Contacts of the helix formed by residues 110 - 126 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109A PHE* 1.3 89.1 - - + +
111A PRO* 1.4 68.8 - - - +
112A ASN* 3.2 2.9 - - - -
113A LEU* 3.1 39.3 + - + +
114A ASN* 3.3 10.0 + - - -
287A VAL* 3.9 15.7 - - + -
290A ARG* 5.4 1.7 - - - +
291A CYS* 3.7 13.8 - - - -
294A ASP* 5.3 2.1 - - - +
378A ASP 5.1 1.6 + - - -
379A TRP* 2.7 61.8 + - + +
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Residues in contact with PRO 111 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96A LEU* 4.1 18.6 - - + -
108A LEU* 3.8 21.1 - - + +
109A PHE 3.1 9.4 - - - +
110A GLN* 1.4 91.4 - - - +
112A ASN* 1.3 58.5 + - - +
114A ASN* 3.1 15.9 + - - +
115A MET* 3.1 31.7 + - + +
136A LEU* 3.8 26.2 - - + -
381A ILE* 3.8 29.2 - - + -
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Residues in contact with ASN 112 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110A GLN 3.2 1.5 + - - -
111A PRO* 1.3 77.0 - - + +
113A LEU* 1.3 62.4 + - + +
115A MET* 3.4 10.9 + - - +
116A ASP* 2.9 40.3 + - - +
132A LYS* 5.3 1.6 + - - +
133A GLU* 2.8 30.1 + - - +
136A LEU* 3.5 22.8 - - - +
381A ILE* 4.1 15.6 - - - +
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Residues in contact with LEU 113 (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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110A GLN* 3.1 43.7 + - - +
112A ASN* 1.3 81.5 - - + +
114A ASN* 1.3 56.6 + - - +
116A ASP* 3.5 17.5 - - + +
117A ARG* 3.0 27.5 + - - +
120A ARG* 5.6 0.2 + - - -
287A VAL* 3.9 29.7 - - + +
290A ARG* 4.7 17.9 - - + -
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Residues in contact with ASN 114 (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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94A GLU* 3.0 33.9 - - + +
95A GLY 3.1 15.1 - - - +
96A LEU* 3.6 30.9 - - + +
109A PHE 4.2 3.4 + - - -
110A GLN 3.3 18.2 + - - -
111A PRO* 3.1 12.7 + - - +
113A LEU* 1.3 74.4 - - - +
115A MET* 1.3 66.4 + - + +
117A ARG* 3.5 9.5 + - - +
118A MET* 2.9 30.7 + - - +
287A VAL* 4.2 14.0 - - - +
331A THR* 5.3 0.2 + - - -
420A PLP 5.0 0.2 + - - -
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Residues in contact with MET 115 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94A GLU* 5.5 0.2 - - + -
96A LEU* 5.0 5.6 - - + -
111A PRO 3.1 16.4 + - - +
112A ASN* 3.7 14.4 - - - +
113A LEU 3.4 0.2 - - - -
114A ASN* 1.3 83.9 - - + +
116A ASP* 1.3 65.0 - - - +
118A MET* 3.4 10.5 + - - +
119A TYR* 3.0 19.9 + - - +
130A PHE* 4.6 2.5 - - + -
132A LYS* 3.3 46.0 - - + +
135A LEU* 3.8 32.3 - - + -
136A LEU* 3.9 22.0 - - + -
139A ILE* 3.8 22.0 - - + -
162A PRO* 4.9 6.1 - - + -
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Residues in contact with ASP 116 (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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112A ASN* 2.9 30.6 + - - +
113A LEU* 3.5 21.4 - - + +
114A ASN 3.3 0.2 - - - -
115A MET* 1.3 76.3 - - - +
117A ARG* 1.3 60.1 + - - +
119A TYR* 3.6 3.1 + - - +
120A ARG* 3.1 55.2 + - - +
132A LYS* 2.9 32.6 + - - +
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Residues in contact with ARG 117 (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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94A GLU* 2.6 40.2 + - - +
95A GLY 4.2 3.8 + - - -
113A LEU 3.0 17.3 + - - +
114A ASN* 3.5 12.1 + - - +
116A ASP* 1.3 73.8 - - - +
118A MET* 1.3 60.0 + - - +
120A ARG* 3.3 15.7 + - + +
121A SER* 2.9 39.5 + - - +
218A ASP 5.5 4.9 - - - +
219A CYS* 5.9 0.4 - - - -
220A LYS* 3.5 25.7 - - + +
284A LEU* 3.5 22.1 - - + +
285A PRO* 3.2 30.7 + - + -
286A GLY* 3.7 1.0 - - - -
287A VAL* 3.7 8.7 - - - +
420A PLP 2.8 30.5 + - - -
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Residues in contact with MET 118 (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 LEU* 3.7 26.9 - - + +
93A PHE 5.6 0.2 - - - -
94A GLU* 3.7 17.6 + - + -
114A ASN 2.9 18.6 + - - +
115A MET* 3.8 7.9 - - - +
116A ASP 3.4 0.2 - - - -
117A ARG* 1.3 73.2 - - - +
