Contacts of the helix formed by residues 254 - 261 (chain A) in PDB entry 2POD
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 SER 254 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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225A LEU* 3.9 13.6 - - - +
247A ILE* 3.7 25.7 - - - +
251A SER 3.7 6.4 + - - -
252A LEU 3.1 1.4 - - - -
253A SER* 1.3 75.9 - - - +
255A LEU* 1.3 60.2 + - - +
256A LYS 3.6 0.9 - - - -
257A ARG* 3.8 22.3 - - - +
258A TYR 4.0 0.5 + - - -
279B ARG* 2.5 34.4 + - - +
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Residues in contact with LEU 255 (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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246A PRO* 4.7 3.6 - - + -
247A ILE* 4.3 17.5 - - + +
249A MSE 3.8 32.1 - - + -
252A LEU* 3.1 20.4 + - + +
253A SER 3.2 0.2 - - - -
254A SER* 1.3 76.3 - - - +
256A LYS* 1.3 62.7 + - - +
257A ARG 3.2 2.5 - - - -
258A TYR* 3.0 11.2 + - + +
259A ALA* 2.9 25.8 + - - +
266A VAL* 4.0 28.0 - - + -
281A LEU* 3.7 30.1 - - + -
284A THR* 4.4 2.7 - - - +
286A ALA* 3.8 18.6 - - + -
287A ALA 4.7 0.7 - - - +
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Residues in contact with LYS 256 (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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252A LEU 4.7 0.6 + - - -
253A SER 4.3 6.8 + - - +
254A SER 3.6 0.2 - - - -
255A LEU* 1.3 77.6 - - - +
257A ARG* 1.3 58.5 + - + +
259A ALA* 4.3 6.3 - - - -
260A GLU* 2.9 61.2 + - - +
284A THR* 3.2 27.2 - - - +
285A ASN* 3.4 30.1 + - - +
286A ALA* 3.7 11.7 - - + +
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Residues in contact with ARG 257 (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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225A LEU* 3.5 35.4 - - + +
229A LEU* 3.8 21.8 - - + +
253A SER 5.2 3.8 + - - +
254A SER* 3.8 18.1 + - - +
256A LYS* 1.3 78.4 - - + +
258A TYR* 1.3 62.1 + - - +
260A GLU* 3.7 22.8 + - - +
261A ARG* 3.8 8.0 + - - -
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Residues in contact with TYR 258 (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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219A PHE* 4.1 6.6 - - - -
225A LEU* 4.4 10.2 - - + +
228A ALA* 3.2 43.6 + - + -
229A LEU* 3.9 13.0 - - + +
232A ALA* 3.6 16.1 - - + +
243A HIS* 2.9 32.1 + - + +
246A PRO* 3.4 38.3 - - + +
247A ILE* 4.8 5.2 - - + -
254A SER 4.0 2.7 + - - +
255A LEU* 3.0 16.5 + - + +
257A ARG* 1.3 75.9 - - - +
259A ALA* 1.3 61.2 + - - +
261A ARG* 3.0 21.0 + - - +
262A SER* 3.2 26.5 + - - -
266A VAL* 3.7 16.4 - - + -
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Residues in contact with ALA 259 (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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255A LEU 2.9 18.5 + - - +
256A LYS* 3.9 8.3 - - - +
258A TYR* 1.3 74.6 - - - +
260A GLU* 1.3 61.0 + - - +
261A ARG 3.2 0.9 + - - -
262A SER* 3.3 21.1 + - - +
266A VAL* 3.9 14.1 - - + +
286A ALA* 3.3 37.5 - - + +
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Residues in contact with GLU 260 (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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236A ARG* 4.3 4.7 + - - -
256A LYS* 2.9 49.5 + - + +
257A ARG* 3.7 17.5 - - - +
259A ALA* 1.3 73.6 - - - +
261A ARG* 1.3 66.2 + - + +
262A SER 3.9 1.0 + - - +
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Residues in contact with ARG 261 (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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229A LEU* 3.8 44.9 - - + +
232A ALA* 4.0 12.7 - - - +
233A GLU* 4.7 2.9 + - - +
236A ARG* 2.9 30.5 + - - +
257A ARG 4.0 8.1 - - - -
258A TYR 3.0 9.3 + - - +
260A GLU* 1.3 84.4 + - + +
262A SER* 1.3 58.5 + - - +
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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