Contacts of the helix formed by residues 138 - 155 (chain O) in PDB entry 2X86
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 ASN 138 (chain O).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39K PHE* 3.4 9.6 - - - -
81O THR* 3.7 34.0 + - - +
84O TRP* 3.5 24.7 - - + -
118O ALA* 5.0 6.4 - - - +
136O PRO* 4.0 2.3 - - - +
137O LEU* 1.3 83.5 + - - +
139O VAL* 1.3 59.6 + - + +
140O PHE* 3.4 8.6 + - - +
141O GLY* 2.7 44.9 + - - -
142O TYR* 2.9 11.8 + - - +
268O LEU* 6.3 1.0 - - - +
271O ARG* 3.9 21.3 + - + +
401O ADP 5.3 1.2 + - - -
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Residues in contact with VAL 139 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33K LEU* 4.1 16.2 - - + -
36K GLY* 3.9 23.8 - - - +
39K PHE* 3.9 8.0 - - + -
83O GLU 3.4 22.9 - - - +
84O TRP* 3.6 24.7 - - + -
86O GLY* 4.1 19.5 - - - -
89O MET* 3.8 15.3 - - + +
90O MET* 5.0 3.8 - - - -
138O ASN* 1.3 71.7 - - + +
140O PHE* 1.3 69.1 + - - +
142O TYR* 3.2 7.8 + - + -
143O SER* 2.9 22.9 + - - -
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Residues in contact with PHE 140 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78O CYS 3.4 27.8 - - - -
79O SER* 3.9 5.4 - - - -
80O SER 3.7 22.0 - - - +
81O THR* 3.8 20.2 + - + -
83O GLU 4.9 0.6 + - - +
89O MET* 3.9 10.8 - - + -
93O ASN* 4.0 5.2 - - - -
116O SER* 3.9 13.9 - - - -
118O ALA* 4.1 6.3 - - + -
138O ASN* 3.2 9.3 + - - +
139O VAL* 1.3 82.0 - - - +
141O GLY* 1.3 65.4 + - - +
143O SER* 2.6 24.5 + - - -
144O LYS* 3.2 26.6 + - + +
400O NAP 3.3 26.2 - - - -
402O BMA 3.5 33.4 - - - -
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Residues in contact with GLY 141 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118O ALA* 4.4 13.9 - - - -
119O THR* 3.9 2.6 - - - +
136O PRO* 3.4 16.2 - - - +
138O ASN* 2.7 22.0 + - - -
140O PHE* 1.3 81.8 - - - +
142O TYR* 1.3 57.8 - - - +
144O LYS* 3.2 6.3 + - - +
145O PHE* 2.8 29.5 + - - +
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Residues in contact with TYR 142 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33K LEU* 4.8 8.1 - - + -
39K PHE* 3.9 37.2 - + + -
42K LEU* 3.5 29.0 + - + +
43K VAL* 4.3 17.5 - - - -
47K ILE* 3.5 28.1 - - - +
50K TYR* 5.5 2.2 - + + +
90O MET* 4.1 28.9 - - + -
136O PRO* 3.6 11.5 - - + +
138O ASN 2.9 7.1 + - - +
139O VAL* 3.5 10.5 - - + +
140O PHE 3.2 0.2 - - - -
141O GLY* 1.3 76.7 - - - +
143O SER* 1.3 58.1 + - - +
145O PHE* 3.2 25.9 + + - +
146O LEU* 2.9 44.0 + - + +
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Residues in contact with SER 143 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89O MET* 3.6 16.8 - - - +
90O MET* 3.9 22.9 - - - -
93O ASN* 3.2 33.6 + - - +
94O TYR* 4.1 13.1 + - - +
139O VAL 2.9 12.6 + - - -
140O PHE 2.6 20.1 + - - -
142O TYR* 1.3 77.9 - - - +
144O LYS* 1.3 62.0 + - - +
146O LEU 4.0 0.2 + - - -
147O PHE* 3.5 19.6 + - - +
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Residues in contact with LYS 144 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76O GLY 5.0 1.0 + - - -
77O ALA* 3.6 13.6 - - - +
93O ASN* 4.6 8.0 - - + +
114O ALA* 3.0 25.3 + - - +
115O SER* 4.1 11.1 - - - +
116O SER* 4.2 11.0 - - - +
119O THR* 3.9 14.4 - - + -
140O PHE* 3.2 31.4 + - + +
141O GLY* 3.2 8.0 + - - +
142O TYR 3.1 0.4 - - - -
143O SER* 1.3 82.7 + - - +
145O PHE* 1.3 66.3 + - - +
147O PHE* 3.1 8.2 + - + +
148O ASP* 3.0 24.3 + - - +
400O NAP 2.9 42.0 + - - -
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Residues in contact with PHE 145 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42K LEU 5.7 0.2 - - - -
43K VAL 4.6 5.2 - - - -
45K LEU 4.9 4.0 - - - -
46K ASN* 5.3 0.2 - - - -
119O THR* 3.5 13.4 - - + +
131O ARG* 3.5 43.5 - - + -
134O GLU* 3.2 40.2 - - + -
136O PRO* 3.9 17.0 - - + -
141O GLY 2.8 16.6 + - - +
142O TYR* 3.5 29.4 - + - +
144O LYS* 1.3 76.8 - - - +
146O LEU* 1.3 72.4 + - + +
148O ASP* 3.0 7.7 + - - +
149O GLU* 3.0 45.7 + - + +
152O ARG* 4.9 0.7 - - - -
166O ARG* 5.6 0.4 - - - -
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Residues in contact with LEU 146 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47K ILE* 3.9 24.5 - - + +
48K ALA 5.5 1.3 - - - +
49K ASP* 5.4 2.5 - - - -
50K TYR* 3.4 34.1 - - + +
90O MET* 3.7 14.4 - - + -
94O TYR* 3.5 30.9 + - + +
142O TYR* 2.9 41.6 + - + +
