Contacts of the helix formed by residues 138 - 155 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81A THR* 3.7 34.9 + - - +
84A TRP* 3.5 24.7 - - + -
118A ALA* 5.0 6.1 - - - +
136A PRO* 4.0 1.6 - - - +
137A LEU* 1.3 82.7 - - - +
139A VAL* 1.3 59.8 + - - +
140A PHE* 3.4 8.7 + - - +
141A GLY* 2.7 45.7 + - - -
142A TYR* 2.9 11.4 + - - +
268A LEU* 6.3 1.0 - - - +
271A ARG* 3.9 21.1 + - + +
401A ADP 5.7 1.0 + - - -
39B PHE* 3.4 9.6 - - - -
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Residues in contact with VAL 139 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A GLU 3.4 24.0 - - - +
84A TRP* 3.6 25.2 - - + -
86A GLY* 4.1 18.4 - - - -
89A MET* 3.8 14.9 - - + +
90A MET* 5.0 3.6 - - - -
138A ASN* 1.3 72.3 - - - +
140A PHE* 1.3 68.7 + - - +
142A TYR* 4.0 7.4 - - + -
143A SER* 2.9 22.7 + - - -
33B LEU* 4.2 15.7 - - + -
36B GLY* 3.8 24.7 - - - +
39B PHE* 3.9 7.6 - - + -
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Residues in contact with PHE 140 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A CYS 3.4 24.5 - - - -
79A SER* 3.9 5.2 - - - -
80A SER 3.7 22.4 - - - +
81A THR* 3.8 20.6 + - + -
83A GLU 4.9 0.4 + - - +
89A MET* 3.9 10.5 - - + -
93A ASN* 4.0 5.6 - - - -
116A SER* 3.9 13.5 - - - -
118A ALA* 4.1 6.1 - - + -
138A ASN* 3.2 8.2 - - - +
139A VAL* 1.3 82.0 - - - +
141A GLY* 1.3 66.2 + - - +
143A SER* 2.6 24.9 + - - -
144A LYS* 3.2 29.1 + - + +
400A NAP 3.1 27.6 - - - -
402A BMA 3.5 31.0 - - - -
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Residues in contact with GLY 141 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118A ALA* 4.4 14.1 - - - -
119A THR* 3.9 2.3 - - - +
136A PRO* 3.4 16.2 - - - +
138A ASN* 2.7 21.8 + - - -
140A PHE* 1.3 82.9 - - - +
142A TYR* 1.3 57.8 + - - +
144A LYS* 3.2 6.5 + - - +
145A PHE* 2.8 30.1 + - - +
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Residues in contact with TYR 142 (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 MET* 4.1 29.6 - - + -
136A PRO* 3.6 9.3 - - + +
138A ASN 2.9 6.6 + - - +
139A VAL* 3.5 7.9 - - + +
140A PHE 3.2 0.2 - - - -
141A GLY* 1.3 77.6 - - - +
143A SER* 1.3 57.3 + - - +
145A PHE* 3.2 25.8 + + - +
146A LEU* 2.9 45.3 + - + +
33B LEU* 4.8 7.0 - - + -
39B PHE* 3.7 42.8 - + + -
42B LEU* 3.4 31.6 + - + +
43B VAL* 4.1 21.5 - - - -
47B ILE* 3.7 20.8 - - - +
50B TYR* 5.8 2.4 - + - +
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Residues in contact with SER 143 (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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89A MET* 3.6 16.6 - - - +
90A MET* 3.9 23.6 - - - -
93A ASN* 3.2 33.1 + - - +
94A TYR* 4.1 12.5 + - - +
139A VAL 2.9 11.6 + - - -
140A PHE 2.6 20.2 + - - -
142A TYR* 1.3 77.1 - - - +
144A LYS* 1.3 63.3 + - - +
147A PHE* 3.5 19.4 + - - +
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Residues in contact with LYS 144 (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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74A HIS 5.9 0.2 + - - -
76A GLY 5.0 1.4 + - - -
77A ALA* 3.6 13.6 - - - +
93A ASN* 4.6 8.4 - - + +
114A ALA* 3.0 27.2 + - - +
115A SER* 4.1 12.7 - - - +
116A SER* 4.2 10.1 - - - +
119A THR* 3.9 14.1 - - + -
140A PHE* 3.7 31.2 - - + +
141A GLY* 3.2 8.0 + - - +
142A TYR 3.1 0.6 - - - -
143A SER* 1.3 82.0 + - - +
145A PHE* 1.3 65.8 + - - +
147A PHE* 3.1 7.7 + - + +
148A ASP* 3.0 25.6 + - - +
400A NAP 3.0 39.0 + - - -
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Residues in contact with PHE 145 (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 THR* 3.5 13.4 - - + +
131A ARG* 3.5 44.0 - - + -
134A GLU* 3.2 39.5 - - + -
136A PRO* 3.9 17.5 - - + -
141A GLY 2.8 17.2 + - - +
142A TYR* 3.5 28.9 - + - +
144A LYS* 1.3 76.7 - - - +
146A LEU* 1.3 72.9 + - + +
148A ASP* 3.0 8.7 + - - +
149A GLU* 3.0 45.9 + - + +
152A ARG* 4.9 0.4 - - - -
166A ARG* 5.6 0.4 - - - -
42B LEU 5.6 0.4 - - - -
43B VAL 4.3 4.9 - - - -
45B LEU 5.0 4.0 - - - -
46B ASN* 5.6 0.2 - - - -
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Residues in contact with LEU 146 (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 MET* 3.7 20.4 - - + -
94A TYR* 3.5 37.0 - - + +
142A TYR* 2.9 44.1 + - + +
143A SER 4.5 0.9 - - - +
145A PHE* 1.3 89.0 - - + +
147A PHE* 1.3 57.6 + - - +
149A GLU* 3.3 11.3 + - + +
150A TYR* 2.9 22.7 + - - +
47B ILE* 4.0 24.2 - - + +
48B ALA 5.8 0.7 - - - +
