Contacts of the helix formed by residues 138 - 155 (chain P) 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 P).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81P THR* 3.7 35.4 + - - +
84P TRP* 3.5 24.5 - - + -
118P ALA* 5.1 5.6 - - - +
136P PRO* 4.0 1.9 - - - +
137P LEU* 1.3 83.7 + - - +
139P VAL* 1.3 59.5 + - + +
140P PHE* 3.4 8.8 + - - +
141P GLY* 2.7 45.7 + - - -
142P TYR* 2.9 11.6 + - - +
268P LEU* 6.2 1.0 - - - +
271P ARG* 3.9 20.3 + - + +
401P ADP 5.3 1.6 + - - -
39Q PHE* 3.3 9.2 - - - -
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Residues in contact with VAL 139 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83P GLU 3.4 23.6 - - - +
84P TRP* 3.6 25.3 - - + -
86P GLY* 4.1 18.6 - - - -
89P MET* 3.8 15.1 - - + +
90P MET* 5.0 4.0 - - - -
138P ASN* 1.3 72.1 - - - +
140P PHE* 1.3 69.2 + - - +
142P TYR* 3.2 8.2 + - + -
143P SER* 2.9 22.3 + - - -
33Q LEU* 4.2 15.3 - - + -
36Q GLY* 3.8 24.5 - - - +
39Q PHE* 3.8 7.4 - - + -
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Residues in contact with PHE 140 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78P CYS 3.4 27.1 - - - -
79P SER* 3.9 5.8 - - - -
80P SER 3.7 21.3 - - - +
81P THR* 3.8 21.5 + - + -
83P GLU 4.9 0.4 + - - -
89P MET* 3.9 10.3 - - + -
93P ASN* 4.0 5.4 - - - -
116P SER* 3.9 14.1 - - - -
118P ALA* 4.1 5.8 - - + -
138P ASN* 3.2 8.4 + - - +
139P VAL* 1.3 82.0 - - - +
141P GLY* 1.3 67.1 + - - +
143P SER* 2.6 25.1 + - - -
144P LYS* 3.2 26.5 + - + +
400P NAP 3.2 26.9 - - - -
402P BMA 3.6 32.3 - - - -
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Residues in contact with GLY 141 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118P ALA* 4.4 14.4 - - - -
119P THR* 3.9 2.8 - - - +
136P PRO* 3.4 16.4 - - - +
138P ASN* 2.7 22.2 + - - -
140P PHE* 1.3 81.9 - - - +
142P TYR* 1.3 56.8 + - - +
144P LYS* 3.2 5.5 + - - +
145P PHE* 2.8 30.1 + - - +
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Residues in contact with TYR 142 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90P MET* 4.0 29.8 - - + -
136P PRO* 3.6 8.6 - - + +
138P ASN 2.9 6.8 + - - +
139P VAL* 3.5 10.1 - - + +
140P PHE 3.2 0.2 - - - -
141P GLY* 1.3 76.7 - - - +
143P SER* 1.3 56.8 + - - +
145P PHE* 3.2 24.7 + + - +
146P LEU* 2.9 45.5 + - + +
33Q LEU* 4.8 6.7 - - + -
39Q PHE* 3.7 41.3 - + + -
42Q LEU* 3.4 31.8 + - + +
43Q VAL* 4.1 22.7 - - - -
47Q ILE* 3.7 21.1 - - - +
50Q TYR* 5.7 2.0 - + + +
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Residues in contact with SER 143 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89P MET* 3.6 16.0 - - - +
90P MET* 3.9 22.2 - - - -
93P ASN* 3.2 33.5 + - - +
94P TYR* 4.1 11.7 + - - +
139P VAL 2.9 12.2 + - - -
140P PHE 2.6 19.8 + - - -
142P TYR* 1.3 78.0 - - - +
144P LYS* 1.3 62.7 + - - +
147P PHE* 3.5 20.1 + - - +
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Residues in contact with LYS 144 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74P HIS 5.9 0.4 + - - -
76P GLY 5.0 1.4 + - - -
77P ALA* 3.6 13.7 - - - +
93P ASN* 4.6 7.1 - - + +
97P SER* 5.6 3.8 + - - -
114P ALA* 3.0 28.7 + - - +
115P SER* 4.1 10.9 - - - +
116P SER* 4.2 10.8 - - - +
119P THR* 3.9 14.4 - - + -
140P PHE* 3.7 29.8 - - + +
141P GLY* 3.2 8.0 + - - +
142P TYR 3.1 0.4 - - - -
143P SER* 1.3 83.1 + - - +
145P PHE* 1.3 66.1 + - - +
147P PHE* 3.1 8.3 + - + +
148P ASP* 3.0 25.2 + - - +
400P NAP 3.1 40.2 + - - -
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Residues in contact with PHE 145 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119P THR* 3.5 13.4 - - + +
131P ARG* 3.5 42.4 - - + -
134P GLU* 3.2 40.6 - - + -
136P PRO* 3.9 17.7 - - + -
141P GLY 2.8 16.6 + - - +
142P TYR* 3.5 28.9 - + - +
144P LYS* 1.3 76.8 - - - +
146P LEU* 1.3 72.6 + - + +
148P ASP* 3.0 8.1 + - - +
149P GLU* 3.0 45.6 + - + +
152P ARG* 4.9 0.2 - - - -
166P ARG* 5.6 0.4 - - - -
42Q LEU 5.6 0.4 - - - -
43Q VAL 4.4 5.6 - - - -
45Q LEU 4.9 4.3 - - - -
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Residues in contact with LEU 146 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90P MET* 3.6 21.5 - - + -
94P TYR* 3.5 36.3 - - + +
142P TYR* 2.9 42.6 + - + +
143P SER 4.5 0.2 - - - +
145P PHE* 1.3 89.3 - - + +
