Contacts of the helix formed by residues 133 - 140 (chain L) in PDB entry 2I5N
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 VAL 133 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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90L THR* 5.2 4.3 - - + -
94L LEU* 5.0 11.4 - - + -
128L PHE* 5.8 0.9 - - + -
129L CYS* 2.9 27.0 + - + +
131L LEU 3.7 0.4 - - - -
132L GLN* 1.3 89.0 - - + +
134L PHE* 1.3 72.0 + - + +
135L ARG 3.5 0.9 - - - -
136L PRO* 3.5 2.3 - - - +
137L LEU* 2.9 53.6 + - + +
142L TRP* 3.9 16.9 - - + -
713L UNL 4.8 8.3 - - + -
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Residues in contact with PHE 134 (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 PHE* 4.2 21.1 - + - -
129L CYS* 2.8 43.2 + - + +
130L VAL* 3.7 20.2 - - + -
133L VAL* 1.3 86.6 - - + +
135L ARG* 1.3 62.3 + - - +
137L LEU* 3.3 12.5 + - + +
138L LEU* 3.0 28.1 + - + +
249L ILE* 4.2 13.2 - - + -
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Residues in contact with ARG 135 (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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18C SER* 5.3 3.0 + - - -
22C VAL* 6.0 0.2 - - - +
130L VAL* 3.0 17.1 + - + +
131L LEU* 4.5 4.2 + - - +
134L PHE* 1.3 76.8 - - - +
136L PRO* 1.3 70.7 - - + +
138L LEU* 3.1 6.6 + - - +
139L LEU* 3.0 47.2 + - + +
144L HIS* 4.1 22.0 + - - +
156L TRP* 4.8 1.4 - - - -
160L PHE* 3.2 43.4 - - - -
163L GLN* 5.0 4.0 + - - -
164L TYR* 3.4 11.9 + - - -
248L THR* 3.4 25.7 + - - -
249L ILE* 3.9 14.5 - - + +
251L SER 2.9 28.7 + - - -
253L PRO* 4.7 7.0 - - + -
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Residues in contact with PRO 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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75L LEU* 4.5 0.9 - - - -
131L LEU 3.3 19.3 - - - +
132L GLN 3.4 19.5 - - - +
133L VAL 3.5 12.8 - - - +
135L ARG* 1.3 95.3 - - + +
137L LEU* 1.3 55.5 + - - +
139L LEU* 3.2 1.3 + - + -
140L GLY 2.8 25.1 + - - -
141L SER 3.2 30.5 + - - +
142L TRP* 4.1 12.8 - - + -
144L HIS* 4.4 9.4 - - + -
145L ALA* 4.0 17.5 - - + +
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Residues in contact with LEU 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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75L LEU* 3.8 37.0 - - + +
133L VAL* 2.9 46.0 + - + +
134L PHE* 3.5 13.7 - - + +
136L PRO* 1.3 70.2 - - - +
138L LEU* 1.3 63.2 + - + +
140L GLY* 3.1 14.2 + - - -
142L TRP* 4.1 15.5 - - + -
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Residues in contact with LEU 138 (chain L).
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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5C PRO* 5.6 11.6 - - + +
6C PRO* 5.7 5.2 - - - +
7C ALA 5.9 0.7 + - - -
134L PHE* 3.0 13.1 + - + +
135L ARG 3.1 6.7 + - - +
137L LEU* 1.3 75.8 - - + +
139L LEU* 1.3 61.9 + - - +
140L GLY 3.7 0.2 + - - -
249L ILE* 3.7 37.7 - - + -
253L PRO* 3.8 29.9 - - + +
254L PHE* 4.5 11.0 - - + -
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Residues in contact with LEU 139 (chain L).
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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7C ALA* 4.2 24.8 - - + +
9C THR* 4.3 17.1 + - + -
135L ARG* 3.0 58.9 + - - +
136L PRO 4.0 0.4 - - - +
138L LEU* 1.3 77.8 - - - +
140L GLY* 1.3 59.4 + - - +
141L SER* 3.6 1.3 + - - -
144L HIS* 3.4 41.4 + - + +
252L GLY* 4.1 8.3 - - - -
253L PRO* 3.9 29.4 - - + -
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Residues in contact with GLY 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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74L GLY* 3.3 16.5 - - - -
75L LEU* 3.7 16.0 - - - +
136L PRO 2.8 9.5 + - - -
137L LEU 3.1 11.2 + - - -
138L LEU 3.4 0.2 - - - -
139L LEU* 1.3 76.8 - - - +
141L SER* 1.3 63.0 + - - -
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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