143O SER 4.5 0.4 - - - +
145O PHE* 1.3 89.3 - - + +
147O PHE* 1.3 57.3 + - - +
149O GLU* 3.3 11.1 + - + +
150O TYR* 2.9 23.4 + - - +
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Residues in contact with PHE 147 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93O ASN 5.6 0.2 - - - +
94O TYR* 3.6 17.9 - + + -
97O SER* 3.6 35.9 - - - -
98O LYS* 3.5 34.1 - - + -
101O LEU* 4.0 17.0 - - + -
111O PHE* 4.0 7.2 - + - -
113O TYR* 3.7 39.5 - + - -
143O SER 3.5 12.2 + - - +
144O LYS* 3.1 11.8 + - + +
146O LEU* 1.3 77.3 - - - +
148O ASP* 1.3 60.3 + - - +
150O TYR* 2.9 10.0 + + + +
151O VAL* 2.8 47.8 + - + +
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Residues in contact with ASP 148 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113O TYR* 2.7 41.5 + - - -
115O SER* 2.6 28.9 + - - -
119O THR* 4.2 3.6 - - - +
134O GLU* 5.5 0.2 - - - +
144O LYS 3.0 15.2 + - - +
145O PHE 3.4 7.2 - - - +
147O PHE* 1.3 75.1 - - - +
149O GLU* 1.3 57.6 + - - +
151O VAL* 3.2 2.4 + - - +
152O ARG* 2.8 40.6 + - - +
166O ARG* 2.8 25.8 + - - +
232O ILE* 3.8 14.2 - - + +
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Residues in contact with GLU 149 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46K ASN* 4.6 7.3 - - - +
47K ILE 5.0 10.0 - - - +
48K ALA 6.0 0.4 - - - +
131O ARG* 3.7 25.4 - - - +
145O PHE* 3.0 39.7 + - + +
146O LEU* 3.4 17.9 - - + +
148O ASP* 1.3 76.4 - - - +
150O TYR* 1.3 62.1 + - - +
152O ARG* 2.9 40.4 + - - +
153O GLN* 3.2 31.4 + - - +
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Residues in contact with TYR 150 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48K ALA 4.1 12.5 + - - +
49K ASP* 4.3 10.8 - - + -
94O TYR* 3.7 19.5 - - + +
98O LYS* 3.6 33.0 + - + +
101O LEU* 4.0 22.4 - - + -
102O HIS* 2.6 38.1 + + - -
146O LEU 2.9 13.6 + - - +
147O PHE* 2.9 15.7 + + + +
149O GLU* 1.3 75.5 - - - +
151O VAL* 1.3 65.5 + - - +
153O GLN* 3.1 28.5 + - + +
154O ILE* 3.2 26.1 + - + +
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Residues in contact with VAL 151 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101O LEU* 4.3 8.1 - - + -
113O TYR* 3.4 29.2 - - + +
147O PHE* 2.8 43.5 + - + +
148O ASP 3.5 7.0 - - - +
150O TYR* 1.3 73.2 - - - +
152O ARG* 1.3 57.4 + - - +
154O ILE* 2.9 10.6 + - - +
155O LEU* 2.8 44.9 + - + +
162O ILE* 3.7 25.1 - - + -
231O GLY 5.8 0.7 - - - +
232O ILE* 4.4 7.9 - - + -
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Residues in contact with ARG 152 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129O GLU* 3.5 24.5 + - - +
130O SER* 3.8 2.4 - - - +
131O ARG* 3.9 10.7 - - - +
134O GLU* 2.5 44.1 + - - -
145O PHE* 4.6 0.6 - - - -
148O ASP* 2.8 23.9 + - - +
149O GLU* 2.9 34.4 + - - +
150O TYR 3.2 0.2 - - - -
151O VAL* 1.3 76.5 - - - +
153O GLN* 1.3 61.1 + - + +
155O LEU* 4.1 12.0 - - + +
156O PRO* 3.4 19.9 - - - +
166O ARG* 3.9 6.6 - - - +
232O ILE* 3.9 26.3 - - + +
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Residues in contact with GLN 153 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47K ILE 4.5 3.8 + - - -
48K ALA* 2.9 46.4 + - - +
149O GLU* 3.2 23.3 + - - +
150O TYR* 3.1 24.2 + - + +
152O ARG* 1.3 77.0 - - - +
154O ILE* 1.3 64.3 + - + +
156O PRO* 3.7 8.5 - - - +
157O GLU* 5.3 2.6 + - - +
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Residues in contact with ILE 154 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101O LEU* 4.3 6.5 - - + -
102O HIS* 4.5 15.5 - - + -
105O LEU* 3.6 27.6 - - + -
150O TYR* 3.2 37.7 + - + +
151O VAL* 2.9 10.4 + - - +
153O GLN* 1.3 83.0 - - + +
155O LEU* 1.3 65.7 + - - +
157O GLU* 3.0 19.6 + - + +
158O ALA* 3.2 10.6 + - + -
162O ILE* 3.9 16.4 - - + -
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Residues in contact with LEU 155 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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289C ASP* 5.6 8.5 - - + +
151O VAL* 2.8 33.6 + - + +
152O ARG* 4.1 14.6 - - + +
154O ILE* 1.3 75.3 - - - +
156O PRO* 1.4 72.1 - - + +
157O GLU 3.0 1.2 + - - -
158O ALA* 3.2 19.4 + - + +
162O ILE* 4.0 30.3 - - + +
230O SER* 4.1 21.8 - - - +
231O GLY* 4.2 19.3 - - - +
232O ILE* 5.0 2.9 - - + +
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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