Contacts of the helix formed by residues 215 - 221 (chain A) in PDB entry 1L2L
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 ARG 215 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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135A HIS* 2.9 20.5 + - + +
136A VAL 3.0 36.9 + - - +
137A PRO 3.2 21.5 + - - +
138A GLN* 4.6 1.6 + - - +
139A LEU* 4.4 10.7 - - - +
155A PRO 5.6 2.2 + - - -
156A THR 5.9 0.6 - - - -
170A PHE* 3.7 29.8 - - - -
213A TYR* 3.8 12.0 - - + +
214A VAL* 1.3 77.2 - - - +
216A GLU* 1.3 65.8 + - - +
217A GLU* 2.7 39.5 + - - +
218A TRP* 3.0 33.6 + - + +
219A ILE* 3.2 8.3 + - - +
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Residues in contact with GLU 216 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213A TYR* 4.8 4.0 + - - +
214A VAL 3.4 3.4 + - - -
215A ARG* 1.3 72.0 - - - +
217A GLU* 1.3 67.8 + - + +
219A ILE* 3.0 20.9 + - - +
220A GLU* 2.9 54.2 + - + +
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Residues in contact with GLU 217 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155A PRO 4.8 0.7 - - - +
156A THR* 3.6 30.5 - - - +
215A ARG* 2.7 45.7 + - - +
216A GLU* 1.3 89.5 + - + +
218A TRP* 1.3 63.1 + - + +
220A GLU* 4.6 3.8 - - - +
221A ARG* 2.8 38.7 + - + +
225A ILE* 4.1 7.2 - - + +
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Residues in contact with TRP 218 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29A LEU* 3.3 35.9 - - + -
30A LEU 4.1 2.5 - - - -
31A ALA* 4.0 14.6 - - + -
32A TYR* 5.2 3.1 - + - -
133A ILE* 4.2 0.7 - - + -
134A ALA 3.6 16.8 + - - -
135A HIS* 3.5 44.0 - + + +
155A PRO* 3.3 30.8 + - + +
214A VAL* 3.7 13.5 - - + -
215A ARG* 3.0 36.8 + - + +
217A GLU* 1.3 79.8 + - + +
219A ILE* 1.3 62.7 + - - +
222A PHE* 3.2 36.4 - + - +
225A ILE* 3.8 20.0 - - + -
255A HIS* 3.2 22.7 - - - +
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Residues in contact with ILE 219 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214A VAL* 3.5 35.2 - - + +
215A ARG 3.2 2.2 + - - +
216A GLU* 3.0 23.6 + - - +
218A TRP* 1.3 80.9 - - - +
220A GLU* 1.3 75.9 + - - +
222A PHE* 4.7 2.8 + - - +
251A LEU* 4.1 35.7 - - + -
254A GLU* 5.6 2.9 - - - +
255A HIS* 4.5 8.3 - - - +
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Residues in contact with GLU 220 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216A GLU* 2.9 43.3 + - + +
217A GLU* 4.3 2.7 - - - +
219A ILE* 1.3 93.5 - - - +
221A ARG* 1.3 72.4 + - + +
222A PHE 3.7 1.0 + - - -
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Residues in contact with ARG 221 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217A GLU* 2.8 25.3 + - + +
220A GLU* 1.3 86.6 - - + +
222A PHE* 1.3 61.3 + - - +
223A GLU* 3.3 3.1 + - - -
224A GLU* 3.5 38.5 + - + +
225A ILE* 3.4 24.2 + - + +
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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