Contacts of the helix formed by residues 110 - 126 (chain J) in PDB entry 2ABJ
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 GLN 110 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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109J PHE* 1.3 89.6 - - + +
111J PRO* 1.4 69.5 - - - +
112J ASN* 3.2 2.9 - - - -
113J LEU* 3.1 40.2 + - + +
114J ASN* 3.3 9.2 + - - -
287J VAL* 3.8 17.7 - - + -
290J ARG* 6.1 0.9 - - - +
291J CYS* 3.8 10.1 - - - -
294J ASP* 5.5 1.2 - - - +
378J ASP 4.8 2.6 + - - -
379J TRP* 2.8 62.2 + - + +
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Residues in contact with PRO 111 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96J LEU* 4.0 17.9 - - + -
108J LEU* 3.8 20.6 - - + +
109J PHE 3.2 10.0 - - - +
110J GLN* 1.4 89.2 - - - +
112J ASN* 1.3 58.3 + - - +
114J ASN* 3.1 15.9 + - - +
115J MET* 3.1 31.6 + - + +
136J LEU* 3.7 28.9 - - + -
379J TRP 4.6 0.7 - - - +
381J ILE* 4.1 28.5 - - + -
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Residues in contact with ASN 112 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110J GLN 3.2 1.5 + - - -
111J PRO* 1.3 76.5 - - - +
113J LEU* 1.3 61.0 + - + +
115J MET* 3.4 9.9 + - - +
116J ASP* 2.9 39.6 + - - +
132J LYS* 5.5 1.4 + - - +
133J GLU* 2.6 30.1 + - - +
136J LEU* 3.5 17.8 - - - +
381J ILE* 4.1 19.8 - - - +
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Residues in contact with LEU 113 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110J GLN* 3.1 40.8 + - + +
112J ASN* 1.3 79.5 - - + +
114J ASN* 1.3 57.9 + - - +
116J ASP* 3.5 16.9 - - + +
117J ARG* 3.0 29.1 + - - +
287J VAL* 4.0 33.0 - - + +
290J ARG* 5.2 13.9 - - + -
291J CYS* 5.8 0.2 - - - -
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Residues in contact with ASN 114 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94J GLU* 2.9 32.7 - - + +
95J GLY 3.2 14.6 - - - +
96J LEU* 3.6 32.1 - - + +
109J PHE 4.2 3.6 + - - -
110J GLN 3.3 18.2 + - - -
111J PRO* 3.1 12.0 + - - +
113J LEU* 1.3 74.6 - - - +
115J MET* 1.3 65.7 + - + +
117J ARG* 3.5 9.4 + - - +
118J MET* 2.9 30.8 + - - +
287J VAL* 4.2 14.5 - - - +
331J THR* 5.3 0.2 + - - -
420J PLP 5.0 0.2 + - - -
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Residues in contact with MET 115 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94J GLU* 5.5 0.4 - - + -
96J LEU* 5.1 5.2 - - + -
111J PRO 3.1 17.0 + - - +
112J ASN* 3.4 12.8 + - - +
114J ASN* 1.3 82.3 - - + +
116J ASP* 1.3 59.8 - - - +
118J MET* 3.4 10.8 + - - +
119J TYR* 3.0 31.4 + - - +
130J PHE* 4.6 2.1 - - + -
132J LYS* 3.4 39.5 - - + +
135J LEU* 3.7 33.2 - - + -
136J LEU* 3.9 22.4 - - + -
139J ILE* 3.8 22.4 - - + -
162J PRO* 4.8 6.3 - - + -
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Residues in contact with ASP 116 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112J ASN* 2.9 29.5 + - - +
113J LEU* 3.5 21.9 - - + +
114J ASN 3.3 0.2 - - - -
115J MET* 1.3 76.6 - - - +
117J ARG* 1.3 56.7 + - - +
119J TYR* 3.5 2.9 + - - +
120J ARG* 3.1 50.3 + - - +
132J LYS* 3.6 27.9 + - - +
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Residues in contact with ARG 117 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94J GLU* 2.7 38.2 + - - +
95J GLY 4.3 3.8 + - - -
113J LEU 3.0 17.7 + - - +
114J ASN* 3.6 10.9 + - - +
116J ASP* 1.3 72.7 - - - +
118J MET* 1.3 60.5 + - - +
120J ARG* 3.3 9.9 + - + +
121J SER* 2.9 40.0 + - - +
218J ASP 5.5 5.2 - - - +
219J CYS* 5.9 0.4 - - - -
220J LYS* 3.6 27.0 - - + +
284J LEU* 3.5 21.3 - - + +
285J PRO* 3.1 32.3 + - + -
286J GLY* 3.7 0.2 - - - -
287J VAL* 3.7 9.1 - - - +
420J PLP 2.8 29.5 + - - +
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Residues in contact with MET 118 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92J LEU* 3.7 28.0 - - + +
93J PHE 5.6 0.4 - - - -
94J GLU* 3.7 17.2 + - + -
114J ASN 2.9 18.6 + - - +