49B ASP 5.7 1.6 - - - +
50B TYR* 3.7 18.4 - - + +
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Residues in contact with PHE 147 (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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93A ASN 5.6 0.2 - - - +
94A TYR* 3.6 17.9 - + + -
97A SER* 3.6 35.0 - - - +
98A LYS* 3.5 33.2 - - + -
101A LEU* 4.0 16.6 - - + -
111A PHE* 4.0 8.1 - + - -
113A TYR* 3.7 38.8 - + - -
143A SER 3.5 12.9 + - - +
144A LYS* 3.1 10.5 + - + +
146A LEU* 1.3 77.1 - - - +
148A ASP* 1.3 60.4 + - - +
150A TYR* 2.9 10.2 + + + +
151A VAL* 2.8 46.8 + - + +
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Residues in contact with ASP 148 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113A TYR* 2.7 41.9 + - - -
115A SER* 2.6 28.8 + - - -
119A THR* 4.2 3.8 - - - +
134A GLU* 5.5 0.2 - - - +
144A LYS 3.0 16.0 + - - +
145A PHE* 3.0 7.6 + - - +
147A PHE* 1.3 74.5 - - - +
149A GLU* 1.3 57.8 + - - +
151A VAL* 3.2 2.6 + - - +
152A ARG* 2.8 40.5 + - - +
166A ARG* 2.8 25.7 + - - +
232A ILE* 3.8 14.6 - - + +
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Residues in contact with GLU 149 (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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131A ARG* 3.7 24.6 - - - +
145A PHE* 3.0 38.0 + - + +
146A LEU* 3.4 17.9 - - + +
148A ASP* 1.3 77.5 - - - +
150A TYR* 1.3 62.4 + - - +
152A ARG* 2.9 40.5 + - - +
153A GLN* 3.2 31.7 + - - +
46B ASN* 4.4 8.7 - - - +
47B ILE 5.4 6.0 - - - +
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Residues in contact with TYR 150 (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 TYR* 3.7 20.0 - - + +
98A LYS* 3.6 31.5 + - + +
101A LEU* 4.0 22.7 - - + -
102A HIS* 2.6 36.5 + + - -
146A LEU 2.9 13.2 + - - +
147A PHE* 2.9 15.7 + + + +
149A GLU* 1.3 74.9 - - - +
151A VAL* 1.3 65.8 + - - +
153A GLN* 3.1 27.7 + - + +
154A ILE* 3.2 27.4 + - + +
48B ALA 4.0 13.9 - - - +
49B ASP* 4.4 9.6 - - + -
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Residues in contact with VAL 151 (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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101A LEU* 4.3 8.7 - - + -
113A TYR* 3.5 28.0 - - + +
147A PHE* 2.8 45.2 + - + +
148A ASP 3.5 7.9 - - - +
150A TYR* 1.3 72.2 - - - +
152A ARG* 1.3 58.6 + - - +
154A ILE* 2.9 8.6 + - - +
155A LEU* 2.8 44.7 + - + +
162A ILE* 3.7 25.8 - - + +
231A GLY 5.8 0.7 - - - +
232A ILE* 4.4 8.1 - - + -
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Residues in contact with ARG 152 (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 GLU* 3.5 24.7 + - - +
130A SER* 3.8 2.3 - - - +
131A ARG* 3.9 10.2 - - - +
134A GLU* 2.5 44.7 + - - -
145A PHE* 4.6 0.4 - - - -
148A ASP* 2.8 22.4 + - - +
149A GLU* 2.9 34.4 + - - +
150A TYR 3.2 0.2 - - - -
151A VAL* 1.3 76.5 - - - +
153A GLN* 1.3 60.2 + - - +
155A LEU* 3.8 12.7 + - + +
156A PRO* 3.4 19.2 - - - +
166A ARG* 3.9 6.8 - - - +
232A ILE* 3.9 26.6 - - + +
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Residues in contact with GLN 153 (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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149A GLU* 3.2 24.2 + - - +
150A TYR* 3.1 23.9 + - + +
152A ARG* 1.3 78.0 - - - +
154A ILE* 1.3 64.4 + - + +
156A PRO* 3.7 8.9 - - - +
157A GLU* 5.2 2.4 + - - +
47B ILE 4.4 4.9 + - - -
48B ALA* 3.2 42.8 + - - +
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Residues in contact with ILE 154 (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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101A LEU* 4.3 7.2 - - + -
102A HIS* 4.5 15.5 - - + -
105A LEU* 3.5 27.8 - - + -
150A TYR* 3.5 37.7 - - + +
151A VAL* 2.9 9.1 + - - +
153A GLN* 1.3 83.1 - - + +
155A LEU* 1.3 65.7 + - - +
156A PRO 3.4 0.2 - - - -
157A GLU* 3.0 18.1 + - + +
158A ALA* 3.2 9.9 + - + +
162A ILE* 3.9 17.5 - - + -
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Residues in contact with LEU 155 (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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151A VAL* 2.8 32.2 + - + +
152A ARG* 4.1 14.4 - - + +
154A ILE* 1.3 75.8 - - - +
156A PRO* 1.4 70.8 - - + +
157A GLU 3.0 1.0 + - - -
158A ALA* 3.2 21.0 + - + +
162A ILE* 4.0 30.1 - - + +
230A SER* 4.1 22.4 - - - +
231A GLY* 4.2 19.7 - - - +
232A ILE* 5.1 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