Contacts of the helix formed by residues 299 - 312 (chain A) in PDB entry 6DXW
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 ASP 299 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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294A ALA* 3.2 24.9 - - - +
295A PRO 3.6 11.0 - - - +
296A LYS* 4.2 9.0 + - - +
297A GLU 4.1 0.2 - - - -
298A ASP* 1.3 72.1 - - - +
300A ARG* 1.3 60.2 + - - +
301A ARG* 3.6 0.3 + - - +
302A THR* 2.5 44.1 + - - +
303A SER* 3.9 11.4 + - - -
329A PRO* 4.7 5.8 - - - +
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Residues in contact with ARG 300 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125A PHE* 4.4 9.7 - - - +
126A ALA 2.7 34.5 + - - +
127A THR* 3.3 17.9 + - - +
145A ASP* 4.1 5.8 + - - -
286A THR* 3.8 19.0 + - + +
287A ASN* 2.8 24.5 + - - +
288A TYR* 4.1 4.8 - - - -
298A ASP* 2.8 42.5 + - - +
299A ASP* 1.3 75.0 - - - +
301A ARG* 1.3 65.1 + - - +
303A SER* 3.5 1.6 + - - -
304A ALA* 3.2 18.9 + - - +
329A PRO* 3.4 40.6 - - + +
330A VAL* 3.4 15.2 - - - +
332A ASN* 4.0 12.8 - - - +
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Residues in contact with ARG 301 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284A VAL* 4.4 19.0 + - + +
285A GLU* 6.3 0.4 - - - +
286A THR* 3.6 26.4 + - + +
288A TYR* 4.1 17.8 + - - +
289A ASP 3.0 30.9 + - - -
290A HIS* 3.7 16.2 + - - +
292A LYS 2.7 20.6 + - - -
293A PRO* 3.8 2.8 - - - +
294A ALA* 3.4 29.7 - - + +
299A ASP* 3.2 6.0 - - - +
300A ARG* 1.3 78.3 - - - +
302A THR* 1.3 66.8 + - - +
304A ALA* 3.1 4.5 + - - +
305A ILE* 3.0 42.0 + - + +
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Residues in contact with THR 302 (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 ALA* 5.3 0.5 - - - +
299A ASP* 2.5 38.0 + - - +
300A ARG 3.4 0.2 - - - -
301A ARG* 1.3 79.5 - - - +
303A SER* 1.3 64.2 + - - +
305A ILE* 3.3 8.4 + - - +
306A LYS* 3.1 49.6 + - + +
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Residues in contact with SER 303 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299A ASP 3.9 6.8 + - - -
300A ARG 3.5 8.4 + - - -
301A ARG 3.2 0.4 - - - -
302A THR* 1.3 78.2 - - - +
304A ALA* 1.3 63.5 + - - +
306A LYS* 3.4 9.0 + - - +
307A ALA* 3.1 22.9 + - - +
327A VAL* 5.0 7.6 - - - +
328A VAL 4.5 4.5 - - - -
329A PRO* 3.3 32.1 - - - +
330A VAL* 3.9 8.3 - - - -
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Residues in contact with ALA 304 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127A THR* 4.5 9.9 - - + -
129A ILE* 4.5 10.1 - - + -
284A VAL* 3.8 22.9 - - + -
300A ARG 3.2 9.8 + - - +
301A ARG 3.1 8.3 + - - +
303A SER* 1.3 79.6 - - - +
305A ILE* 1.3 62.9 + - - +
307A ALA* 3.2 7.1 + - - +
308A LEU* 3.0 28.1 + - - +
324A ILE* 4.2 4.7 - - + +
330A VAL* 3.7 14.9 - - + +
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Residues in contact with ILE 305 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282A PHE* 4.1 19.2 - - + -
284A VAL* 3.9 23.3 - - + -
301A ARG* 3.0 42.3 + - + +
302A THR* 3.8 8.1 - - - +
303A SER 3.3 0.2 - - - -
304A ALA* 1.3 75.7 - - - +
306A LYS* 1.3 61.2 + - + +
308A LEU* 3.3 5.3 + - - +
309A ASN* 2.8 38.8 + - - +
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Residues in contact with LYS 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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302A THR* 3.1 40.4 + - + +
303A SER* 3.8 6.5 - - - +
305A ILE* 1.3 79.1 - - + +
307A ALA* 1.3 57.1 + - - +
309A ASN* 3.2 11.3 + - - +
310A ALA* 2.8 30.6 + - - +
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Residues in contact with ALA 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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303A SER 3.1 17.2 + - - +
304A ALA* 3.2 4.2 + - - +
306A LYS* 1.3 76.4 - - - +
308A LEU* 1.3 57.9 + - - +
310A ALA* 3.2 6.5 + - - +
311A THR* 2.8 34.2 + - - -
324A ILE* 3.8 28.7 - - + +
327A VAL* 4.5 16.6 - - + -
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Residues in contact with LEU 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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129A ILE* 3.9 28.3 - - + -
131A ALA* 4.7 0.7 - - + -
281A TRP* 3.4 32.2 - - + -
282A PHE* 3.7 27.1 - - + -
284A VAL* 3.4 32.5 - - + -
304A ALA 3.0 17.4 + - - +
305A ILE 3.7 3.8 - - - +
307A ALA* 1.3 73.3 - - - +
309A ASN* 1.3 66.3 + - - +
311A THR* 3.2 1.6 + - - -
312A GLY 3.0 20.3 + - - -
316A LEU* 4.6 5.6 - - + -
321A LEU* 4.2 5.8 - - + -
324A ILE* 3.7 26.0 - - + -
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Residues in contact with ASN 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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281A TRP* 5.0 4.6 + - - -
282A PHE* 3.8 19.1 - - - -
305A ILE* 2.8 26.2 + - - +
306A LYS* 3.3 15.5 - - - +
308A LEU* 1.3 77.6 - - - +
310A ALA* 1.3 62.5 + - - +
312A GLY* 3.5 9.5 + - - -
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Residues in contact with ALA 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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306A LYS 2.8 19.9 + - - +
307A ALA* 3.7 7.0 - - - +
309A ASN* 1.3 71.7 - - - +
311A THR* 1.3 67.6 + - - +
312A GLY* 3.5 0.5 + - - -
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Residues in contact with THR 311 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281A TRP* 5.5 1.1 - - + -
307A ALA 2.8 23.1 + - - -
308A LEU* 3.2 4.9 + - - -
310A ALA* 1.3 76.0 - - - +
312A GLY* 1.3 68.4 + - - +
315A ASN* 3.1 49.4 + - + +
316A LEU* 4.5 5.4 - - + +
320A ALA* 4.0 17.1 + - + +
324A ILE* 3.5 22.4 - - + +
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Residues in contact with GLY 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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281A TRP* 3.7 10.2 - - - -
308A LEU 3.0 13.2 + - - -
309A ASN 3.5 7.6 + - - -
310A ALA 3.3 2.4 - - - -
311A THR* 1.3 86.0 - - - +
313A GLN* 1.3 66.7 + - - -
314A ALA* 3.2 3.6 - - - -
315A ASN* 3.2 7.8 + - - -
316A LEU* 3.5 8.1 + - - -
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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