Contacts of the helix formed by residues 256 - 266 (chain A) in PDB entry 4I5L
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 256 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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218A ASP* 2.8 29.8 + - - +
221A ARG* 3.7 9.2 - - - -
254A ASP* 2.8 22.1 + - - +
255A LYS* 1.3 73.8 - - - +
257A TRP* 1.3 64.5 + - - +
258A ARG* 3.3 15.6 + - - +
259A VAL* 3.2 17.5 + - - +
260A ARG* 3.3 16.2 + - - +
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Residues in contact with TRP 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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255A LYS 3.5 2.4 + - - -
256A SER* 1.3 72.6 + - - +
258A ARG* 1.3 78.7 + - + +
260A ARG* 3.3 25.5 + - - +
261A TYR* 2.7 51.7 + + + +
295A GLU* 3.7 33.4 + - + -
297A GLU* 3.7 38.6 - - + -
298A VAL* 3.6 5.0 - - + +
411B PHE* 5.1 12.8 - + + -
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Residues in contact with ARG 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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218A ASP* 3.0 33.1 + - - +
219A SER* 3.6 14.3 + - - -
222A LEU* 3.8 31.4 - - + +
256A SER* 3.1 7.5 - - - +
257A TRP* 1.3 111.2 - - + +
259A VAL* 1.3 61.3 + - + +
261A TYR* 3.3 5.9 - - - +
262A MET* 3.2 25.5 + - - +
403B ASP* 5.2 6.1 + - - -
409B SER* 5.4 2.2 + - - -
411B PHE* 3.5 58.8 - - - +
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Residues in contact with VAL 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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218A ASP* 4.2 6.3 - - + +
221A ARG* 3.9 21.8 - - + +
222A LEU* 3.8 23.8 - - + +
225A VAL* 4.2 1.9 - - + +
251A ALA* 3.3 22.4 - - + +
254A ASP* 3.3 48.5 - - + +
256A SER* 3.2 14.8 + - - +
258A ARG* 1.3 73.1 - - - +
260A ARG* 1.3 65.9 + - - +
261A TYR 3.1 0.2 - - - -
262A MET* 3.0 13.8 + - - +
263A VAL* 3.2 15.2 + - - +
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Residues in contact with ARG 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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251A ALA 3.9 6.3 - - - +
252A ALA 3.4 23.8 - - - +
253A GLU* 4.0 4.5 - - - +
254A ASP 2.7 50.4 + - - +
255A LYS* 3.1 22.4 + - - +
256A SER 3.3 2.9 + - - +
257A TRP* 3.5 30.4 - - - +
259A VAL* 1.3 74.5 - - - +
261A TYR* 1.3 63.0 + - - +
263A VAL* 3.2 8.4 + - - +
264A ALA* 3.2 16.3 + - - +
290A LEU* 3.9 10.3 - - + +
293A ASP* 2.7 45.6 + - - +
294A CYS* 3.8 18.5 - - - -
295A GLU* 4.0 1.4 - - - +
298A VAL* 4.3 7.6 - - + -
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Residues in contact with TYR 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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257A TRP* 2.7 32.6 + + + +
258A ARG* 3.3 11.7 - - - +
260A ARG* 1.3 73.1 - - - +
262A MET* 1.3 65.4 + - - +
264A ALA* 3.1 5.6 + - - +
265A ASP* 2.8 53.2 + - + -
297A GLU* 3.6 51.8 + - + -
298A VAL* 4.0 9.4 - - + +
301A ALA* 3.6 17.9 - - + +
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Residues in contact with MET 262 (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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222A LEU* 3.7 37.5 - - + +
223A LEU* 6.2 1.8 - - + -
225A VAL* 3.7 18.8 - - + -
226A GLU* 5.6 4.0 - - + -
258A ARG 3.2 14.1 + - - +
259A VAL* 3.0 9.8 + - - +
261A TYR* 1.3 93.5 - - - +
263A VAL* 1.3 57.3 + - - +
265A ASP* 3.7 10.7 - - - +
266A LYS* 2.9 68.7 + - + +
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Residues in contact with VAL 263 (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 VAL* 3.9 12.5 - - + +
248A LEU* 4.5 7.9 - - + -
251A ALA* 3.8 29.4 - - + +
252A ALA* 3.8 21.3 - - + +
259A VAL 3.2 15.9 + - - +
260A ARG 3.2 6.3 + - - +
262A MET* 1.3 75.1 - - - +
264A ALA* 1.3 62.2 + - - +
266A LYS 3.4 1.7 + - - -
267A PHE* 3.1 35.0 + - + -
270A LEU* 3.8 14.0 - - + +
286A ALA* 6.1 0.2 - - + -
290A LEU* 3.7 21.3 - - + -
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Residues in contact with ALA 264 (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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260A ARG 3.2 10.6 + - - +
261A TYR* 3.1 10.4 + - - +
263A VAL* 1.3 77.7 - - - +
265A ASP* 1.3 61.9 + - - +
267A PHE* 3.2 19.3 + - - +
287A PHE* 6.2 0.9 - - + -
290A LEU* 4.1 18.2 - - + -
298A VAL* 4.3 7.9 - - + +
301A ALA* 3.9 8.5 - - + -
302A ALA* 3.9 27.6 - - + +
305A LYS* 3.4 16.0 - - - +
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Residues in contact with ASP 265 (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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261A TYR* 2.8 44.6 + - + +
262A MET* 3.3 15.2 + - - +
264A ALA* 1.3 72.5 - - - +
266A LYS* 1.3 74.0 + - - +
267A PHE 3.3 1.1 + - - -
269A GLU* 4.8 2.9 - - - +
301A ALA* 4.5 6.5 - - + +
305A LYS* 2.8 29.8 + - - +
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Residues in contact with LYS 266 (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 VAL* 3.8 20.2 - - + -
226A GLU* 3.0 35.1 + - - +
229A VAL* 4.5 7.9 - - + -
262A MET* 2.9 43.8 + - + +
263A VAL 3.6 2.9 - - - +
265A ASP* 1.3 85.6 + - - +
267A PHE* 1.3 64.8 + - - +
268A THR 3.3 2.5 - - - -
269A GLU* 3.2 30.5 + - - +
270A LEU* 3.0 24.6 + - + +
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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