Contacts of the helix formed by residues 231 - 240 (chain A) in PDB entry 2V53
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 231 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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224A HIS 4.3 5.8 + - - -
230A LEU* 1.3 78.3 - - - +
232A HIS* 1.3 67.6 + - - +
233A THR* 3.8 8.9 + - - -
234A GLU* 2.7 54.9 + - - +
235A LEU* 3.4 7.3 + - - +
263A TYR* 3.8 30.5 - - - -
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Residues in contact with HIS 232 (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 LEU 3.7 0.8 + - - -
231A SER* 1.3 72.7 - - - +
233A THR* 1.3 61.9 + - - +
235A LEU* 3.0 31.7 + - + +
236A ALA 3.4 4.5 + - - -
239A ARG* 3.7 45.5 + - - -
250A THR* 6.1 3.0 - - + +
253A PHE* 6.3 2.7 - - + -
254A GLU* 6.2 4.9 - - + -
262A LYS 4.6 12.9 + - - +
263A TYR* 5.9 0.2 - - - -
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Residues in contact with THR 233 (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 HIS* 5.4 8.7 + - - +
224A HIS* 6.3 4.0 - - + -
231A SER* 3.2 9.0 + - - -
232A HIS* 1.3 78.3 - - - +
234A GLU* 1.3 62.3 + - + +
235A LEU 3.1 0.7 + - - -
236A ALA* 3.5 21.1 - - + +
237A PRO* 3.9 3.1 - - - +
239A ARG* 5.6 0.4 - - - +
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Residues in contact with GLU 234 (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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221A LEU* 3.6 26.5 - - - +
222A ASP* 3.6 4.3 - - - -
223A GLN 2.4 35.2 + - - +
224A HIS* 2.8 27.3 + - + +
229A TYR 2.8 14.2 - - - +
230A LEU* 3.2 9.7 - - + -
231A SER* 2.7 45.4 + - - +
233A THR* 1.3 80.4 - - + +
235A LEU* 1.3 59.9 + - - +
237A PRO* 3.5 10.6 - - - +
301A CA 2.6 25.2 - - - -
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Residues in contact with LEU 235 (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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221A LEU* 3.9 21.5 - - + -
230A LEU* 4.3 20.0 - - + +
231A SER 3.6 16.8 - - - +
232A HIS* 3.3 26.0 - - + +
234A GLU* 1.3 76.5 - - - +
236A ALA* 1.3 68.6 + - - +
237A PRO* 3.1 4.9 - - - +
238A LEU* 2.5 19.5 + - + +
239A ARG* 2.9 21.7 + - + +
253A PHE* 4.1 40.4 - - + +
264A ILE* 4.6 15.0 - - + -
269A TRP* 4.7 1.3 - - + -
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Residues in contact with ALA 236 (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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126A LEU 6.2 0.4 - - - +
232A HIS 3.4 5.4 + - - +
233A THR* 3.5 17.0 - - + +
235A LEU* 1.3 76.7 - - - +
237A PRO* 1.3 60.3 - - + +
238A LEU 2.6 13.5 + - - -
239A ARG* 3.9 19.6 - - - +
240A ALA* 2.8 34.5 + - + +
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Residues in contact with PRO 237 (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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221A LEU* 4.9 10.8 - - + -
233A THR 3.9 2.2 - - - +
234A GLU* 3.5 15.0 - - - +
235A LEU 3.1 6.5 - - - -
236A ALA* 1.3 94.0 - - + +
238A LEU* 1.3 59.5 + - - +
240A ALA* 5.3 0.7 - - + -
241A PRO* 3.3 17.5 - - + +
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Residues in contact with LEU 238 (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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150A MET* 4.9 7.6 - - - -
153A TRP* 4.2 25.1 - - + -
154A LEU* 5.7 0.4 - - + -
217A GLN* 3.6 35.4 - - + +
221A LEU* 4.6 18.8 - - + -
235A LEU* 2.5 15.3 + - - +
236A ALA 2.6 0.4 + - - -
237A PRO* 1.3 79.2 - - - +
239A ARG* 1.3 60.3 + - - +
241A PRO* 3.1 11.2 - - + +
242A LEU* 2.9 42.8 - - + +
253A PHE* 4.2 21.3 - - + -
269A TRP* 4.9 3.1 - - + -
21C MET* 5.3 1.8 - - + -
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Residues in contact with ARG 239 (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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126A LEU 5.6 3.2 + - - -
127A ASP* 3.6 33.5 + - - +
232A HIS* 3.7 51.2 + - - -
233A THR* 5.6 0.6 - - - +
235A LEU* 2.9 21.1 + - + +
236A ALA* 2.9 17.9 + - - +
238A LEU* 1.3 78.8 - - - +
240A ALA* 1.3 58.7 + - - +
242A LEU* 3.2 0.5 + - - +
243A ILE* 2.7 48.2 + - + +
249A THR* 4.2 16.8 - - + -
250A THR* 4.5 19.9 - - - +
253A PHE* 4.3 22.1 - - + -
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Residues in contact with ALA 240 (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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126A LEU* 5.4 4.5 - - + +
127A ASP 3.9 6.2 + - - +
128A TYR* 3.1 43.8 - - - +
129A ILE* 3.3 9.6 + - + +
236A ALA* 2.8 24.3 + - + +
237A PRO* 5.3 0.4 - - + -
239A ARG* 1.3 70.1 - - - +
241A PRO* 1.3 63.7 - - + +
242A LEU 2.8 10.6 + - - -
243A ILE* 4.1 0.2 - - - +
244A PRO* 3.6 6.4 - - - +
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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