* 1.3 75.2 - - - +
132A CYS* 1.3 55.5 + - - +
134A GLU* 3.7 9.3 - - + +
135A ALA* 2.9 31.9 + - - +
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Residues in contact with CYS 132 (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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95A LEU* 4.1 8.1 - - - -
101A VAL* 3.7 35.9 - - - -
128A VAL* 2.9 34.6 + - - +
129A ILE 3.4 6.5 - - - +
130A GLU 3.1 0.2 - - - -
131A THR* 1.3 76.9 + - - +
133A LYS* 1.3 58.0 + - - +
136A GLY 3.3 2.3 + - - -
137A VAL* 2.7 44.9 + - + +
140A LEU* 4.4 8.5 - - - -
193A PHE* 3.7 20.2 - - + -
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Residues in contact with LYS 133 (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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129A ILE* 3.1 25.1 - - + +
130A GLU* 2.8 11.7 + - + +
132A CYS* 1.3 73.8 - - - +
134A GLU* 1.3 64.6 + - - +
135A ALA 3.1 2.2 - - - -
136A GLY* 3.2 13.0 + - - +
186A ALA* 4.7 4.9 + - + +
188A ASP* 3.2 30.3 + - - +
191A LYS* 3.5 42.6 + - - +
193A PHE* 3.5 41.6 - - + -
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Residues in contact with GLU 134 (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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88A ARG* 3.6 33.8 + - - +
89A GLN* 4.5 5.0 - - - +
92A TYR* 3.3 33.7 + - + -
130A GLU* 2.4 32.2 + - + +
131A THR* 3.3 10.2 + - - +
133A LYS* 1.3 67.7 - - - +
135A ALA* 1.3 55.8 + - - +
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Residues in contact with ALA 135 (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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92A TYR* 3.9 19.3 - - + -
95A LEU* 4.4 10.1 - - + +
96A LYS* 4.2 23.2 - - + +
97A GLY 5.3 4.2 + - - -
98A VAL 5.3 1.7 - - - +
131A THR 2.9 16.5 + - - +
134A GLU* 1.3 78.8 - - - +
136A GLY* 1.3 62.7 + - - +
137A VAL* 3.3 9.6 + - + +
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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