Contacts of the helix formed by residues 138 - 155 (chain H) 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 H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81H THR* 3.7 34.8 + - - +
84H TRP* 3.5 25.4 - - + -
118H ALA* 5.0 5.4 - - - +
136H PRO* 4.0 1.7 - - - +
137H LEU* 1.3 84.6 + - - +
139H VAL* 1.3 59.2 - - - +
140H PHE* 3.4 8.6 + - - +
141H GLY* 2.7 45.4 + - - -
142H TYR* 2.9 11.4 + - - +
268H LEU* 6.3 1.0 - - - +
271H ARG* 3.9 19.9 + - + +
401H ADP 5.1 2.2 + - - -
39I PHE* 3.3 9.6 - - - -
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Residues in contact with VAL 139 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83H GLU 3.4 22.9 - - - +
84H TRP* 3.6 26.4 - - + -
86H GLY* 4.1 18.6 - - - -
89H MET* 3.8 15.7 - - + +
90H MET* 5.0 3.6 - - - -
138H ASN* 1.3 71.0 - - - +
140H PHE* 1.3 68.3 + - - +
142H TYR* 4.0 8.1 - - + -
143H SER* 2.9 22.9 + - - -
33I LEU* 4.1 15.7 - - + -
36I GLY* 3.7 25.6 - - - +
39I PHE* 3.9 6.9 - - + -
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Residues in contact with PHE 140 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78H CYS 3.4 26.9 - - - -
79H SER* 3.9 6.3 - - - -
80H SER 3.7 21.5 - - - +
81H THR* 3.8 20.8 + - + -
83H GLU 4.9 0.2 + - - -
89H MET* 3.9 9.4 - - + -
93H ASN* 4.0 4.7 - - - -
116H SER* 3.9 14.4 - - - -
118H ALA* 4.1 5.2 - - + -
138H ASN* 3.2 9.0 - - - +
139H VAL* 1.3 81.8 - - - +
141H GLY* 1.3 66.3 + - - +
143H SER* 2.6 25.3 + - - -
144H LYS* 3.2 26.7 + - + +
400H NAP 3.3 26.7 - - - -
402H BMA 3.5 31.2 - - - -
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Residues in contact with GLY 141 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118H ALA* 4.4 13.9 - - - -
119H THR* 3.9 2.4 - - - +
136H PRO* 3.4 17.0 - - - +
138H ASN* 2.7 22.4 + - - -
140H PHE* 1.3 81.5 - - - +
142H TYR* 1.3 57.4 + - - +
144H LYS* 3.2 6.2 + - - +
145H PHE* 2.8 29.6 + - - +
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Residues in contact with TYR 142 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90H MET* 4.1 29.4 - - + -
136H PRO* 3.6 10.4 - - + +
138H ASN 2.9 6.7 + - - +
139H VAL* 3.5 7.6 - - + +
140H PHE 3.2 0.2 - - - -
141H GLY* 1.3 77.8 - - - +
143H SER* 1.3 57.3 + - - +
145H PHE* 3.2 25.1 + + - +
146H LEU* 2.9 44.8 + - + +
33I LEU* 4.7 7.4 - - + -
39I PHE* 3.7 44.9 - + + -
42I LEU* 3.5 33.1 + - + +
43I VAL* 4.2 18.2 - - - -
47I ILE* 3.6 22.0 - - - +
50I TYR* 5.7 2.2 - + + -
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Residues in contact with SER 143 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89H MET* 3.6 16.0 - - - +
90H MET* 3.9 22.2 - - - -
93H ASN* 3.2 33.8 + - - +
94H TYR* 4.1 12.0 + - - +
139H VAL 2.9 12.1 + - - -
140H PHE 2.6 20.1 + - - -
142H TYR* 1.3 77.5 - - - +
144H LYS* 1.3 62.1 + - - +
147H PHE* 3.5 19.4 + - - +
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Residues in contact with LYS 144 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76H GLY 5.1 1.0 + - - -
77H ALA* 3.6 14.4 - - - +
93H ASN* 4.6 8.8 - - + +
97H SER* 5.6 3.4 + - - -
113H TYR* 6.4 0.2 - - + -
114H ALA* 3.0 28.8 + - - +
115H SER* 4.1 10.3 - - - +
116H SER* 4.2 11.7 - - - +
119H THR* 3.9 15.0 - - + -
140H PHE* 3.7 32.1 - - + +
141H GLY 3.2 7.5 + - - +
142H TYR 3.1 0.2 - - - -
143H SER* 1.3 83.4 + - - +
145H PHE* 1.3 65.2 + - - +
147H PHE* 3.1 8.5 + - + +
148H ASP* 3.0 25.0 + - - +
400H NAP 3.1 38.5 + - - -
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Residues in contact with PHE 145 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119H THR* 3.5 12.9 - - + +
131H ARG* 3.5 43.7 - - + -
134H GLU* 3.2 38.6 - - + -
136H PRO* 3.9 17.5 - - + -
141H GLY 2.8 17.2 + - - +
142H TYR* 3.5 29.2 - + - +
144H LYS* 1.3 76.8 - - - +
146H LEU* 1.3 74.1 + - + +
148H ASP* 3.0 8.9 + - - +
149H GLU* 3.0 45.2 + - + +
152H ARG* 4.9 0.4 - - - -
166H ARG* 5.6 0.2 - - - -
42I LEU 5.6 0.4 - - - -
43I VAL 4.5 4.7 - - - -
45I LEU 5.0 3.8 - - - -
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Residues in contact with LEU 146 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90H MET* 3.6 13.9 - - + -
94H TYR* 3.5 31.0 - - + +
142H TYR* 2.9 41.8 + - + +
145H PHE* 1.3 88.9 - - + +
147H PHE* 1.3 58.2 + - - +
149H GLU* 3.3 11.6 + - + +
150H TYR* 2.9 22.7 + - - +
47I ILE* 4.0 23.8 - - + +
