Contacts of the helix formed by residues 241 - 249 (chain A) in PDB entry 2LD1
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 LYS 241 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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227A GLY 4.8 0.6 + - - -
228A ASN* 3.3 42.1 + - + +
230A ILE* 5.6 1.0 - - - +
240A CYS* 1.3 74.6 - - - +
242A LYS* 1.3 61.8 + - + +
243A CYS 3.1 0.2 + - - -
244A ILE 3.4 0.2 + - - -
245A LEU* 2.9 41.0 + - + +
250A ARG* 3.9 35.4 - - + +
253A LEU* 3.3 30.5 - - + -
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Residues in contact with LYS 242 (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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173A ALA 5.1 5.9 - - - +
223A CYS* 5.8 1.8 - - - -
225A GLU* 3.6 30.9 + - - +
226A GLY 5.6 4.3 + - - +
240A CYS* 3.3 14.4 - - + -
241A LYS* 1.3 80.3 - - + +
243A CYS* 1.3 61.0 + - - +
245A LEU* 4.2 11.0 - - + +
246A ARG* 3.6 24.9 + - - +
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Residues in contact with CYS 243 (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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2A ZN 2.3 36.3 - - - -
172A THR* 4.9 6.1 + - - +
173A ALA* 4.0 21.5 - - - -
220A CYS* 3.8 6.7 - - - -
222A TRP* 3.9 31.2 - - + -
223A CYS* 3.9 5.2 - - - -
239A PHE* 5.0 2.5 - - + -
240A CYS* 3.3 8.2 + - - +
241A LYS 3.1 0.6 - - - -
242A LYS* 1.3 79.8 - - - +
244A ILE* 1.3 67.1 + - + +
246A ARG* 3.4 5.6 + - - +
247A ASN* 3.1 23.1 + - - +
266A TYR* 5.3 0.9 - - + -
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Residues in contact with ILE 244 (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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230A ILE* 3.0 38.4 - - + -
239A PHE* 4.8 7.0 - - + -
240A CYS 3.6 9.6 + - - +
241A LYS 3.4 1.6 + - - +
243A CYS* 1.3 74.1 - - + +
245A LEU* 1.3 61.8 + - - +
247A ASN* 3.0 6.0 + - - +
248A LEU* 2.6 63.5 + - + -
249A GLY 3.0 10.4 + - - +
253A LEU* 3.6 22.7 - - + -
256A ILE* 4.0 9.9 - - + -
263A TRP* 4.7 8.7 - - + -
266A TYR* 3.9 19.1 - - + +
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Residues in contact with LEU 245 (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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241A LYS* 2.9 27.3 + - + +
242A LYS* 4.3 11.0 - - + +
244A ILE* 1.3 77.5 - - - +
246A ARG* 1.3 72.7 + - + +
249A GLY* 3.2 28.3 + - - -
250A ARG* 3.5 31.9 - - + +
253A LEU* 5.1 0.6 - - - +
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Residues in contact with ARG 246 (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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172A THR* 4.2 17.4 + - - +
173A ALA 6.0 0.2 - - - +
174A CYS 4.0 11.2 + - - +
175A GLY* 3.7 33.8 + - - +
176A GLN* 5.9 0.4 - - - +
242A LYS 3.6 17.8 + - - +
243A CYS 3.4 4.8 + - - +
244A ILE 3.2 0.4 - - - -
245A LEU* 1.3 92.1 + - + +
247A ASN* 1.3 60.7 + - - +
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Residues in contact with ASN 247 (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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172A THR* 4.9 7.6 - - - +
222A TRP* 5.6 1.8 - - + -
243A CYS 3.1 15.7 + - - +
244A ILE 3.0 2.5 + - - +
246A ARG* 1.3 80.6 - - - +
248A LEU* 1.3 65.9 + - - +
249A GLY 4.0 0.2 - - - -
266A TYR* 3.1 25.3 + - + +
272A PRO 2.7 27.2 + - - +
273A LEU* 4.5 2.0 - - - +
276A LEU* 3.2 37.1 - - + +
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Residues in contact with LEU 248 (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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244A ILE* 2.6 30.5 + - + -
247A ASN* 1.3 81.1 - - - +
249A GLY* 1.3 66.9 + - - +
251A LYS* 6.1 0.2 - - - +
252A GLU* 3.3 45.1 + - + +
253A LEU 4.5 0.2 - - - +
256A ILE* 5.5 5.8 - - + -
266A TYR* 3.7 22.0 - - - +
272A PRO* 4.7 12.8 - - + +
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Residues in contact with GLY 249 (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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244A ILE* 3.0 19.7 + - - +
245A LEU* 3.2 27.7 + - - -
247A ASN 4.0 0.2 - - - -
248A LEU* 1.3 91.1 - - - +
250A ARG* 1.3 60.9 + - - -
251A LYS* 3.7 2.0 - - - -
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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