Contacts of the helix formed by residues 137 - 149 (chain J) 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 ASP 137 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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169I LYS* 5.8 1.4 + - - -
173I ASP* 5.5 1.8 - - + +
130J VAL* 4.5 5.1 - - - +
135J VAL* 3.0 9.1 + - - +
136J HIS* 1.3 72.3 - - - +
138J ILE* 1.3 57.6 + - + +
139J GLY 3.3 1.3 - - - -
140J LYS* 2.9 28.9 + - - +
141J ASN* 2.8 48.2 + - - +
158J GLY* 5.4 0.2 - - - -
159J ARG* 3.0 48.8 + - - +
500J B13 3.1 12.6 + - - +
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Residues in contact with ILE 138 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173I ASP* 3.4 38.6 - - + +
176I VAL* 4.5 4.0 - - + -
177I LEU* 4.5 11.9 - - + -
225I THR* 3.7 23.1 - - + -
229I ILE* 4.1 13.7 - - + -
136J HIS 3.5 0.2 - - - -
137J ASP* 1.3 79.4 - - + +
139J GLY* 1.3 64.7 + - - +
141J ASN* 3.3 8.4 + - - +
142J ILE* 3.0 43.7 + - + +
500J B13 2.9 44.2 + - + +
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Residues in contact with GLY 139 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136J HIS 4.7 1.6 + - - -
137J ASP 3.3 0.6 - - - -
138J ILE* 1.3 81.7 - - - +
140J LYS* 1.3 60.6 + - - +
142J ILE* 3.2 4.7 + - - +
143J VAL* 3.1 21.1 + - - +
181J THR* 4.6 2.5 - - - -
500J B13 3.4 55.1 + - - +
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Residues in contact with LYS 140 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128J CYS* 4.4 13.7 - - + -
129J HIS* 4.4 8.1 - - - +
130J VAL* 3.6 27.8 - - + +
137J ASP* 2.9 34.2 + - - +
139J GLY* 1.3 72.4 - - - -
141J ASN* 1.3 80.8 + - - +
143J VAL* 3.0 8.4 + - + +
144J THR* 2.7 39.8 + - - +
156J ASP* 3.5 30.5 + - - +
158J GLY* 3.6 18.2 + - - +
179J THR* 5.3 2.0 - - - +
181J THR* 3.7 24.6 + - + +
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Residues in contact with ASN 141 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173I ASP* 6.3 1.6 - - - +
177I LEU* 4.8 14.5 - - + +
99J MET* 5.0 2.1 - - + +
137J ASP* 2.8 33.4 + - - +
138J ILE* 3.6 14.1 - - - +
139J GLY 3.2 0.2 - - - -
140J LYS* 1.3 95.3 + - - +
142J ILE* 1.3 59.7 + - - +
144J THR* 3.6 7.4 - - - +
145J ALA* 2.9 31.4 + - - +
156J ASP* 4.0 6.6 - - - +
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Residues in contact with ILE 142 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177I LEU* 4.2 18.6 - - + -
229I ILE* 5.4 4.3 - - + -
237I ASN* 5.6 1.3 - - - +
88J TYR* 5.4 1.3 - - - +
95J LEU* 3.7 45.8 - - + -
99J MET* 5.1 3.8 - - - -
138J ILE* 3.0 27.9 + - + +
139J GLY* 3.6 5.8 - - - +
141J ASN* 1.3 75.1 - - - +
143J VAL* 1.3 56.3 + - - +
145J ALA* 3.9 4.8 + - - +
146J LEU* 3.2 29.7 + - + +
231J ALA* 3.7 22.0 - - + -
500J B13 3.7 34.1 - - + -
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Residues in contact with VAL 143 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128J CYS* 4.6 2.5 - - + -
139J GLY 3.1 12.3 + - - +
140J LYS* 3.0 12.9 + - - +
142J ILE* 1.3 74.7 - - - +
144J THR* 1.3 67.9 + - - +
146J LEU* 3.1 7.7 + - - +