115J MET* 3.8 7.4 - - - +
116J ASP 3.4 0.2 - - - -
117J ARG* 1.3 76.6 - - - +
119J TYR* 1.3 57.5 + - - +
121J SER* 3.3 6.8 + - - -
122J ALA* 2.9 28.2 + - - +
130J PHE* 4.1 7.6 - - + -
135J LEU* 3.6 23.1 - - - -
162J PRO* 3.8 38.1 - - + +
164J PHE* 4.0 15.5 - - + -
181J LEU* 4.1 22.9 - - + -
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Residues in contact with TYR 119 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115J MET 3.0 18.2 + - - +
116J ASP 3.6 4.5 - - - +
118J MET* 1.3 76.5 - - - +
120J ARG* 1.3 66.9 + - + +
122J ALA* 3.2 4.8 + - - +
123J VAL* 3.2 31.1 + - + +
129J VAL* 3.3 41.5 - - + +
130J PHE* 3.0 45.2 - + + -
132J LYS* 3.7 32.3 - - + -
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Residues in contact with ARG 120 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116J ASP* 3.1 41.5 + - - +
117J ARG* 3.6 9.2 - - + +
118J MET 3.3 0.2 - - - -
119J TYR* 1.3 80.8 - - + +
121J SER* 1.3 64.1 + - - +
123J VAL* 3.5 8.0 + - - +
124J ARG* 3.2 21.9 + - - +
132J LYS* 5.2 6.1 - - - +
219J CYS* 4.8 5.2 - - - -
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Residues in contact with SER 121 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92J LEU* 3.8 23.5 - - - +
93J PHE 5.8 0.2 - - - -
117J ARG* 2.9 20.5 + - - +
118J MET* 3.3 6.7 + - - -
120J ARG* 1.3 74.4 - - - +
122J ALA* 1.3 59.1 + - - +
124J ARG* 3.3 8.5 + - - +
125J ALA* 2.8 30.7 + - - +
219J CYS* 3.7 15.3 - - - +
220J LYS* 3.4 26.4 + - - +
221J MET* 4.2 3.3 - - - +
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Residues in contact with ALA 122 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92J LEU* 3.8 10.7 - - - +
118J MET 2.9 14.3 + - - +
119J TYR* 3.2 13.2 + - - +
121J SER* 1.3 77.5 - - - +
123J VAL* 1.3 56.9 + - + +
125J ALA 3.2 0.9 + - - -
126J THR 2.9 8.7 + - - -
127J LEU* 2.8 38.3 + - + +
128J PRO 4.3 4.3 - - - +
129J VAL* 5.4 2.5 - - - -
130J PHE* 4.5 3.1 - - + -
164J PHE* 3.9 29.4 - - + -
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Residues in contact with VAL 123 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230G PHE* 3.3 30.5 - - + -
119J TYR* 3.2 26.3 + - + +
120J ARG* 3.7 8.3 - - - +
122J ALA* 1.3 74.9 - - - +
124J ARG* 1.3 63.4 + - - +
126J THR* 3.2 13.4 + - - +
127J LEU 4.8 2.5 - - - -
129J VAL* 3.9 24.2 - - + -
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Residues in contact with ARG 124 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208G TYR* 6.2 2.2 - - - -
226G GLY 4.9 3.1 - - - +
227G SER* 5.8 1.6 - - - -
230G PHE* 3.4 44.9 + - + +
120J ARG 3.2 13.3 + - - +
121J SER 3.5 8.5 - - - +
123J VAL* 1.3 81.2 - - - +
125J ALA* 1.3 57.9 + - - +
215J GLY 3.1 22.4 + - - -
216J THR* 3.9 12.4 - - + +
218J ASP* 2.7 32.0 + - - -
219J CYS* 3.0 25.9 - - - -
221J MET* 3.4 25.2 - - + +
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Residues in contact with ALA 125 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226G GLY 4.6 6.5 - - - +
229G LEU* 3.8 15.1 - - - +
90J VAL* 4.5 7.1 - - + +
91J GLU 4.9 6.3 - - - +
92J LEU* 4.1 5.6 - - + -
121J SER 2.8 16.2 + - - +
122J ALA 3.2 4.7 + - - +
124J ARG* 1.3 75.6 - - - +
126J THR* 1.3 74.6 + - - +
127J LEU* 3.5 24.9 + - + -
221J MET* 4.0 16.1 - - + -
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Residues in contact with THR 126 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229G LEU* 3.4 24.8 - - + +
230G PHE* 3.6 36.8 - - + +
233G CYS* 4.1 10.1 - - + -
122J ALA 2.9 5.4 + - - -
123J VAL* 3.2 12.2 + - - +
125J ALA* 1.3 84.9 + - - +
127J LEU* 1.3 62.9 + - - +
128J PRO* 4.1 0.7 - - - +
175J LYS* 3.4 38.7 - - - +
176J PRO* 3.6 13.5 - - - +
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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
------------------------------------------------------------
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