Contacts of the helix formed by residues 305 - 314 (chain A) in PDB entry 2CT8
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 305 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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19A VAL* 5.5 3.3 - - - +
20A PRO 5.0 3.2 - - - +
303A VAL 3.4 5.1 + - - +
304A VAL* 1.3 73.2 - - - +
306A PRO* 1.3 78.0 - - - +
307A TYR* 3.4 16.9 + - - -
308A GLU* 2.9 35.7 + - + +
309A VAL* 2.9 22.0 + - - +
310B VAL 5.0 2.4 - - - +
311B GLN* 4.9 11.7 - - - +
495B ARG* 3.4 30.9 + - - -
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Residues in contact with PRO 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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20A PRO* 4.0 5.2 - - + +
21A HIS* 3.4 34.5 - - - +
22A LEU* 3.4 8.5 - - + +
25A ALA* 4.3 10.3 - - + -
83A LEU* 3.8 32.5 - - + -
86A PHE* 5.1 0.7 - - - -
87A LEU* 4.9 4.9 - - + -
304A VAL* 3.4 10.0 - - + +
305A ASP* 1.3 91.8 - - - +
307A TYR* 1.3 64.3 + - + +
309A VAL* 3.2 9.3 + - + +
310A VAL* 3.1 31.8 + - + +
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Residues in contact with TYR 307 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A PRO* 6.0 4.5 - - + -
79A ARG 4.0 2.5 + - - -
82A LYS* 3.4 6.9 - - - +
83A LEU* 3.2 42.3 + - + +
86A PHE* 3.4 44.5 - + + -
305A ASP* 3.2 17.8 + - - +
306A PRO* 1.3 81.8 - - + +
308A GLU* 1.3 58.3 + - + +
310A VAL* 3.5 3.1 + - - +
311A GLN* 2.8 32.9 + - + +
458B LYS* 6.0 0.2 - - - +
493B PRO* 3.6 28.3 - - + -
494B LYS 5.7 0.4 - - - -
495B ARG* 3.4 63.8 - - + +
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Residues in contact with GLU 308 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305A ASP* 2.9 28.5 + - + +
307A TYR* 1.3 73.2 - - + +
309A VAL* 1.3 65.5 + - - +
310A VAL 3.2 2.2 - - - -
311A GLN* 3.2 21.1 + - + +
312A GLU* 3.4 21.2 + - - +
88B LYS* 5.9 3.3 - - - -
310B VAL* 4.8 5.1 - - - +
314B GLY* 3.4 12.3 - - - -
315B LEU* 3.3 32.8 + - - +
317B GLU* 4.9 1.4 - - - +
458B LYS* 4.9 8.5 + - - +
495B ARG* 4.0 6.4 + - - +
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Residues in contact with VAL 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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22A LEU* 4.7 8.7 - - + -
304A VAL* 3.4 29.6 - - + -
305A ASP 2.9 11.9 + - - +
306A PRO* 3.7 6.7 - - + +
308A GLU* 1.3 77.5 - - - +
310A VAL* 1.3 72.6 + - + +
312A GLU* 3.8 4.0 + - - +
313A TYR* 3.0 39.2 + - + +
318A VAL* 4.1 16.8 - - + -
334A PHE* 3.5 36.1 - - + -
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Residues in contact with VAL 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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86A PHE* 4.1 17.9 - - + -
87A LEU* 3.9 21.3 - - + -
306A PRO* 3.1 19.2 + - + +
307A TYR 3.8 3.8 - - - +
309A VAL* 1.3 81.2 - - + +
311A GLN* 1.3 63.4 + - - +
312A GLU 3.3 0.7 - - - -
314A GLY* 3.0 18.3 + - - +
315A LEU* 3.4 36.6 - - + +
318A VAL* 3.9 25.1 - - + -
489B LYS* 5.4 1.4 + - - +
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Residues in contact with GLN 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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86A PHE* 4.2 8.1 - - - -
307A TYR 2.8 25.7 + - - +
308A GLU* 3.2 13.0 + - + +
310A VAL* 1.3 80.4 - - - +
312A GLU* 1.3 61.4 + - - +
458B LYS* 3.2 22.8 - - - +
461B GLU* 2.9 49.5 - - - +
489B LYS* 4.0 23.0 + - - +
490B ILE 3.1 28.0 + - - +
491B LEU 3.3 1.6 + - - -
493B PRO* 3.2 23.6 - - - +
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Residues in contact with GLU 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 GLU* 3.4 16.6 + - - +
309A VAL* 4.7 2.9 - - - +
311A GLN* 1.3 80.4 - - + +
313A TYR* 1.3 93.4 + - + +
336A LYS* 4.8 3.0 + - - -
495A ARG* 2.7 24.0 + - - -
497A GLY* 2.9 34.6 - - - +
88B LYS* 5.6 8.0 + - - -
461B GLU* 4.9 7.4 - - + +
464B GLN* 5.4 2.8 + - - -
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Residues in contact with TYR 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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309A VAL* 3.0 28.8 + - + +
312A GLU* 1.3 97.8 + - + +
314A GLY* 1.3 63.6 + - - +
317A GLU* 3.3 18.2 - - + +
318A VAL* 4.5 6.1 - - + -
334A PHE* 4.4 14.3 - + - -
336A LYS* 3.1 34.3 + - - +
339A ILE* 3.9 32.7 - - + +
340A LEU* 4.2 26.0 - - + -
343A ILE* 3.9 23.5 - - + +
495A ARG* 3.0 28.0 + - - +
497A GLY* 4.3 13.9 - - - -
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Residues in contact with GLY 314 (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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310A VAL* 3.0 18.4 + - - -
313A TYR* 1.3 79.1 - - - +
315A LEU* 1.3 58.8 + - - +
317A GLU* 3.1 12.9 + - - -
318A VAL* 2.7 37.4 + - - +
495A ARG* 3.4 9.8 - - - +
487B GLU* 5.8 2.5 - - - -
489B LYS* 5.4 2.7 - - - -
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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