Contacts of the helix formed by residues 142 - 155 (chain I) in PDB entry 2I2X
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 LYS 142 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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93I ASN* 4.5 8.8 + - - +
129I ILE* 3.8 34.2 + - + +
130I ARG* 4.3 10.8 - - + -
131I GLU 2.8 36.4 + - - +
132I ASN* 4.2 8.5 - - - +
137I GLN* 4.8 15.3 - - + +
140I GLY 3.1 1.8 + - - -
141I ASP* 1.3 87.3 - - + +
143I TYR* 1.3 63.4 + - - +
144I SER 3.2 2.9 - - - -
145I VAL* 3.0 15.8 + - + +
146I PHE* 2.9 23.8 + - - +
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Residues in contact with TYR 143 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130I ARG* 3.9 11.7 - - - +
137I GLN 5.5 0.4 + - - -
138I LEU 3.2 23.6 - - - +
139I ARG* 4.4 5.2 - - - -
140I GLY 3.2 20.3 + - - +
142I LYS* 1.3 76.7 - - - +
144I SER* 1.3 58.7 + - - +
146I PHE* 3.1 10.8 - + - +
147I LEU* 3.1 47.5 + - + +
198I LEU* 3.1 46.8 + - + +
199I ILE* 3.4 22.2 - - + -
202I ASP* 2.7 30.5 + - - +
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Residues in contact with SER 144 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140I GLY 4.8 0.4 + - - -
141I ASP 3.9 11.8 + - - -
142I LYS 3.2 0.2 - - - -
143I TYR* 1.3 77.4 - - - +
145I VAL* 1.3 67.0 + - - +
147I LEU* 3.4 9.7 + - - +
148I GLU* 2.9 38.0 + - - +
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Residues in contact with VAL 145 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92I SER 3.9 10.1 - - - +
93I ASN* 3.5 25.6 - - - +
95I PRO* 3.9 10.4 - - + +
129I ILE* 4.0 10.8 - - + -
141I ASP 4.3 8.7 - - - +
142I LYS* 3.0 17.4 + - + +
144I SER* 1.3 81.7 - - - +
146I PHE* 1.3 61.0 + - - +
148I GLU* 3.1 14.9 + - - +
149I ALA* 2.9 30.0 + - - +
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Residues in contact with PHE 146 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126I ILE* 3.9 18.8 - - + -
127I GLY 3.9 13.9 - - - -
128I ASP* 4.0 13.2 - - - -
129I ILE* 3.9 18.2 - - + +
130I ARG* 3.8 30.5 - - + -
142I LYS 2.9 11.6 + - - +
143I TYR* 3.1 20.4 - + - +
145I VAL* 1.3 76.5 - - - +
147I LEU* 1.3 71.5 + - + +
149I ALA* 3.3 12.6 + - - +
150I PHE* 3.2 43.8 + + - -
163I VAL* 4.0 15.0 - - + -
199I ILE* 4.0 30.1 - - + -
203I ILE* 4.8 0.9 - - + -
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Residues in contact with LEU 147 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143I TYR* 3.1 43.5 + - + +
144I SER* 3.4 10.3 + - - +
146I PHE* 1.3 89.2 - - + +
148I GLU* 1.3 65.1 + - - +
150I PHE* 3.2 13.3 + - + +
151I GLU* 3.0 23.8 + - - +
199I ILE 5.2 0.7 - - - +
202I ASP* 3.7 34.1 - - + +
203I ILE* 5.0 3.4 - - + -
206I ILE* 3.6 24.0 - - + +
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Residues in contact with GLU 148 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95I PRO* 4.0 18.2 - - + +
144I SER* 2.9 26.2 + - - +
145I VAL* 3.1 17.0 + - - +
147I LEU* 1.3 76.5 - - - +
149I ALA* 1.3 50.7 + - - +
151I GLU* 3.9 15.8 - - + +
152I GLN* 2.8 49.6 + - + +
