Contacts of the helix formed by residues 135 - 140 (chain L) in PDB entry 1IJ4
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 ILE 135 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16L LEU* 4.5 5.2 - - + -
20L GLU* 4.0 40.1 - - + +
23L LYS* 4.5 9.4 - - + -
24L ILE* 3.9 23.8 - - + -
111L ILE* 4.3 2.0 - - + -
112L THR* 3.5 32.9 + - - +
113L ASP* 3.7 10.7 - - + +
134L GLY* 1.3 71.6 - - - -
136L GLY* 1.3 58.5 + - - +
137L LYS* 2.9 14.4 + - - +
138L HIS* 3.0 13.1 + - - +
163L LEU* 3.7 24.5 - - + -
164L ASP* 3.3 24.5 - - - +
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Residues in contact with GLY 136 (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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20L GLU* 6.1 0.2 - - - -
134L GLY 3.9 1.8 + - - -
135L ILE* 1.3 66.9 - - - +
137L LYS* 1.3 57.4 + - - -
138L HIS 3.3 5.5 + - - -
139L PHE* 3.7 16.2 + - - +
140L GLN* 4.7 5.1 - - - +
162L ILE* 4.8 5.4 - - - +
164L ASP* 2.7 21.0 + - - -
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Residues in contact with LYS 137 (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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37I LEU 3.9 21.5 - - - -
39I LYS* 4.0 39.3 - - + +
41I GLU* 5.0 4.8 - - - +
15L SER 3.0 12.9 + - - -
17L GLN* 4.2 5.9 - - - +
20L GLU* 2.7 46.4 + - - +
113L ASP* 2.9 32.1 + - + +
135L ILE 2.9 6.5 + - - +
136L GLY* 1.3 68.2 - - - -
138L HIS* 1.3 61.0 + - - +
139L PHE 3.5 1.0 + - - -
140L GLN* 3.1 31.7 + - - +
144L SER* 4.2 11.1 - - - -
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Residues in contact with HIS 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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112L THR* 3.1 38.9 + - + +
113L ASP 3.4 23.1 + - - +
114L GLY 4.0 0.9 - - - -
132L ILE* 3.9 18.4 - - + +
134L GLY* 3.7 10.7 - - - -
135L ILE 3.0 19.9 + - - +
136L GLY 3.3 0.4 - - - -
137L LYS* 1.3 75.7 - - - +
139L PHE* 1.3 79.3 + + + +
140L GLN 3.7 0.9 - - - -
144L SER* 3.3 31.5 - - - +
145L GLN* 4.6 0.9 - - - -
147L THR* 3.4 36.0 + - + +
148L LEU* 3.6 14.5 - - + +
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Residues in contact with PHE 139 (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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132L ILE 5.0 1.8 - - - -
134L GLY* 3.7 30.1 - - - -
136L GLY 3.7 11.8 + - - +
137L LYS 3.5 1.2 - - - -
138L HIS* 1.3 98.5 - + + +
140L GLN* 1.3 57.6 + - - +
145L GLN* 3.0 27.7 + - + +
148L LEU* 3.4 38.4 - - + -
160L VAL* 4.0 12.8 - - + -
161L LYS 4.5 4.5 - - - -
162L ILE* 3.6 49.4 - - + -
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Residues in contact with GLN 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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39I LYS 4.9 2.6 - - - +
40I LYS* 4.9 6.7 - - - +
41I GLU* 2.9 38.3 + - + +
136L GLY 4.7 3.3 - - - +
137L LYS* 3.1 40.5 - - - +
138L HIS 3.7 0.2 - - - -
139L PHE* 1.3 76.8 - - - +
141L THR* 1.3 69.1 + - + +
144L SER* 3.5 9.9 + - - +
145L GLN* 3.5 10.4 + - - -
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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