147J LEU* 2.9 42.3 + - + +
179J THR* 4.2 19.7 - - + +
181J THR* 5.8 0.2 - - - +
231J ALA* 3.9 26.0 - - + +
234J ALA* 4.0 11.4 - - + +
235J PRO* 5.3 0.2 - - - +
500J B13 3.7 33.4 - - + +
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Residues in contact with THR 144 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128J CYS* 4.0 14.2 - - - +
140J LYS* 2.7 22.2 + - - +
141J ASN* 3.6 11.0 - - - +
143J VAL* 1.3 73.9 - - - +
145J ALA* 1.3 65.0 + - + +
147J LEU* 3.2 4.7 + - - +
148J ARG* 3.0 58.8 + - - +
154J VAL* 3.8 18.2 - - + +
156J ASP* 3.5 21.6 + - - +
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Residues in contact with ALA 145 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99J MET* 3.6 37.7 - - + -
102J ALA* 4.4 10.6 - - + +
141J ASN 2.9 17.9 + - - +
142J ILE 4.1 2.0 - - - +
144J THR* 1.3 78.0 - - + +
146J LEU* 1.3 58.9 + - - +
148J ARG* 3.7 8.5 + - - +
149J ALA* 3.0 27.5 + - - +
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Residues in contact with LEU 146 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85J ILE* 6.1 3.4 - - + -
88J TYR* 4.3 13.9 - - + -
95J LEU* 4.3 16.8 - - + -
98J VAL* 3.7 29.8 - - + -
99J MET* 5.3 0.9 - - - -
142J ILE* 3.2 24.1 + - + +
143J VAL* 3.1 7.9 + - - +
145J ALA* 1.3 78.1 - - + +
147J LEU* 1.3 63.7 + - - +
149J ALA* 3.7 3.3 + - + -
150J ASN* 2.8 37.0 + - - +
231J ALA* 4.7 3.6 - - + +
232J ALA* 3.7 36.1 - - + +
235J PRO* 3.4 18.8 - - + +
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Residues in contact with LEU 147 (chain J).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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126J VAL* 3.8 33.0 - - + -
128J CYS* 3.8 11.0 - - - -
143J VAL* 2.9 34.5 + - + +
144J THR 3.6 3.6 - - - +
146J LEU* 1.3 76.6 - - - +
148J ARG* 1.3 59.9 + - - +
150J ASN 3.2 7.6 + - - -
152J TYR* 3.2 33.0 + - + +
154J VAL* 3.5 17.5 - - + -
177J MET* 5.8 0.4 - - - -
179J THR* 4.2 5.2 - - + -
234J ALA* 3.8 6.7 - - + +
235J PRO* 3.5 38.8 - - + -
238J ALA* 4.4 11.0 - - + -
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Residues in contact with ARG 148 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78J MET* 5.0 0.2 - - - +
102J ALA* 6.0 1.1 - - + -
105J MET* 3.9 14.5 - - - +
106J LEU* 4.4 35.9 - - + +
144J THR* 3.0 38.0 + - - +
145J ALA* 3.9 7.5 - - - +
147J LEU* 1.3 75.9 - - - +
149J ALA* 1.3 60.9 + - - +
151J GLY* 3.2 13.5 + - - -
152J TYR 3.8 18.6 + - - +
154J VAL* 3.2 41.0 + - + +
156J ASP* 4.2 15.2 + - - +
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Residues in contact with ALA 149 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78J MET* 4.1 6.0 - - - +
81J MET* 3.3 50.5 - - + +
85J ILE* 3.4 9.8 - - + +
98J VAL* 4.9 7.0 - - + -
102J ALA* 4.2 7.1 - - + +
105J MET* 4.5 6.1 - - - -
145J ALA 3.0 19.7 + - - +
146J LEU* 3.9 9.0 - - + +
147J LEU 3.3 0.2 - - - -
148J ARG* 1.3 75.8 - - - +
150J ASN* 1.3 61.8 + - - +
151J GLY 3.3 1.5 + - - -
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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