Contacts of the helix formed by residues 110 - 126 (chain G) 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 G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109G PHE* 1.3 93.1 - - + +
111G PRO* 1.4 69.0 - - - +
112G ASN* 3.2 3.1 - - - -
113G LEU* 3.1 45.2 + - + +
114G ASN* 3.2 10.4 + - - -
287G VAL* 4.2 7.2 - - + -
290G ARG* 5.1 4.6 - - - +
291G CYS* 3.6 17.3 - - - -
294G ASP* 5.1 1.4 + - - -
378G ASP 5.3 0.2 - - - +
379G TRP* 2.7 62.6 + - + +
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Residues in contact with PRO 111 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96G LEU* 3.9 15.5 - - + -
108G LEU* 3.7 22.4 - - + +
109G PHE* 3.1 10.9 - - - +
110G GLN* 1.4 89.4 - - - +
112G ASN* 1.3 62.4 + - - +
113G LEU 3.2 0.2 - - - -
114G ASN* 3.2 15.7 + - - +
115G MET* 3.1 30.2 + - - +
136G LEU* 3.7 31.9 - - + -
379G TRP 4.5 0.4 - - - +
381G ILE* 4.4 18.8 - - + -
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Residues in contact with ASN 112 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110G GLN 3.2 0.8 + - - -
111G PRO* 1.3 82.4 - - - +
113G LEU* 1.3 62.8 + - + +
115G MET* 3.3 9.9 + - - +
116G ASP* 2.9 41.4 + - - +
132G LYS* 5.6 1.9 - - - +
133G GLU* 5.3 8.7 - - - +
136G LEU* 3.4 25.4 - - - +
381G ILE* 5.2 10.1 - - - +
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Residues in contact with LEU 113 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110G GLN* 3.1 46.9 + - + +
112G ASN* 1.3 80.7 - - + +
114G ASN* 1.3 55.9 + - - +
116G ASP* 3.6 15.9 + - + +
117G ARG* 3.1 26.9 + - - +
287G VAL* 3.9 30.7 - - + +
290G ARG* 4.3 18.2 - - + -
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Residues in contact with ASN 114 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94G GLU* 3.0 31.9 - - + +
95G GLY 3.1 14.4 - - - +
96G LEU* 3.7 33.9 - - + +
109G PHE 4.2 4.2 + - - -
110G GLN 3.2 18.4 + - - -
111G PRO* 3.2 10.2 + - - +
113G LEU* 1.3 75.7 - - - +
115G MET* 1.3 65.6 + - + +
117G ARG* 3.5 10.5 + - - +
118G MET* 2.9 30.5 + - - +
287G VAL* 4.0 13.7 - - - +
331G THR* 5.2 0.3 + - - -
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Residues in contact with MET 115 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94G GLU* 5.4 0.4 - - + -
96G LEU* 5.0 6.5 - - + -
111G PRO 3.1 16.9 + - - +
112G ASN* 3.3 11.9 + - - +
114G ASN* 1.3 87.9 - - + +
116G ASP* 1.3 62.1 + - - +
118G MET* 3.5 11.3 + - - +
119G TYR* 3.1 18.4 + - - +
130G PHE* 4.7 2.1 - - - -
132G LYS* 3.3 42.8 - - + +
135G LEU* 3.8 32.8 - - + -
136G LEU* 3.9 27.4 - - + -
139G ILE* 3.8 21.1 - - + -
162G PRO* 4.7 6.5 - - + -
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Residues in contact with ASP 116 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112G ASN* 2.9 29.9 + - - +
113G LEU* 3.7 18.2 - - + +
115G MET* 1.3 77.2 - - - +
117G ARG* 1.3 56.7 + - - +
119G TYR* 3.5 4.2 + - - +
120G ARG* 3.1 31.9 + - - +
132G LYS* 2.8 38.4 + - - +
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Residues in contact with ARG 117 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94G GLU* 2.7 38.2 + - - +
95G GLY 4.4 3.6 + - - -
113G LEU 3.1 15.2 + - - +
114G ASN* 3.6 8.7 + - - +
116G ASP* 1.3 78.2 - - - +
118G MET* 1.3 59.8 + - - +
120G ARG* 3.4 32.7 + - - +
121G SER* 3.0 36.6 + - - +
220G LYS* 3.6 24.9 - - + +
284G LEU* 3.5 22.4 - - + +
285G PRO 3.2 26.8 + - - -
286G GLY* 3.6 0.6 - - - -
287G VAL* 3.7 11.0 - - - +
420G PLP 2.8 29.7 + - - -
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Residues in contact with MET 118 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92G LEU* 3.8 15.9 - - + +
94G GLU* 3.7 16.3 + - + -
114G ASN 2.9 19.6 + - - +
115G MET* 3.7 9.2 - - - +
117G ARG* 1.3 76.6 - - - +
119G TYR* 1.3 56.3 + - - +
121G SER* 3.3 7.0 + - - -