147P PHE* 1.3 56.9 + - - +
149P GLU* 3.3 11.6 + - + +
150P TYR* 2.9 23.0 + - - +
47Q ILE* 4.0 23.1 - - + +
48Q ALA 5.8 1.3 - - - +
49Q ASP 4.8 2.0 - - - +
50Q TYR* 3.7 19.1 - - + +
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Residues in contact with PHE 147 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93P ASN 6.0 0.2 - - - -
94P TYR* 3.6 17.6 - + + -
97P SER* 3.6 35.4 - - - -
98P LYS* 3.5 33.7 - - + -
101P LEU* 4.0 16.6 - - + -
111P PHE* 4.0 8.5 - + - -
113P TYR* 3.7 39.5 - + - -
143P SER 3.5 13.1 + - - +
144P LYS* 3.1 9.9 + - + +
146P LEU* 1.3 77.8 - - - +
148P ASP* 1.3 60.5 + - - +
150P TYR* 2.9 9.3 + + + +
151P VAL* 2.8 47.1 + - + +
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Residues in contact with ASP 148 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113P TYR* 2.7 42.3 + - - -
115P SER* 2.6 28.4 + - - -
119P THR* 4.2 3.8 - - - +
144P LYS 3.0 14.9 + - - +
145P PHE 3.4 7.9 - - - +
147P PHE* 1.3 73.7 - - - +
149P GLU* 1.3 58.0 + - - +
151P VAL* 3.2 3.0 + - - +
152P ARG* 2.8 40.8 + - - +
166P ARG* 2.8 26.6 + - - +
232P ILE* 3.8 14.2 - - + +
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Residues in contact with GLU 149 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131P ARG* 3.7 26.2 - - - +
145P PHE* 3.0 39.5 + - + +
146P LEU* 3.4 17.7 - - + +
148P ASP* 1.3 77.3 - - - +
150P TYR* 1.3 61.8 + - - +
152P ARG* 2.9 40.2 + - - +
153P GLN* 3.2 32.3 + - - +
46Q ASN* 4.4 9.0 - - - +
47Q ILE 5.3 7.7 - - - +
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Residues in contact with TYR 150 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94P TYR* 3.7 19.3 - - + +
98P LYS* 3.6 32.1 + - + +
101P LEU* 4.0 23.3 - - + -
102P HIS* 2.6 36.9 + + - -
146P LEU 2.9 13.9 + - - +
147P PHE* 3.2 15.3 - + + +
149P GLU* 1.3 75.3 - - - +
151P VAL* 1.3 65.7 + - - +
153P GLN* 3.1 28.1 + - + +
154P ILE* 3.2 23.8 + - + +
48Q ALA 4.1 13.7 - - - +
49Q ASP* 4.5 9.4 - - + -
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Residues in contact with VAL 151 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101P LEU* 4.3 9.2 - - + -
113P TYR* 3.5 30.7 - - + +
147P PHE* 2.8 42.3 + - + +
148P ASP 3.2 7.4 + - - +
150P TYR* 1.3 72.5 - - - +
152P ARG* 1.3 59.4 + - - +
154P ILE* 2.9 8.3 + - - +
155P LEU* 2.8 44.0 + - + +
162P ILE* 3.7 25.4 - - + -
231P GLY 5.8 0.9 - - - +
232P ILE* 4.3 8.5 - - + -
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Residues in contact with ARG 152 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129P GLU* 3.5 25.1 + - - +
130P SER* 3.8 2.0 - - - +
131P ARG* 3.8 10.6 - - - +
134P GLU* 2.5 45.4 + - - -
145P PHE* 4.6 0.4 - - - -
148P ASP* 2.8 24.1 + - - +
149P GLU* 2.9 33.6 + - - +
150P TYR 3.2 0.2 - - - -
151P VAL* 1.3 75.5 - - - +
153P GLN* 1.3 60.9 + - + +
155P LEU* 4.1 12.4 - - + +
156P PRO* 3.4 19.1 - - - +
166P ARG* 4.0 5.7 - - - +
232P ILE* 3.9 27.4 - - + +
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Residues in contact with GLN 153 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149P GLU* 3.2 23.9 + - - +
150P TYR* 3.1 24.0 + - + +
152P ARG* 1.3 76.6 - - - +
154P ILE* 1.3 65.6 + - + +
156P PRO* 3.7 9.1 - - - +
157P GLU* 5.2 2.3 + - - +
47Q ILE 4.5 4.0 + - - -
48Q ALA* 3.2 43.9 + - - +
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Residues in contact with ILE 154 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101P LEU* 4.3 6.5 - - + -
102P HIS* 4.5 16.2 - - + -
105P LEU* 3.5 28.7 - - + -
150P TYR* 3.5 36.8 - - + +
151P VAL* 2.9 9.7 + - - +
153P GLN* 1.3 82.5 - - + +
155P LEU* 1.3 67.7 + - - +
157P GLU* 3.0 17.9 + - + +
158P ALA* 3.2 9.1 + - + +
162P ILE* 3.9 17.5 - - + -
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Residues in contact with LEU 155 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151P VAL* 2.8 34.5 + - + +
152P ARG* 4.1 15.0 - - + +
154P ILE* 1.3 72.2 - - - +
156P PRO* 1.4 71.8 - - + +
157P GLU 3.0 0.9 + - - -
158P ALA* 3.2 20.6 + - + +
162P ILE* 4.0 30.3 - - + +
230P SER* 4.1 21.1 - - - +
231P GLY* 4.3 19.5 - - - +
232P 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
------------------------------------------------------------
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