Contacts of the helix formed by residues 202 - 211 (chain A) in PDB entry 1LCJ
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 LEU 202 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127A TRP* 4.0 16.2 - - + -
128A PHE* 4.4 19.3 - - + -
153A ILE* 4.2 24.5 - - + -
163A PHE* 4.4 18.2 - - + -
183A ILE* 4.0 39.7 - - + -
191A PHE* 3.8 25.1 - - + -
201A GLY* 1.3 69.8 - - - -
203A HIS* 1.3 63.8 + - - +
205A LEU* 3.4 7.6 + - + +
206A VAL* 3.0 27.7 + - - +
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Residues in contact with HIS 203 (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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125A GLU* 2.7 35.4 + - - +
127A TRP* 4.0 15.3 - + + -
201A GLY* 3.2 2.2 - - - -
202A LEU* 1.3 81.1 - - - +
204A GLU* 1.3 70.2 + - + +
206A VAL* 3.5 3.8 + - + +
207A ARG* 3.0 59.8 + - + +
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Residues in contact with GLU 204 (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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199A PHE* 3.7 17.7 - - + -
200A PRO* 3.8 23.8 - - + -
201A GLY* 3.4 10.3 + - - +
202A LEU 3.3 0.4 - - - -
203A HIS* 1.3 100.7 - - + +
205A LEU* 1.3 66.7 + - - +
207A ARG* 3.2 31.2 + - - +
208A HIS* 3.0 24.3 + - - +
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Residues in contact with LEU 205 (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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153A ILE* 4.6 2.5 - - + -
165A LEU* 5.5 6.1 - - + -
183A ILE* 4.0 42.6 - - + -
191A PHE* 4.2 9.4 - - + -
192A TYR* 4.4 4.3 - - - -
193A ILE* 4.2 19.3 - - + -
199A PHE* 3.6 39.5 - - + -
201A GLY 3.5 8.4 + - - +
202A LEU* 3.4 10.7 + - + +
203A HIS 3.3 0.2 - - - -
204A GLU* 1.3 76.5 - - - +
206A VAL* 1.3 75.7 + - + +
208A HIS* 3.2 11.1 + - - +
209A TYR* 3.2 32.2 + - + -
220A LEU* 5.7 1.3 - - + -
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Residues in contact with VAL 206 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127A TRP* 3.9 26.7 - - + +
151A PHE* 3.6 34.3 - - + -
153A ILE* 3.5 27.6 - - + -
202A LEU 3.0 20.2 + - - +
203A HIS* 3.9 5.2 - - + +
205A LEU* 1.3 78.1 - - + +
207A ARG* 1.3 64.2 + - - +
209A TYR* 3.2 2.1 + - - +
210A THR* 3.0 31.3 + - - +
220A LEU* 4.3 9.4 - - + +
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Residues in contact with ARG 207 (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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203A HIS* 3.0 53.7 + - + +
204A GLU* 3.2 29.8 + - - +
205A LEU 3.3 0.2 - - - -
206A VAL* 1.3 74.2 - - - +
208A HIS* 1.3 64.0 + - - +
210A THR* 3.3 7.3 + - - -
211A ASN* 3.1 42.6 + - - +
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Residues in contact with HIS 208 (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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197A ILE* 4.2 14.7 - - + +
199A PHE* 3.4 34.3 - + + -
204A GLU 3.0 6.9 + - - +
205A LEU 3.2 5.6 + - - +
207A ARG* 1.3 76.7 - - - +
209A TYR* 1.3 88.9 + + - +
211A ASN* 3.1 23.3 + - - +
212A ALA* 3.2 14.9 + - + +
214A ASP* 2.9 33.9 + - + +
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Residues in contact with TYR 209 (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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165A LEU* 6.1 0.2 - - + -
193A ILE* 4.4 15.7 + - + +
194A SER 5.0 1.7 + - - -
197A ILE* 3.6 22.0 + - - +
199A PHE* 3.9 18.9 - + - -
205A LEU* 3.2 32.9 + - + +
206A VAL 3.2 2.6 + - - -
208A HIS* 1.3 95.5 - + - +
210A THR* 1.3 61.3 + - - +
211A ASN 3.4 0.2 - - - -
212A ALA 3.3 10.8 - - - +
213A SER* 3.2 27.9 + - - -
214A ASP* 3.9 10.8 - - + -
216A LEU* 3.7 24.9 - - + -
219A ARG* 3.7 5.0 - - - +
220A LEU* 2.9 37.5 + - + -
207B ILE* 3.6 23.7 - - + +
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Residues in contact with THR 210 (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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151A PHE* 4.8 2.1 - - - -
206A VAL* 3.0 26.1 + - - +
207A ARG* 3.7 7.6 - - - -
209A TYR* 1.3 78.0 - - - +
211A ASN* 1.3 65.1 + - - +
212A ALA 3.3 0.2 - - - -
219A ARG* 3.0 35.0 + - - +
220A LEU* 3.4 29.6 + - - +
221A SER 4.6 10.2 + - - +
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Residues in contact with ASN 211 (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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207A ARG* 3.1 33.7 + - - +
208A HIS* 3.1 11.1 + - - +
210A THR* 1.3 85.9 - - - +
212A ALA* 1.3 62.7 + - + +
219A ARG* 4.0 17.8 + - - +
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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