Contacts of the helix formed by residues 137 - 150 (chain L) 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 L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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173K ASP* 4.9 2.8 - - + +
130L VAL* 4.8 4.9 - - - +
135L VAL 3.3 7.0 + - - +
136L HIS* 1.3 69.9 - - - +
138L ILE* 1.3 55.3 + - + +
139L GLY 3.2 2.5 - - - -
140L LYS* 2.7 54.8 + - - +
141L ASN* 2.8 28.8 + - - +
159L ARG* 3.2 29.9 + - - +
500L B13 2.8 24.7 + - - +
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Residues in contact with ILE 138 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173K ASP* 4.3 10.3 - - + +
176K VAL* 5.4 1.8 - - + -
177K LEU* 4.3 19.3 - - + -
225K THR* 3.5 31.9 - - + -
229K ILE* 4.0 20.2 - - + -
136L HIS 3.7 0.2 - - - -
137L ASP* 1.3 79.9 - - + +
139L GLY* 1.3 57.0 + - - +
141L ASN* 3.4 8.6 + - - +
142L ILE* 3.0 46.8 + - + +
500L B13 3.1 55.5 + - + +
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Residues in contact with GLY 139 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136L HIS* 4.8 2.2 + - - +
137L ASP 2.9 4.8 + - - -
138L ILE* 1.3 73.6 - - - +
140L LYS* 1.3 63.0 + - - -
142L ILE* 3.4 2.5 + - - +
143L VAL* 3.2 25.6 + - - +
181L THR* 4.6 1.6 - - - -
183L LEU* 5.6 0.4 - - - +
500L B13 3.4 54.1 + - - +
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Residues in contact with LYS 140 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128L CYS* 4.5 23.1 - - + +
129L HIS 4.7 4.3 - - - +
130L VAL* 3.6 24.2 - - + +
137L ASP* 2.7 38.3 + - - +
139L GLY* 1.3 70.3 - - - -
141L ASN* 1.3 76.3 + - - +
143L VAL* 3.1 8.8 + - + +
144L THR* 2.7 35.6 + - - +
156L ASP* 3.3 31.2 + - - +
158L GLY* 3.4 31.0 + - - +
159L ARG* 4.7 0.2 - - - +
179L THR* 5.7 0.7 - - - +
181L THR* 3.9 18.0 + - - +
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Residues in contact with ASN 141 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177K LEU* 4.6 19.8 - - + +
99L MET* 4.5 8.3 - - + +
137L ASP* 2.8 33.2 + - - +
138L ILE* 3.6 12.2 - - - +
139L GLY 3.3 0.2 - - - -
140L LYS* 1.3 98.7 + - - +
142L ILE* 1.3 64.2 + - - +
144L THR* 3.6 9.4 + - - +
145L ALA* 3.1 22.5 + - - +
156L ASP* 4.1 5.4 - - - +
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Residues in contact with ILE 142 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177K LEU* 5.5 3.4 - - + -
229K ILE* 5.8 1.8 - - + -
237K ASN* 5.4 5.8 - - - +
88L TYR* 5.1 5.8 - - + +
95L LEU* 3.6 41.7 - - + -
99L MET* 5.1 3.8 - - - -
138L ILE* 3.0 38.2 + - + +
139L GLY* 3.9 4.9 - - - +
140L LYS 3.3 0.4 - - - -
141L ASN* 1.3 73.7 - - + +
143L VAL* 1.3 67.0 + - - +
145L ALA* 3.1 5.3 + - - +
146L LEU* 3.0 39.7 + - + +
231L ALA* 3.6 20.4 - - + -
500L B13 4.3 22.0 - - + -
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Residues in contact with VAL 143 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128L CYS* 4.6 2.9 - - + -
139L GLY 3.2 10.8 + - - +
140L LYS* 3.1 12.4 + - - +
142L ILE* 1.3 75.6 - - - +
144L THR* 1.3 56.2 + - - +
146L LEU* 3.7 0.5 - - - +
147L LEU* 2.8 50.8 + - + +
179L THR* 4.1 20.4 - - + +
231L ALA* 3.7 22.4 - - + -
234L ALA* 3.9 15.7 - - + -
500L B13 3.6 36.8 - - + -