119A TYR* 1.3 59.6 + - - +
121A SER* 3.4 6.7 + - - -
122A ALA* 2.9 28.6 + - - +
130A PHE* 4.1 7.6 - - + -
135A LEU* 3.7 22.9 - - + -
162A PRO* 3.7 38.6 - - + +
164A PHE* 4.1 15.3 - - + -
181A LEU* 4.1 22.2 - - + -
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Residues in contact with TYR 119 (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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115A MET 3.0 17.4 + - - +
116A ASP 3.6 4.7 - - - +
118A MET* 1.3 76.7 - - - +
120A ARG* 1.3 67.2 + - + +
122A ALA* 3.2 6.1 + - + +
123A VAL* 3.1 31.0 + - + +
129A VAL* 3.3 40.2 - - + +
130A PHE* 3.1 46.3 - + + -
132A LYS* 3.7 27.1 - - + -
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Residues in contact with ARG 120 (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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116A ASP* 3.1 46.2 + - - +
117A ARG* 3.6 12.5 - - + +
118A MET 3.3 0.2 - - - -
119A TYR* 1.3 83.4 - - + +
121A SER* 1.3 63.8 + - - +
123A VAL* 3.4 7.3 + - - +
124A ARG* 3.1 22.0 + - - +
132A LYS* 5.8 1.0 - - - +
219A CYS* 4.8 5.0 - - - -
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Residues in contact with SER 121 (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 LEU* 3.8 23.2 - - - +
93A PHE 5.8 0.2 - - - -
94A GLU* 5.2 0.2 + - - -
117A ARG* 2.9 22.5 + - - +
118A MET* 3.7 6.7 - - - -
120A ARG* 1.3 71.5 - - - +
122A ALA* 1.3 60.9 + - - +
124A ARG* 3.3 8.0 + - - +
125A ALA* 2.9 30.5 + - - +
219A CYS* 3.9 13.3 - - - +
220A LYS* 3.5 28.4 + - - +
221A MET* 4.2 3.8 - - - +
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Residues in contact with ALA 122 (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 LEU* 3.8 10.7 - - + +
118A MET 2.9 15.1 + - - +
119A TYR* 3.2 13.4 + - - +
121A SER* 1.3 77.4 - - - +
123A VAL* 1.3 56.7 + - + +
125A ALA 3.2 0.7 + - - -
126A THR 2.9 24.6 + - - -
127A LEU* 2.9 25.3 + - - +
128A PRO 4.3 4.7 - - - +
129A VAL* 5.4 2.2 - - - -
130A PHE* 4.6 3.4 - - + -
164A PHE* 4.1 24.9 - - + -
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Residues in contact with VAL 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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119A TYR* 3.1 28.0 + - + +
120A ARG* 3.7 9.4 - - - +
122A ALA* 1.3 73.5 - - - +
124A ARG* 1.3 62.7 + - - +
126A THR* 3.3 11.3 + - - +
127A LEU 4.8 2.5 - - - -
129A VAL* 3.9 24.5 - - + -
230D PHE* 3.3 28.6 - - + -
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Residues in contact with ARG 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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120A ARG 3.1 17.4 + - - +
121A SER 3.7 5.2 - - - +
123A VAL* 1.3 77.3 - - - +
125A ALA* 1.3 59.0 + - - +
215A GLY 3.0 23.0 + - - -
216A THR* 3.8 13.6 - - + +
218A ASP* 2.7 33.0 + - - -
219A CYS* 3.1 28.0 - - - -
221A MET* 3.3 28.1 - - + +
208D TYR* 6.1 4.1 - - - -
226D GLY 5.0 3.5 - - - +
227D SER* 5.8 1.7 - - - -
230D PHE* 3.4 40.0 + - + +
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Residues in contact with ALA 125 (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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90A VAL* 4.4 8.2 - - + +
91A GLU 4.9 6.7 - - - +
92A LEU* 4.1 5.2 - - + -
121A SER 2.9 17.3 + - - +
122A ALA 3.2 4.2 + - - +
124A ARG* 1.3 75.6 - - - +
126A THR* 1.3 73.2 + - - +
127A LEU* 3.6 23.7 + - + -
221A MET* 3.9 17.2 - - + -
226D GLY 4.6 6.7 - - - +
229D LEU* 3.9 14.3 - - - +
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Residues in contact with THR 126 (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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122A ALA 2.9 5.4 + - - -
123A VAL* 3.3 9.7 + - - +
125A ALA* 1.3 84.7 + - - +
127A LEU* 1.3 64.1 + - - +
128A PRO* 4.0 0.7 - - - +
175A LYS* 3.4 37.8 - - - +
176A PRO* 3.6 13.7 - - - +
229D LEU* 3.5 24.1 - - - +
230D PHE* 3.6 39.3 - - + +
233D CYS* 4.0 9.2 - - + -
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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