122G ALA* 2.9 28.6 + - - +
130G PHE* 3.9 8.1 - - + -
135G LEU* 3.6 21.8 - - + -
162G PRO* 3.7 34.1 - - + -
164G PHE* 4.1 18.8 - - + -
181G LEU* 3.8 34.1 - - + -
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Residues in contact with TYR 119 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115G MET 3.1 17.9 + - - +
116G ASP* 3.5 5.8 - - - +
118G MET* 1.3 76.5 - - - +
120G ARG* 1.3 65.2 + - + +
122G ALA* 3.3 3.3 + - - +
123G VAL* 3.1 38.8 + - + +
129G VAL* 3.2 40.4 - - + +
130G PHE* 3.2 43.6 - + + -
132G LYS* 3.9 28.5 - - + +
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Residues in contact with ARG 120 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116G ASP* 3.1 13.5 + - + +
117G ARG* 3.5 33.6 - - - +
119G TYR* 1.3 83.8 - - + +
121G SER* 1.3 62.0 + - - +
123G VAL* 3.4 8.0 + - - +
124G ARG* 3.1 22.9 + - - +
218G ASP* 3.0 37.4 + - - +
219G CYS* 3.9 17.7 - - - +
285G PRO* 3.8 18.8 - - - +
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Residues in contact with SER 121 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92G LEU* 3.6 24.2 - - - -
93G PHE 5.7 0.4 - - - -
117G ARG* 3.0 21.6 + - - +
118G MET* 3.6 7.5 - - - -
120G ARG* 1.3 73.3 + - - +
122G ALA* 1.3 60.5 + - - +
124G ARG* 3.3 3.8 + - - +
125G ALA* 2.8 30.0 + - - +
219G CYS* 3.7 16.1 - - - +
220G LYS* 3.2 30.6 + - - +
221G MET* 4.1 3.3 - - - +
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Residues in contact with ALA 122 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92G LEU* 3.8 10.9 - - - +
118G MET 2.9 16.5 + - - +
119G TYR 3.5 6.7 - - - +
121G SER* 1.3 73.2 - - - +
123G VAL* 1.3 59.8 + - + +
125G ALA* 3.2 1.0 + - - -
126G THR 2.9 24.8 + - - -
127G LEU* 3.0 22.0 + - + +
128G PRO 4.2 4.0 - - - +
129G VAL* 5.3 2.5 - - - -
130G PHE* 4.4 6.5 - - + -
164G PHE* 3.9 30.3 - - + -
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Residues in contact with VAL 123 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119G TYR* 3.1 28.6 + - + +
120G ARG* 3.6 10.8 - - - +
121G SER 3.3 0.2 - - - -
122G ALA* 1.3 75.1 - - - +
124G ARG* 1.3 61.2 + - - +
126G THR* 3.2 13.3 + - - +
127G LEU 4.8 2.2 - - - -
129G VAL* 3.8 24.7 - - + -
230J PHE* 3.4 28.1 - - + -
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Residues in contact with ARG 124 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120G ARG 3.1 16.5 + - - +
121G SER 3.7 4.7 - - - +
123G VAL* 1.3 78.4 - - - +
125G ALA* 1.3 58.3 + - - +
214G GLY* 4.0 15.8 + - - -
215G GLY* 2.7 26.9 + - - -
216G THR* 3.5 18.0 - - + +
218G ASP* 5.4 2.0 + - - -
219G CYS* 3.8 20.4 - - - -
221G MET* 3.7 21.6 - - - +
208J TYR* 4.1 23.6 - - - +
209J VAL 5.8 0.4 + - - -
226J GLY 4.9 1.9 - - - +
227J SER* 3.3 23.6 + - - +
230J PHE* 3.7 39.5 + - - +
231J ALA* 5.9 0.4 - - - +
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Residues in contact with ALA 125 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90G VAL* 4.3 7.2 - - + +
91G GLU 5.0 6.1 - - - +
92G LEU* 4.1 5.8 - - + -
121G SER 2.8 17.4 + - - +
122G ALA 3.7 4.5 - - - +
123G VAL 3.2 0.2 - - - -
124G ARG* 1.3 77.1 - - - +
126G THR* 1.3 73.5 + - - +
127G LEU* 3.6 23.5 + - + -
221G MET* 4.0 21.5 - - + -
226J GLY 4.5 3.0 - - - +
229J LEU* 3.8 14.6 - - - +
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Residues in contact with THR 126 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122G ALA 2.9 5.2 + - - -
123G VAL* 3.2 9.4 + - - +
125G ALA* 1.3 84.1 + - - +
127G LEU* 1.3 62.8 + - - +
128G PRO* 4.1 0.9 - - - +
175G LYS* 3.5 39.8 - - - +
176G PRO* 3.5 13.5 - - - +
229J LEU* 3.4 23.8 - - - +
230J PHE* 3.7 40.8 - - + +
233J CYS* 4.0 10.3 - - + -
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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