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Residues in contact with THR 144 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128L CYS* 4.2 7.7 - - - +
140L LYS* 2.7 21.4 + - - +
141L ASN* 3.6 12.6 - - + +
143L VAL* 1.3 73.8 - - - +
145L ALA* 1.3 65.2 + - + +
147L LEU* 3.3 7.0 + - - +
148L ARG* 3.1 60.9 + - - +
154L VAL* 3.7 17.3 - - + +
156L ASP* 3.4 21.5 + - - +
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Residues in contact with ALA 145 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81L MET* 5.5 0.2 - - - +
98L VAL* 5.3 2.9 - - + -
99L MET* 3.6 37.2 - - + -
102L ALA* 4.8 15.8 - - + +
141L ASN 3.1 8.4 + - - +
142L ILE 3.1 9.0 + - - +
144L THR* 1.3 79.6 - - + +
146L LEU* 1.3 64.6 + - + +
148L ARG* 3.4 8.7 + - - +
149L ALA* 2.9 29.3 + - - +
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Residues in contact with LEU 146 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85L ILE* 4.5 20.4 - - + -
88L TYR* 4.5 26.5 - - + -
89L ASP* 6.1 0.4 - - - +
95L LEU* 4.8 2.9 - - + -
98L VAL* 4.3 19.3 - - + -
142L ILE* 3.0 35.4 + - + +
143L VAL 3.9 3.1 - - - +
145L ALA* 1.3 84.1 - - + +
147L LEU* 1.3 64.5 + - - +
149L ALA* 4.0 5.2 - - + -
150L ASN* 2.9 32.1 + - - +
231L ALA 4.1 15.7 - - - +
232L ALA* 4.9 10.8 - - + -
235L PRO* 3.2 16.7 - - + +
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Residues in contact with LEU 147 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126L VAL* 3.7 28.9 - - + -
128L CYS* 3.6 31.4 - - - -
143L VAL* 2.8 27.3 + - + +
144L THR 3.3 1.1 + - - +
146L LEU* 1.3 76.9 - - - +
148L ARG* 1.3 62.3 + - - +
150L ASN* 3.2 7.2 + - - -
152L TYR* 3.2 32.8 + - + +
154L VAL* 3.5 15.3 - - + -
177L MET* 6.1 0.9 - - - -
179L THR* 4.2 3.1 - - + -
234L ALA* 3.5 32.3 - - + +
235L PRO* 3.5 18.2 - - + -
238L ALA* 6.0 1.3 - - + -
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Residues in contact with ARG 148 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78L MET* 4.4 4.9 - - - +
102L ALA* 6.5 1.1 - - + -
105L MET* 4.7 18.5 - - + +
106L LEU* 4.2 35.8 - - + +
144L THR* 3.1 38.7 + - - +
145L ALA* 3.6 9.6 - - - +
147L LEU* 1.3 75.7 - - - +
149L ALA* 1.3 56.6 + - - +
151L GLY* 3.1 20.3 + - - -
152L TYR 3.5 17.8 + - - +
154L VAL* 3.6 35.7 + - + +
156L ASP* 4.2 17.4 + - - +
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Residues in contact with ALA 149 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78L MET* 3.8 14.7 - - - +
81L MET* 3.7 37.5 - - + +
85L ILE* 3.1 33.7 - - + +
98L VAL* 5.7 2.5 - - + -
105L MET* 4.8 5.1 - - - -
145L ALA 2.9 17.9 + - - +
146L LEU* 4.1 9.0 - - + +
148L ARG* 1.3 75.1 - - - +
150L ASN* 1.3 58.2 + - - +
151L GLY 3.3 3.0 + - - -
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Residues in contact with ASN 150 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78L MET* 4.1 5.2 - - - -
85L ILE* 3.9 26.5 - - - +
123L LYS* 3.5 15.3 + - - +
146L LEU* 2.9 25.9 + - - +
147L LEU 3.2 5.4 + - - +
148L ARG 3.1 1.6 - - - -
149L ALA* 1.3 79.6 + - - +
151L GLY* 1.3 58.2 + - - +
152L TYR* 3.3 22.1 - - + -
235L PRO* 3.3 31.8 - - + +
239L ASP* 5.0 6.3 - - - +
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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