48I ALA 5.7 1.1 - - - +
49I ASP* 5.5 2.2 - - - -
50I TYR* 3.5 34.5 - - + +
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Residues in contact with PHE 147 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94H TYR* 3.6 17.0 - + + -
97H SER* 3.6 36.1 - - - +
98H LYS* 3.5 34.3 - - + -
101H LEU* 4.0 16.4 - - + -
111H PHE* 4.0 7.6 - + - -
113H TYR* 3.7 39.0 - + - -
114H ALA 5.8 0.2 - - - -
143H SER 3.5 12.6 + - - +
144H LYS* 3.1 11.0 + - + +
146H LEU* 1.3 77.3 - - - +
148H ASP* 1.3 60.4 + - - +
150H TYR* 2.9 9.0 + + + +
151H VAL* 2.8 46.9 + - + +
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Residues in contact with ASP 148 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113H TYR* 2.7 40.7 + - - -
115H SER* 2.6 28.5 + - - -
119H THR* 4.2 3.6 - - - +
144H LYS 3.0 14.5 + - - +
145H PHE* 3.4 7.9 - - - +
147H PHE* 1.3 75.0 - - - +
149H GLU* 1.3 58.1 + - - +
151H VAL* 3.2 2.8 + - - +
152H ARG* 2.8 40.8 + - - +
166H ARG* 2.8 26.5 + - - +
232H ILE* 3.8 14.3 - - + +
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Residues in contact with GLU 149 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131H ARG* 3.7 25.4 - - - +
145H PHE* 3.0 39.4 + - + +
146H LEU* 3.4 18.4 - - + +
147H PHE 3.1 0.2 - - - -
148H ASP* 1.3 76.8 - - - +
150H TYR* 1.3 61.6 + - - +
152H ARG* 2.9 39.2 + - - +
153H GLN* 3.2 32.1 + - - +
46I ASN* 4.5 7.8 - - - +
47I ILE 5.2 8.4 - - - +
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Residues in contact with TYR 150 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94H TYR* 3.7 19.3 - - + +
98H LYS* 3.6 32.8 + - + +
101H LEU* 4.0 22.4 - - + -
102H HIS* 2.6 38.0 + + - -
146H LEU 2.9 13.6 + - - +
147H PHE* 2.9 15.7 + + + +
149H GLU* 1.3 75.1 - - - +
151H VAL* 1.3 66.3 + - - +
153H GLN* 3.1 28.4 + - + +
154H ILE* 3.2 26.2 + - + +
48I ALA 4.2 12.3 - - - -
49I ASP* 4.4 10.8 - - + -
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Residues in contact with VAL 151 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101H LEU* 4.3 9.6 - - + -
113H TYR* 3.5 27.8 - - + +
147H PHE* 2.8 44.4 + - + +
148H ASP 3.5 7.6 - - - +
150H TYR* 1.3 72.4 - - - +
152H ARG* 1.3 58.2 + - - +
154H ILE* 2.9 10.3 + - - +
155H LEU* 2.8 43.8 + - + +
162H ILE* 3.7 25.1 - - + -
231H GLY 5.8 0.9 - - - +
232H ILE* 4.4 7.9 - - + -
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Residues in contact with ARG 152 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129H GLU* 3.5 24.9 + - - +
130H SER* 3.8 1.8 - - - +
131H ARG* 3.9 10.5 - - - +
134H GLU* 2.5 45.6 + - - -
145H PHE* 4.6 0.6 - - - -
148H ASP* 2.8 23.0 + - - +
149H GLU* 2.9 33.7 + - - +
150H TYR 3.2 0.4 - - - -
151H VAL* 1.3 77.7 - - - +
153H GLN* 1.3 60.5 + - - +
155H LEU* 3.8 11.8 + - + +
156H PRO* 3.4 19.2 - - - +
166H ARG* 3.9 5.9 - - - +
232H ILE* 3.9 27.0 - - + +
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Residues in contact with GLN 153 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149H GLU* 3.2 23.4 + - - +
150H TYR* 3.1 25.1 + - + +
152H ARG* 1.3 77.2 - - - +
154H ILE* 1.3 64.4 + - + +
156H PRO* 3.7 8.9 - - - +
157H GLU* 5.3 2.3 + - - +
47I ILE 4.5 4.0 + - - -
48I ALA* 3.0 44.0 + - - +
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Residues in contact with ILE 154 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101H LEU* 4.3 7.2 - - + -
102H HIS* 4.5 15.7 - - + -
105H LEU* 3.5 28.3 - - + -
150H TYR* 3.5 37.2 - - + +
151H VAL* 2.9 10.4 + - - +
153H GLN* 1.3 82.7 - - + +
155H LEU* 1.3 65.2 + - - +
156H PRO 3.4 0.2 - - - -
157H GLU* 3.0 18.7 + - + +
158H ALA* 3.2 10.6 + - + +
162H ILE* 3.9 16.8 - - + -
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Residues in contact with LEU 155 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151H VAL* 2.8 32.2 + - + +
152H ARG* 4.1 14.8 - - + +
154H ILE* 1.3 76.2 - - - +
156H PRO* 1.4 71.7 - - + +
157H GLU 3.0 1.4 + - - -
158H ALA* 3.2 19.3 + - + +
162H ILE* 4.0 30.1 - - + +
230H SER* 4.1 21.1 - - - -
231H GLY* 4.2 18.8 - - - +
232H ILE* 5.1 2.7 - - + +
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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) + - + + + + + -
------------------------------------------------------------
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