Contacts of the helix formed by residues 295 - 302 (chain D) in PDB entry 1D7W
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 295 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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291D ILE* 3.0 23.8 + - - +
294D ARG* 1.3 122.6 + - - +
296D TYR* 1.3 66.4 + - - +
298D PRO* 3.6 2.1 - - - +
299D LEU* 3.4 13.7 - - - +
532D SER* 5.2 2.4 - - - -
533D LEU* 5.4 1.2 + - - +
549D ASN* 5.9 4.4 + - - +
550D ASN* 3.1 42.7 + - - +
551D ILE* 5.5 3.0 - - + +
552D PHE* 3.6 12.4 - - + -
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Residues in contact with TYR 296 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86B PHE* 3.4 43.1 + + - -
89B TRP* 3.5 24.7 - + + -
90B GLY* 3.4 19.9 - - - -
93B LEU* 4.0 19.3 - - + -
605B HEM 4.0 0.9 - - - +
291D ILE 3.0 8.4 + - - +
292D THR* 3.3 8.0 + - - +
295D ASP* 1.3 76.0 - - - +
297D LEU* 1.4 82.2 + - + +
299D LEU* 2.9 27.9 + - - +
300D VAL* 3.2 25.8 + - + +
332D PHE* 3.4 22.7 - + - -
334D TYR* 3.0 18.7 + - - -
552D PHE* 3.5 18.4 - + + -
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Residues in contact with LEU 297 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292D THR* 2.7 24.4 + - + +
293D TYR* 3.6 36.6 - - + +
296D TYR* 1.4 82.8 - - + +
298D PRO* 1.4 70.7 - - + +
300D VAL* 3.0 10.4 + - + +
301D LEU* 3.0 33.7 + - + +
306D MET* 4.5 2.0 - - - -
310D LEU* 3.9 15.5 - - + -
499D ILE* 4.7 5.8 - - + -
503D PHE* 3.6 53.8 - - + -
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Residues in contact with PRO 298 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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293D TYR 3.5 19.7 - - - +
294D ARG 3.3 17.7 - - - +
295D ASP 3.6 9.6 - - - +
296D TYR 3.4 4.9 - - - -
297D LEU* 1.4 91.0 - - + +
299D LEU* 1.4 65.5 + - + +
302D GLY* 2.9 29.1 + - - -
303D PRO* 4.4 0.7 - - + +
306D MET* 3.8 31.2 - - + -
488D LYS 3.9 1.7 - - - +
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Residues in contact with LEU 299 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82B ARG* 2.9 56.7 + - - +
86B PHE* 3.6 10.1 - - + -
295D ASP 3.4 12.3 - - - +
296D TYR 2.9 10.9 + - - +
298D PRO* 1.4 84.2 - - + +
300D VAL* 1.3 63.3 - - - +
488D LYS 4.1 3.6 - - - +
489D GLY* 3.8 0.3 - - - -
490D ARG 3.7 6.1 + - - -
550D ASN* 3.8 17.3 - - - +
552D PHE* 3.6 36.3 - - + -
553D MET* 4.0 19.5 - - + +
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Residues in contact with VAL 300 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86B PHE* 3.8 8.7 - - + -
296D TYR* 3.3 51.4 - - + +
297D LEU* 3.0 10.3 + - + +
299D LEU* 1.3 79.7 - - - +
301D LEU* 1.3 71.6 + - + +
332D PHE* 5.3 0.2 - - + -
334D TYR* 3.5 29.6 - - + +
489D GLY* 3.5 0.2 - - - -
490D ARG* 2.8 25.4 + - - +
491D VAL* 3.6 21.8 + - + +
499D ILE* 4.6 13.2 - - + -
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Residues in contact with LEU 301 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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297D LEU* 3.0 23.3 + - + +
300D VAL* 1.3 90.8 - - + +
302D GLY* 1.3 63.5 + - - +
305D ALA* 3.3 28.5 + - + +
306D MET* 3.9 16.6 - - + +
310D LEU* 4.0 26.9 - - + -
486D LYS* 3.8 17.7 - - - +
489D GLY* 3.9 1.6 - - - -
491D VAL* 4.5 3.3 - - + +
496D ALA* 3.5 39.5 - - + +
499D ILE* 4.6 4.7 - - + -
500D GLY* 4.1 18.4 - - - +
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Residues in contact with GLY 302 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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298D PRO 2.9 15.9 + - - -
300D VAL 3.5 1.8 - - - -
301D LEU* 1.3 77.8 - - - +
303D PRO* 1.3 76.7 - - - +
304D THR 3.4 2.2 + - - -
306D MET* 3.1 23.1 + - - +
486D LYS* 5.3 0.2 - - - -
487D ARG 3.7 4.7 - - - -
488D LYS 3.3 20.0 - - - -
489D GLY* 3.6 2.2 - - - -
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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