Contacts of the helix formed by residues 303 - 314 (chain A) in PDB entry 2HW6
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 303 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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144A GLU* 2.6 35.3 + - - -
301A HIS 3.6 2.6 + - - -
302A ILE* 1.3 75.6 - - - +
304A SER* 1.3 62.5 + - - +
305A GLU* 2.9 34.3 + - - +
306A ALA* 3.6 6.3 - - - +
307A LYS* 3.3 20.3 + - - +
332A TRP* 4.1 2.1 - - - -
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Residues in contact with SER 304 (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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302A ILE 3.5 2.3 + - - -
303A SER* 1.3 70.7 + - - +
305A GLU* 1.3 73.9 + - - +
307A LYS* 3.4 10.9 + - - +
308A ASP* 2.8 30.2 + - - +
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Residues in contact with GLU 305 (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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303A SER* 2.9 20.1 + - - +
304A SER* 1.3 89.6 + - - +
306A ALA* 1.3 56.5 + - - +
308A ASP* 3.2 8.7 - - - +
309A LEU 3.0 23.0 + - - -
330A HIS* 3.3 12.6 - - + -
331A PRO* 4.9 17.3 - - + -
332A TRP* 4.0 20.6 - - + +
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Residues in contact with ALA 306 (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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144A GLU* 4.0 1.8 - - - +
250A LEU* 4.7 1.4 - - - +
254A LEU* 4.0 16.2 - - + -
302A ILE* 4.1 4.7 - - + -
303A SER* 3.5 16.7 + - - +
304A SER 3.3 0.2 - - - -
305A GLU* 1.3 77.0 - - - +
307A LYS* 1.3 59.4 + - - +
309A LEU* 3.3 5.5 + - - +
310A ILE* 3.1 32.4 + - - +
332A TRP* 3.5 41.1 - - + +
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Residues in contact with LYS 307 (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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294A PHE* 3.9 43.7 + - + +
296A ASP* 5.0 5.5 + - - -
299A TRP* 3.3 48.0 + - + +
300A ALA* 4.5 4.8 - - - +
302A ILE* 3.4 16.4 - - + -
303A SER 3.3 12.5 + - - +
304A SER* 3.8 10.5 - - - +
306A ALA* 1.3 71.7 - - - +
308A ASP* 1.3 60.5 + - - +
310A ILE* 3.4 6.3 + - - +
311A SER* 2.9 31.4 + - - -
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Residues in contact with ASP 308 (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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304A SER 2.8 15.4 + - - +
305A GLU* 3.2 12.6 - - - +
307A LYS* 1.3 73.2 - - - +
309A LEU* 1.3 64.4 + - - +
311A SER* 3.0 11.5 + - - -
312A LYS* 3.0 55.4 + - - +
330A HIS* 3.0 22.9 + - - -
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Residues in contact with LEU 309 (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 VAL* 4.4 5.8 - - + -
250A LEU* 4.0 15.7 - - + -
305A GLU 3.0 13.5 + - - +
306A ALA* 3.3 9.4 + - - +
308A ASP* 1.3 75.4 - - - +
310A ILE* 1.3 62.8 + - - +
312A LYS* 3.0 14.0 + - - +
313A LEU* 3.2 23.8 + - + +
322A LEU* 3.9 22.7 - - + -
327A VAL* 4.3 10.8 - - + -
330A HIS* 3.7 25.8 - - + +
332A TRP* 3.5 28.7 - - + -
333A VAL* 3.8 19.1 - - + -
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Residues in contact with ILE 310 (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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247A GLY* 4.6 5.4 - - - +
250A LEU* 3.7 25.1 - - + -
251A TYR* 4.2 10.1 - - + -
254A LEU* 4.0 11.7 - - + -
292A TYR* 4.6 0.4 - - + -
294A PHE* 3.8 20.0 - - + -
299A TRP* 3.4 37.9 - - + -
306A ALA 3.1 18.8 + - - +
307A LYS 3.7 6.7 - - - +
308A ASP 3.3 0.2 - - - -
309A LEU* 1.3 76.5 - - - +
311A SER* 1.3 60.3 + - - +
313A LEU* 3.0 9.5 + - - +
314A LEU* 2.8 53.8 + - + +
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Residues in contact with SER 311 (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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292A TYR* 2.9 30.5 + - - -
294A PHE* 4.9 4.0 - - - -
307A LYS 2.9 15.5 + - - -
308A ASP* 3.0 19.1 + - - -
310A ILE* 1.3 78.1 - - - +
312A LYS* 1.3 61.5 + - - +
313A LEU 3.5 0.5 + - - -
314A LEU 4.0 0.6 - - - +
315A VAL* 3.6 19.8 + - - +
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Residues in contact with LYS 312 (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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308A ASP* 3.0 45.7 + - - +
309A LEU 3.0 9.9 + - - +
311A SER* 1.3 78.5 + - - +
313A LEU* 1.3 58.3 + - - +
315A VAL* 3.5 15.3 - - - +
320A GLN 4.6 0.9 - - - +
321A ARG* 3.6 0.3 - - - -
322A LEU* 3.4 56.2 + - + +
330A HIS* 4.7 7.4 - - + -
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Residues in contact with LEU 313 (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 VAL* 5.8 0.4 - - + -
243A LEU* 3.5 34.8 - - + +
244A TRP* 3.6 8.4 - - - -
246A LEU* 4.4 11.7 - - + +
247A GLY* 3.7 26.9 - - - +
250A LEU* 4.9 4.7 - - + -
309A LEU* 3.2 35.2 + - + +
310A ILE* 3.0 7.7 + - - +
312A LYS* 1.3 78.0 - - - +
314A LEU* 1.3 57.6 + - - +
315A VAL 3.1 7.1 + - - -
321A ARG* 3.2 27.1 + - - -
322A LEU* 4.0 12.6 - - + +
327A VAL* 3.8 26.0 - - + -
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Residues in contact with LEU 314 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244A TRP* 3.8 31.5 + - + +
247A GLY 4.4 7.0 - - - +
248A VAL* 3.7 32.1 - - + +
251A TYR* 4.4 2.9 - - + -
259A PRO* 4.2 23.3 - - + -
260A PHE* 4.2 11.5 - - + -
290A GLY* 5.6 4.3 - - - -
292A TYR* 3.8 37.2 - - + -
310A ILE* 2.8 38.8 + - + +
311A SER 3.9 3.1 + - - -
312A LYS 3.7 0.2 - - - -
313A LEU* 1.3 74.7 - - - +
315A VAL* 1.3 62.7 + - - +
316A ARG* 3.8 1.4 + - - +
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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