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Residues in contact with ALA 149 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87I HIS* 5.0 2.7 - - + -
91I MET 4.8 1.6 - - - +
92I SER* 3.8 26.2 - - - +
95I PRO* 3.8 15.2 - - + +
126I ILE* 4.0 19.5 - - + -
145I VAL 2.9 11.8 + - - +
146I PHE* 3.5 10.8 - - - +
147I LEU 3.2 0.4 - - - -
148I GLU* 1.3 73.0 - - - +
150I PHE* 1.3 66.6 + - - +
152I GLN* 4.3 0.9 - - - -
153I CYS* 2.9 30.0 + - - -
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Residues in contact with PHE 150 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126I ILE* 3.7 26.0 - - + +
146I PHE* 3.2 51.2 + + - -
147I LEU* 3.2 11.1 + - + +
149I ALA* 1.3 78.4 - - - +
151I GLU* 1.3 58.7 + - - +
153I CYS* 3.9 1.2 - - - +
154I ALA* 2.9 30.3 + - - +
161I LEU* 4.0 19.6 - - + +
162I SER 3.4 24.9 - - - -
163I VAL* 3.7 20.4 - - + -
203I ILE* 3.4 43.7 - - + -
206I ILE* 4.1 18.2 - - + -
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Residues in contact with GLU 151 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147I LEU* 3.0 15.9 + - - +
148I GLU* 3.9 22.0 + - + +
150I PHE* 1.3 76.7 - - - +
152I GLN* 1.3 65.4 + - - +
154I ALA* 3.8 2.4 - - - +
155I GLU* 3.0 42.1 + - - +
206I ILE* 3.6 29.3 - - + +
209I LYS* 2.8 35.8 + - - +
210I THR* 4.4 6.7 - - + -
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Residues in contact with GLN 152 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95I PRO* 3.9 27.6 - - + +
96I SER* 4.3 12.6 - - - -
99I ALA* 3.6 13.5 - - + +
148I GLU* 2.8 39.9 + - + +
149I ALA 3.7 3.6 - - - +
151I GLU* 1.3 79.2 - - - +
153I CYS* 1.3 61.5 + - - +
155I GLU* 3.5 18.2 + - - +
156I ASN* 3.0 35.4 + - - +
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Residues in contact with CYS 153 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87I HIS* 3.4 37.5 - - - -
95I PRO 4.8 1.8 - - - -
98I GLY* 3.5 17.9 - - - -
99I ALA* 3.9 6.1 - - - +
102I ALA* 4.1 1.6 - - - +
124I HIS* 3.5 22.0 - - + -
126I ILE* 4.6 4.7 - - + -
149I ALA 2.9 19.9 + - - +
150I PHE 3.9 2.7 - - - +
152I GLN* 1.3 74.5 - - - +
154I ALA* 1.3 58.4 + - - +
156I ASN* 3.0 18.2 + - - -
157I GLY 3.4 1.0 + - - -
158I ALA* 3.2 26.7 + - + +
161I LEU* 4.8 1.3 - - + -
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Residues in contact with ALA 154 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150I PHE 2.9 18.2 + - - +
151I GLU* 3.8 6.1 - - - +
153I CYS* 1.3 77.7 - - - +
155I GLU* 1.3 59.2 + - - +
156I ASN 3.5 0.7 + - - -
157I GLY 4.2 2.4 + - - -
158I ALA 3.8 13.5 - - - +
161I LEU* 4.1 14.9 - - + +
206I ILE* 4.7 0.9 - - + -
210I THR* 3.3 30.1 - - + +
212I THR* 3.5 27.6 - - - +
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Residues in contact with GLU 155 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151I GLU* 3.0 32.2 + - - +
152I GLN* 3.7 24.2 + - - +
153I CYS 3.2 0.4 - - - -
154I ALA* 1.3 75.9 - - - +
156I ASN* 1.3 67.7 + - - +
157I GLY 3.7 1.1 - - - -
209I LYS* 4.5 8.1 + - - -
210I THR* 3.9 22.5 - - + +
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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